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From: <ko...@us...> - 2015-05-10 21:10:55
|
Revision: 2288
http://sourceforge.net/p/jsbml/code/2288
Author: kofiav
Date: 2015-05-10 21:10:53 +0000 (Sun, 10 May 2015)
Log Message:
-----------
More test cases added to ASTNodeInfixParsingTest.java. Test cases are now more or less exhaustive.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
Modified: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-05-10 02:58:57 UTC (rev 2287)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-05-10 21:10:53 UTC (rev 2288)
@@ -171,6 +171,62 @@
}
+ @Test public void notParsingTests() {
+
+ try {
+ // not(x)
+ ASTNode n = ASTNode.parseFormula("not(x)", l3Parser);
+ String formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'not(x)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ // !(x)
+ n = ASTNode.parseFormula("!(x)", l3Parser);
+ formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula '!(x)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ } catch (ParseException e) {
+ // should never happen
+ e.printStackTrace();
+ assertTrue(false);
+ }
+ }
+
+ @Test public void orParsingTests() {
+
+ try {
+ // or(x, y)
+ ASTNode n = ASTNode.parseFormula("or(x,y)", l3Parser);
+ String formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'or(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ // x || y
+ n = ASTNode.parseFormula("x || y", l3Parser);
+ formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'x || y' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ // x or y
+ n = ASTNode.parseFormula("x or y", parser); // or(x,y) does not work ==> difference compared to the L1 supported syntax?
+ formula = ASTNode.formulaToString(n);
+ System.out.println("formula 'x or y)' = " + formula);
+ n = ASTNode.parseFormula(formula, parser);
+
+ // or(x, y)
+ n = ASTNode.parseFormula("or(x,y)", l3Parser);
+ formula = ASTNode.formulaToString(n, oldL1Compiler);
+ System.out.println("formula 'or(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ } catch (ParseException e) {
+ // should never happen
+ e.printStackTrace();
+ assertTrue(false);
+ }
+ }
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1127,6 +1183,54 @@
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@Test
+ public void testExpCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode exp = ASTNode.parseFormula("Exp(-1)", caseInsensitiveParser);
+ status = (exp.getType() == ASTNode.Type.FUNCTION_EXP) && (exp.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = exp.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testExpCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode exp = ASTNode.parseFormula("Exp(-1)", caseSensitiveParser);
+ status = (exp.getType() != ASTNode.Type.FUNCTION_EXP) && (exp.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = exp.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
public void testFalseCaseInsensitive() {
boolean status = false;
try {
@@ -1229,7 +1333,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1292,7 +1396,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1336,7 +1440,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1359,7 +1463,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1387,6 +1491,58 @@
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@Test
+ public void testNanCaseInsensitive() {
+ boolean status = false;
+ try {
+ // Verify 'NaN'
+ ASTNode nan = ASTNode.parseFormula("Nan", caseInsensitiveParser);
+ status = (nan.getType() == ASTNode.Type.REAL) && (nan.getType() != ASTNode.Type.NAME);
+ if (status) {
+ status = nan.getReal() == Double.NaN;
+ }
+ // Verify 'NotANumber'
+ nan = ASTNode.parseFormula("NotANumber", caseInsensitiveParser);
+ status = status && (nan.getType() == ASTNode.Type.REAL) && (nan.getType() != ASTNode.Type.NAME);
+ if (status) {
+ status = nan.getReal() == Double.NaN;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testNanCaseSensitive() {
+ boolean status = false;
+ try {
+ // Verify 'NaN'
+ ASTNode nan = ASTNode.parseFormula("Nan", caseSensitiveParser);
+ status = (nan.getType() != ASTNode.Type.REAL) && (nan.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = nan.getName().equals("Nan");
+ }
+ // Verify 'NotANumber'
+ nan = ASTNode.parseFormula("NotANumber", caseSensitiveParser);
+ status = status && (nan.getType() != ASTNode.Type.REAL) && (nan.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = nan.getName().equals("Nan");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
public void testPiCaseInsensitive() {
boolean status = false;
try {
@@ -1405,7 +1561,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1456,7 +1612,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1516,7 +1672,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1568,7 +1724,7 @@
}
assertTrue(status);
}
-
+
/**
* Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
*/
@@ -1865,4 +2021,32 @@
assertTrue(status);
}
+ @Test public void xorParsingTests() {
+
+ try {
+ // xor(x, y)
+ ASTNode n = ASTNode.parseFormula("xor(x,y)", l3Parser);
+ String formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'xor(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ // x xor y
+ n = ASTNode.parseFormula("x xor y", parser); // xor(x,y) does not work ==> difference compared to the L1 supported syntax?
+ formula = ASTNode.formulaToString(n);
+ System.out.println("formula 'x xor y)' = " + formula);
+ n = ASTNode.parseFormula(formula, parser);
+
+ // xor(x, y)
+ n = ASTNode.parseFormula("xor(x,y)", l3Parser);
+ formula = ASTNode.formulaToString(n, oldL1Compiler);
+ System.out.println("formula 'xor(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
+ } catch (ParseException e) {
+ // should never happen
+ e.printStackTrace();
+ assertTrue(false);
+ }
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ko...@us...> - 2015-05-10 02:58:59
|
Revision: 2287
http://sourceforge.net/p/jsbml/code/2287
Author: kofiav
Date: 2015-05-10 02:58:57 +0000 (Sun, 10 May 2015)
Log Message:
-----------
Added additional test cases to ASTNodeInfixParsingTest for functions in the facade class
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNode2.java
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNode2.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNode2.java 2015-05-09 16:26:38 UTC (rev 2286)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNode2.java 2015-05-10 02:58:57 UTC (rev 2287)
@@ -261,6 +261,11 @@
*/
public void unsetParentSBMLObject();
+ /**
+ * Set the strictness of this node
+ *
+ * @param {@code boolean} strict
+ */
public abstract void setStrictness(boolean strict);
}
Modified: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-05-09 16:26:38 UTC (rev 2286)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-05-10 02:58:57 UTC (rev 2287)
@@ -41,14 +41,23 @@
* Tests related to {@link ASTNode#parseFormula(String)} and {@link ASTNode#parseFormula(String, IFormulaParser)}.
*
* @author Nicolas Rodriguez
+ * @author Victor Kofia
* @version $Rev$
* @since 1.0
+ * @date May 9, 2015
*/
public class ASTNodeInfixParsingTest {
/**
*
*/
+ @BeforeClass public static void init() {
+ caseInsensitiveParser.setCaseSensitive(false);
+ }
+
+ /**
+ *
+ */
final static FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader(""));
/**
@@ -65,100 +74,56 @@
*
*/
final static FormulaParserLL3 caseInsensitiveParser = new FormulaParserLL3(new StringReader(""));
-
- /**
- *
- */
- final static FormulaCompiler l3Compiler = new FormulaCompilerLibSBML();
/**
*
*/
- final static FormulaCompiler oldJsbmlCompiler = new FormulaCompiler();
+ final static FormulaCompiler l3Compiler = new FormulaCompilerLibSBML();
/**
*
*/
- final static FormulaCompiler oldL1Compiler = new LibSBMLFormulaCompiler();
+ final static FormulaCompiler oldJsbmlCompiler = new FormulaCompiler();
/**
*
*/
- @BeforeClass public static void init() {
- caseInsensitiveParser.setCaseSensitive(false);
- }
+ final static FormulaCompiler oldL1Compiler = new LibSBMLFormulaCompiler();
+
+ @Test public void andParsingTests() {
- /**
- *
- */
- @Test public void caseSensitivityTests() {
-
try {
- ASTNode n = ASTNode.parseFormula("Cos(x)", caseSensitiveParser);
+ // and(x, y)
+ ASTNode n = ASTNode.parseFormula("and(x,y)", l3Parser);
+ String formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'and(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
- assertTrue(n.getType() != ASTNode.Type.FUNCTION_COS);
- assertTrue(n.getType() == ASTNode.Type.FUNCTION);
- assertTrue(n.getName().equals("Cos"));
+ // x && y
+ n = ASTNode.parseFormula("x && y", l3Parser);
+ formula = ASTNode.formulaToString(n, l3Compiler);
+ System.out.println("formula 'x && y' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
- n = ASTNode.parseFormula("1 + Pi", caseSensitiveParser);
+ // x and y
+ n = ASTNode.parseFormula("x and y", parser); // and(x,y) does not work ==> difference compared to the L1 supported syntax?
+ formula = ASTNode.formulaToString(n);
+ System.out.println("formula 'x and y)' = " + formula);
+ n = ASTNode.parseFormula(formula, parser);
- assertTrue(n.getChild(1).getType() != ASTNode.Type.CONSTANT_PI);
- assertTrue(n.getChild(1).getType() == ASTNode.Type.NAME);
- assertTrue(n.getChild(1).getName().equals("Pi"));
-
-
+ // and(x, y)
+ n = ASTNode.parseFormula("and(x,y)", l3Parser);
+ formula = ASTNode.formulaToString(n, oldL1Compiler);
+ System.out.println("formula 'and(x, y)' = " + formula);
+ n = ASTNode.parseFormula(formula, l3Parser);
+
} catch (ParseException e) {
// should never happen
e.printStackTrace();
assertTrue(false);
}
}
-
- /**
- *
- */
- @Test public void caseInsensitivityTests() {
-
- try {
- ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
-
- assertTrue(n.getType() == ASTNode.Type.FUNCTION_COS);
- assertTrue(n.isFunction() == true);
- assertTrue(n.isName() == false);
- assertTrue(n.getChildCount() == 1);
- assertTrue(n.getName() == null); // TODO - should the original String be conserved and accessible through getName()
- assertTrue(n.toFormula().equals("cos(x)"));
-
- n = ASTNode.parseFormula("COS(x)", caseInsensitiveParser);
-
- assertTrue(n.getType() == ASTNode.Type.FUNCTION_COS);
- assertTrue(n.toFormula().equals("cos(x)"));
-
- n = ASTNode.parseFormula("cos(x)", caseInsensitiveParser);
-
- assertTrue(n.getType() == ASTNode.Type.FUNCTION_COS);
- assertTrue(n.toFormula().equals("cos(x)"));
-
- n = ASTNode.parseFormula("coS(x)", caseInsensitiveParser);
-
- assertTrue(n.getType() == ASTNode.Type.FUNCTION_COS);
- assertTrue(n.toFormula().equals("cos(x)"));
-
-
- n = ASTNode.parseFormula("1 + Pi", caseInsensitiveParser);
-
- assertTrue(n.getChild(1).getType() == ASTNode.Type.CONSTANT_PI);
- assertTrue(n.getChild(1).getName() == null); // TODO - should the original String be conserved and accessible through getName()
- assertTrue(n.toFormula().equals("1+pi"));
-
-
- } catch (ParseException e) {
- // should never happen
- e.printStackTrace();
- assertTrue(false);
- }
- }
@Test public void factorialParsingTests() {
@@ -205,39 +170,1699 @@
}
}
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testAbsCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode abs = ASTNode.parseFormula("Abs(-1)", caseInsensitiveParser);
+ status = (abs.getType() == ASTNode.Type.FUNCTION_ABS) && (abs.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = abs.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testAbsCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode abs = ASTNode.parseFormula("Abs(-1)", caseSensitiveParser);
+ status = (abs.getType() != ASTNode.Type.FUNCTION_ABS) && (abs.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = abs.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCosCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccos = ASTNode.parseFormula("ArcCos(x)", caseInsensitiveParser);
+ status = arccos.getType() == ASTNode.Type.FUNCTION_ARCCOS;
+ if (status) {
+ ASTNode n = arccos.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCosCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccos = ASTNode.parseFormula("ArcCos(x)", caseSensitiveParser);
+ status = (arccos.getType() != ASTNode.Type.FUNCTION_ARCCOS) && (arccos.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccos.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCoshCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccosh = ASTNode.parseFormula("ArcCosh(x)", caseInsensitiveParser);
+ status = arccosh.getType() == ASTNode.Type.FUNCTION_ARCCOSH;
+ if (status) {
+ ASTNode n = arccosh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCoshCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccosh = ASTNode.parseFormula("ArcCosh(x)", caseSensitiveParser);
+ status = (arccosh.getType() != ASTNode.Type.FUNCTION_ARCCOSH) && (arccosh.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccosh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCotCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccot = ASTNode.parseFormula("ArcCot(x)", caseInsensitiveParser);
+ status = arccot.getType() == ASTNode.Type.FUNCTION_ARCCOT;
+ if (status) {
+ ASTNode n = arccot.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCotCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccot = ASTNode.parseFormula("ArcCot(x)", caseSensitiveParser);
+ status = (arccot.getType() != ASTNode.Type.FUNCTION_ARCCOT) && (arccot.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccot.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCothCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccoth = ASTNode.parseFormula("ArcCoth(x)", caseInsensitiveParser);
+ status = arccoth.getType() == ASTNode.Type.FUNCTION_ARCCOTH;
+ if (status) {
+ ASTNode n = arccoth.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCothCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccoth = ASTNode.parseFormula("ArcCoth(x)", caseSensitiveParser);
+ status = (arccoth.getType() != ASTNode.Type.FUNCTION_ARCCOTH) && (arccoth.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccoth.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCscCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccsc = ASTNode.parseFormula("ArcCsc(x)", caseInsensitiveParser);
+ status = arccsc.getType() == ASTNode.Type.FUNCTION_ARCCSCH;
+ if (status) {
+ ASTNode n = arccsc.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCscCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccsc = ASTNode.parseFormula("ArcCsc(x)", caseSensitiveParser);
+ status = (arccsc.getType() != ASTNode.Type.FUNCTION_ARCCSCH) && (arccsc.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccsc.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCschCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccsch = ASTNode.parseFormula("ArcCsch(x)", caseInsensitiveParser);
+ status = arccsch.getType() == ASTNode.Type.FUNCTION_ARCCSCH;
+ if (status) {
+ ASTNode n = arccsch.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcCschCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arccsch = ASTNode.parseFormula("ArcCsch(x)", caseSensitiveParser);
+ status = (arccsch.getType() != ASTNode.Type.FUNCTION_ARCCSCH) && (arccsch.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arccsch.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSecCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsec = ASTNode.parseFormula("ArcSec(x)", caseInsensitiveParser);
+ status = arcsec.getType() == ASTNode.Type.FUNCTION_ARCSEC;
+ if (status) {
+ ASTNode n = arcsec.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSecCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsec = ASTNode.parseFormula("ArcSec(x)", caseSensitiveParser);
+ status = (arcsec.getType() != ASTNode.Type.FUNCTION_ARCSEC) && (arcsec.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arcsec.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSechCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsech = ASTNode.parseFormula("ArcSech(x)", caseInsensitiveParser);
+ status = arcsech.getType() == ASTNode.Type.FUNCTION_ARCSECH;
+ if (status) {
+ ASTNode n = arcsech.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSechCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsech = ASTNode.parseFormula("ArcSech(x)", caseSensitiveParser);
+ status = (arcsech.getType() != ASTNode.Type.FUNCTION_ARCSECH) && (arcsech.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arcsech.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSinCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsin = ASTNode.parseFormula("ArcSin(x)", caseInsensitiveParser);
+ status = arcsin.getType() == ASTNode.Type.FUNCTION_ARCSIN;
+ if (status) {
+ ASTNode n = arcsin.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSinCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsin = ASTNode.parseFormula("ArcSin(x)", caseSensitiveParser);
+ status = (arcsin.getType() != ASTNode.Type.FUNCTION_ARCSIN) && (arcsin.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arcsin.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSinhCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsinh = ASTNode.parseFormula("ArcSinh(x)", caseInsensitiveParser);
+ status = arcsinh.getType() == ASTNode.Type.FUNCTION_ARCSINH;
+ if (status) {
+ ASTNode n = arcsinh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcSinhCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arcsinh = ASTNode.parseFormula("ArcSinh(x)", caseSensitiveParser);
+ status = (arcsinh.getType() != ASTNode.Type.FUNCTION_ARCSINH) && (arcsinh.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arcsinh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcTanCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arctan = ASTNode.parseFormula("ArcTan(x)", caseInsensitiveParser);
+ status = arctan.getType() == ASTNode.Type.FUNCTION_ARCTAN;
+ if (status) {
+ ASTNode n = arctan.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcTanCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arctan = ASTNode.parseFormula("ArcTan(x)", caseSensitiveParser);
+ status = (arctan.getType() != ASTNode.Type.FUNCTION_ARCTAN) && (arctan.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arctan.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcTanhCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode arctanh = ASTNode.parseFormula("ArcTanh(x)", caseInsensitiveParser);
+ status = arctanh.getType() == ASTNode.Type.FUNCTION_ARCTANH;
+ if (status) {
+ ASTNode n = arctanh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testArcTanhCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode arctanh = ASTNode.parseFormula("ArcTanh(x)", caseSensitiveParser);
+ status = (arctanh.getType() != ASTNode.Type.FUNCTION_ARCTANH) && (arctanh.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = arctanh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testAvogadroCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode avogadro = ASTNode.parseFormula("Avogadro", caseInsensitiveParser);
+ status = (avogadro.getType() == ASTNode.Type.NAME_AVOGADRO) && (avogadro.getType() != ASTNode.Type.NAME);
+ if (status) {
+ status = avogadro.getName() == null;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testAvogadroCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode avogadro = ASTNode.parseFormula("Avogadro", caseSensitiveParser);
+ status = (avogadro.getType() != ASTNode.Type.NAME_AVOGADRO) && (avogadro.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = avogadro.getName().equals("Avogadro");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCeilCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode ceil = ASTNode.parseFormula("Ceil(-x)", caseInsensitiveParser);
+ status = (ceil.getType() == ASTNode.Type.FUNCTION_CEILING) && (ceil.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = ceil.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
- @Test public void andParsingTests() {
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCeilCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode ceil = ASTNode.parseFormula("Ceil(-x)", caseSensitiveParser);
+ status = (ceil.getType() != ASTNode.Type.FUNCTION_CEILING) && (ceil.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = ceil.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCosCaseInsensitive() {
+ boolean status = false;
try {
- // and(x, y)
- ASTNode n = ASTNode.parseFormula("and(x,y)", l3Parser);
- String formula = ASTNode.formulaToString(n, l3Compiler);
- System.out.println("formula 'and(x, y)' = " + formula);
- n = ASTNode.parseFormula(formula, l3Parser);
+ ASTNode cos = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
+ status = cos.getType() == ASTNode.Type.FUNCTION_COS;
+ if (status) {
+ ASTNode n = cos.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCosCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode cos = ASTNode.parseFormula("Cos(x)", caseSensitiveParser);
+ status = (cos.getType() != ASTNode.Type.FUNCTION_COS) && (cos.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = cos.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCoshCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode cosh = ASTNode.parseFormula("Cosh(x)", caseInsensitiveParser);
+ status = cosh.getType() == ASTNode.Type.FUNCTION_COSH;
+ if (status) {
+ ASTNode n = cosh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCoshCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode cosh = ASTNode.parseFormula("Cosh(x)", caseSensitiveParser);
+ status = (cosh.getType() != ASTNode.Type.FUNCTION_COSH) && (cosh.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = cosh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCotCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode cot = ASTNode.parseFormula("Cot(x)", caseInsensitiveParser);
+ status = cot.getType() == ASTNode.Type.FUNCTION_COT;
+ if (status) {
+ ASTNode n = cot.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCotCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode cot = ASTNode.parseFormula("Cot(x)", caseSensitiveParser);
+ status = (cot.getType() != ASTNode.Type.FUNCTION_COT) && (cot.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = cot.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCothCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode coth = ASTNode.parseFormula("Coth(x)", caseInsensitiveParser);
+ status = coth.getType() == ASTNode.Type.FUNCTION_COTH;
+ if (status) {
+ ASTNode n = coth.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCothCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode coth = ASTNode.parseFormula("Coth(x)", caseSensitiveParser);
+ status = (coth.getType() != ASTNode.Type.FUNCTION_COTH) && (coth.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = coth.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCscCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode csc = ASTNode.parseFormula("Csc(x)", caseInsensitiveParser);
+ status = csc.getType() == ASTNode.Type.FUNCTION_CSC;
+ if (status) {
+ ASTNode n = csc.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCscCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode csc = ASTNode.parseFormula("Csc(x)", caseSensitiveParser);
+ status = (csc.getType() != ASTNode.Type.FUNCTION_CSC) && (csc.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = csc.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCschCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode csch = ASTNode.parseFormula("Csch(x)", caseInsensitiveParser);
+ status = csch.getType() == ASTNode.Type.FUNCTION_CSCH;
+ if (status) {
+ ASTNode n = csch.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testCschCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode csch = ASTNode.parseFormula("Csch(x)", caseSensitiveParser);
+ status = (csch.getType() != ASTNode.Type.FUNCTION_CSCH) && (csch.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = csch.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testDelayCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode delay = ASTNode.parseFormula("Delay(-x)", caseInsensitiveParser);
+ status = (delay.getType() == ASTNode.Type.FUNCTION_DELAY) && (delay.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = delay.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
- // x && y
- n = ASTNode.parseFormula("x && y", l3Parser);
- formula = ASTNode.formulaToString(n, l3Compiler);
- System.out.println("formula 'x && y' = " + formula);
- n = ASTNode.parseFormula(formula, l3Parser);
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testDelayCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode delay = ASTNode.parseFormula("Delay(-x)", caseSensitiveParser);
+ status = (delay.getType() != ASTNode.Type.FUNCTION_DELAY) && (delay.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = delay.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
- // x and y
- n = ASTNode.parseFormula("x and y", parser); // and(x,y) does not work ==> difference compared to the L1 supported syntax?
- formula = ASTNode.formulaToString(n);
- System.out.println("formula 'x and y)' = " + formula);
- n = ASTNode.parseFormula(formula, parser);
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testEulersConstantCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode e = ASTNode.parseFormula("1 + exponentialE", caseInsensitiveParser);
+ status = e.getType() == ASTNode.Type.PLUS;
+ if (status) {
+ ASTNode n = e.getChild(1);
+ status = n.getType() == ASTNode.Type.CONSTANT_E;
+ if (status) {
+ status = n.toFormula().equals("e") && n.getName() == null;
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testEulersConstantCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode e = ASTNode.parseFormula("1 + exponentialE", caseSensitiveParser);
+ status = e.getType() == ASTNode.Type.PLUS;
+ if (status) {
+ ASTNode n = e.getChild(1);
+ status = (n.getType() != ASTNode.Type.CONSTANT_E) && (n.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = n.toFormula().equals("exponentialE") && n.getName().equals("exponentialE");
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testFalseCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode booleanFalse = ASTNode.parseFormula("False", caseInsensitiveParser);
+ status = (booleanFalse.getType() == ASTNode.Type.CONSTANT_FALSE) && (booleanFalse.getType() != null);
+ if (status) {
+ status = booleanFalse.getName() == null;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testFalseCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode booleanFalse = ASTNode.parseFormula("False", caseSensitiveParser);
+ status = (booleanFalse.getType() != ASTNode.Type.CONSTANT_FALSE) && (booleanFalse.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = booleanFalse.getName().equals("False");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testFloorCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode floor = ASTNode.parseFormula("Floor(-x)", caseSensitiveParser);
+ status = (floor.getType() == ASTNode.Type.FUNCTION_FLOOR) && (floor.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = floor.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
- // and(x, y)
- n = ASTNode.parseFormula("and(x,y)", l3Parser);
- formula = ASTNode.formulaToString(n, oldL1Compiler);
- System.out.println("formula 'and(x, y)' = " + formula);
- n = ASTNode.parseFormula(formula, l3Parser);
-
- } catch (ParseException e) {
- // should never happen
+ } catch (Exception e) {
e.printStackTrace();
- assertTrue(false);
+ status = false;
}
+ assertTrue(status);
}
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testFloorCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode floor = ASTNode.parseFormula("Floor(-x)", caseSensitiveParser);
+ status = (floor.getType() != ASTNode.Type.FUNCTION_FLOOR) && (floor.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = floor.getChild(0);
+ status = n.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ n = n.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testInfinityCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode infinity = ASTNode.parseFormula("Infinity", caseInsensitiveParser);
+ status = (infinity.getType() == ASTNode.Type.REAL) && (infinity.getType() != ASTNode.Type.NAME);
+ if (status) {
+ status = infinity.getReal() == Double.POSITIVE_INFINITY;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testInfinityCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode infinity = ASTNode.parseFormula("Infinity", caseSensitiveParser);
+ status = (infinity.getType() != ASTNode.Type.REAL) && (infinity.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = infinity.getName().equals("Infinity");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testLnCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode ln = ASTNode.parseFormula("Ln(1000)", caseInsensitiveParser);
+ status = (ln.getType() == ASTNode.Type.FUNCTION_LN) && (ln.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode base = ln.getChild(0);
+ status = (base.getType() == ASTNode.Type.CONSTANT_E);
+ if (status) {
+ ASTNode n = ln.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testLnCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode ln = ASTNode.parseFormula("Ln(1000)", caseSensitiveParser);
+ status = (ln.getType() != ASTNode.Type.FUNCTION_LN) && (ln.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = ln.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testLogCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode log = ASTNode.parseFormula("Log(1000)", caseInsensitiveParser);
+ status = (log.getType() == ASTNode.Type.FUNCTION_LOG) && (log.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode base = log.getChild(0);
+ status = (base.getType() == ASTNode.Type.INTEGER) && (base.getInteger() == 10);
+ if (status) {
+ ASTNode n = log.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testLogCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode log = ASTNode.parseFormula("Log(1000)", caseSensitiveParser);
+ status = (log.getType() != ASTNode.Type.FUNCTION_LOG) && (log.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = log.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testMinusInfinityCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode infinity = ASTNode.parseFormula("-Infinity", caseInsensitiveParser);
+ status = infinity.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ ASTNode n = infinity.getChild(0);
+ status = (n.getType() == ASTNode.Type.REAL) && (n.getType() != ASTNode.Type.NAME);
+ if (status) {
+ status = infinity.getReal() == Double.POSITIVE_INFINITY;
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testMinusInfinityCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode infinity = ASTNode.parseFormula("-Infinity", caseSensitiveParser);
+ status = infinity.getType() == ASTNode.Type.MINUS;
+ if (status) {
+ ASTNode n = infinity.getChild(0);
+ status = (n.getType() != ASTNode.Type.REAL) && (n.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = infinity.getName().equals("Infinity");
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testPiCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode pi = ASTNode.parseFormula("1 + Pi", caseInsensitiveParser);
+ status = pi.getType() == ASTNode.Type.PLUS;
+ if (status) {
+ ASTNode n = pi.getChild(1);
+ status = n.getType() == ASTNode.Type.CONSTANT_PI;
+ if (status) {
+ status = n.toFormula().equals("pi") && n.getName() == null;
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testPiCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode pi = ASTNode.parseFormula("1 + Pi", caseSensitiveParser);
+ status = pi.getType() == ASTNode.Type.PLUS;
+ if (status) {
+ ASTNode n = pi.getChild(1);
+ status = (n.getType() != ASTNode.Type.CONSTANT_PI) && (n.getType() == ASTNode.Type.NAME);
+ if (status) {
+ status = n.toFormula().equals("Pi") && n.getName().equals("Pi");
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testPowerCaseInsensitive() {
+ boolean status = false;
+ try {
+ // Verify 'pow'
+ ASTNode power = ASTNode.parseFormula("Pow(1000)", caseInsensitiveParser);
+ status = (power.getType() == ASTNode.Type.FUNCTION_POWER) && (power.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = power.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ // Verify 'power'
+ power = ASTNode.parseFormula("Power(1000)", caseInsensitiveParser);
+ status = status && (power.getType() == ASTNode.Type.FUNCTION_POWER) && (power.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = power.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testPowerCaseSensitive() {
+ boolean status = false;
+ try {
+ // Verify 'pow'
+ ASTNode power = ASTNode.parseFormula("Pow(1000)", caseSensitiveParser);
+ status = (power.getType() != ASTNode.Type.FUNCTION_POWER) && (power.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = power.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ // Verify 'power'
+ power = ASTNode.parseFormula("Power(1000)", caseSensitiveParser);
+ status = status && (power.getType() != ASTNode.Type.FUNCTION_POWER) && (power.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = power.getChild(0);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 1000);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testRootCaseInsensitive() {
+ boolean status = false;
+ try {
+ // Verify 'sqr'
+ ASTNode root = ASTNode.parseFormula("Sqr(2, 3)", caseInsensitiveParser);
+ status = (root.getType() == ASTNode.Type.FUNCTION_ROOT) && (root.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = root.getChild(0), radicand = root.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 2)
+ && (radicand.getType() == ASTNode.Type.INTEGER) && (radicand.getInteger() == 3);
+
+ }
+ // Verify 'sqrt'
+ root = ASTNode.parseFormula("Sqrt(2, 3)", caseInsensitiveParser);
+ status = (root.getType() == ASTNode.Type.FUNCTION_ROOT) && (root.getType() != ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = root.getChild(0), radicand = root.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 2)
+ && (radicand.getType() == ASTNode.Type.INTEGER) && (radicand.getInteger() == 3);
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testRootCaseSensitive() {
+ boolean status = false;
+ try {
+ // Verify 'sqr'
+ ASTNode root = ASTNode.parseFormula("Sqr(2, 3)", caseSensitiveParser);
+ status = (root.getType() != ASTNode.Type.FUNCTION_ROOT) && (root.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = root.getChild(0), radicand = root.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 2)
+ && (radicand.getType() == ASTNode.Type.INTEGER) && (radicand.getInteger() == 3);
+
+ }
+ // Verify 'sqrt'
+ root = ASTNode.parseFormula("Sqrt(2, 3)", caseSensitiveParser);
+ status = (root.getType() != ASTNode.Type.FUNCTION_ROOT) && (root.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = root.getChild(0), radicand = root.getChild(1);
+ status = (n.getType() == ASTNode.Type.INTEGER) && (n.getInteger() == 2)
+ && (radicand.getType() == ASTNode.Type.INTEGER) && (radicand.getInteger() == 3);
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSecCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode sec = ASTNode.parseFormula("Sec(x)", caseInsensitiveParser);
+ status = sec.getType() == ASTNode.Type.FUNCTION_SEC;
+ if (status) {
+ ASTNode n = sec.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSecCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode sec = ASTNode.parseFormula("Sec(x)", caseSensitiveParser);
+ status = (sec.getType() != ASTNode.Type.FUNCTION_SEC) && (sec.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = sec.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSechCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode sech = ASTNode.parseFormula("Sech(x)", caseInsensitiveParser);
+ status = sech.getType() == ASTNode.Type.FUNCTION_SECH;
+ if (status) {
+ ASTNode n = sech.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSechCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode sech = ASTNode.parseFormula("Sech(x)", caseSensitiveParser);
+ status = (sech.getType() != ASTNode.Type.FUNCTION_SECH) && (sech.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = sech.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSinCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode sin = ASTNode.parseFormula("Sin(x)", caseInsensitiveParser);
+ status = sin.getType() == ASTNode.Type.FUNCTION_SIN;
+ if (status) {
+ ASTNode n = sin.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSinCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode sin = ASTNode.parseFormula("Sin(x)", caseSensitiveParser);
+ status = (sin.getType() != ASTNode.Type.FUNCTION_SIN) && (sin.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = sin.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSinhCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode sinh = ASTNode.parseFormula("Sinh(x)", caseInsensitiveParser);
+ status = sinh.getType() == ASTNode.Type.FUNCTION_SINH;
+ if (status) {
+ ASTNode n = sinh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testSinhCaseSensitive() {
+ boolean status = false;
+ try {
+ ASTNode sinh = ASTNode.parseFormula("Sinh(x)", caseSensitiveParser);
+ status = (sinh.getType() != ASTNode.Type.FUNCTION_SINH) && (sinh.getType() == ASTNode.Type.FUNCTION);
+ if (status) {
+ ASTNode n = sinh.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testTanCaseInsensitive() {
+ boolean status = false;
+ try {
+ ASTNode tan = ASTNode.parseFormula("Tan(x)", caseInsensitiveParser);
+ status = tan.getType() == ASTNode.Type.FUNCTION_TAN;
+ if (status) {
+ ASTNode n = tan.getChild(0);
+ status = n.getType() == ASTNode.Type.NAME && n.getName().equals("x");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ status = false;
+ }
+ assertTrue(status);
+ }
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#parseFormula(java.lang.String, org.sbml.jsbml.text.parser.IFormulaParser)}.
+ */
+ @Test
+ public void testTanCaseSensitive() {
+ ...
[truncated message content] |
|
From: <ko...@us...> - 2015-05-09 16:26:40
|
Revision: 2286
http://sourceforge.net/p/jsbml/code/2286
Author: kofiav
Date: 2015-05-09 16:26:38 +0000 (Sat, 09 May 2015)
Log Message:
-----------
Added new test case for getMantissa() in relation to nodes of type REAL
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeTest.java
Modified: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeTest.java 2015-05-08 15:55:31 UTC (rev 2285)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeTest.java 2015-05-09 16:26:38 UTC (rev 2286)
@@ -144,7 +144,7 @@
* {@link org.sbml.jsbml.ASTNode#getReal()}.
*/
@Test
- public final void testRealE() {
+ public void testRealE() {
ASTNode realENode = new ASTNode(0.14, 4);
assertTrue(realENode.isReal());
assertTrue(realENode.getReal() == 1400.0);
@@ -155,8 +155,22 @@
assertTrue(realENode.getMantissa() == 0.27);
assertTrue(realENode.getExponent() == 3);
}
+
+ /**
+ * Test method for {@link org.sbml.jsbml.ASTNode#getMantissa()},
+ * {@link org.sbml.jsbml.ASTNode#getMantissa()},
+ * {@link org.sbml.jsbml.ASTNode#isReal()} and
+ * {@link org.sbml.jsbml.ASTNode#getReal()}.
+ */
+ @Test
+ public void testGetMantissaForReal() {
+ ASTNode realNode = new ASTNode(1.0001);
+ assertTrue(realNode.isReal());
+ assertTrue(realNode.getReal() == 1.0001);
+ assertTrue(realNode.getExponent() == 1);
+ assertTrue(realNode.getMantissa() == 1.0001);
+ }
-
/**
* Test method for {@link org.sbml.jsbml.ASTNode#setValue(int numerator, int denominator)},
* {@link org.sbml.jsbml.ASTNode#getNumerator()} and
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|
|
From: <nik...@us...> - 2015-05-08 15:55:34
|
Revision: 2285
http://sourceforge.net/p/jsbml/code/2285
Author: niko-rodrigue
Date: 2015-05-08 15:55:31 +0000 (Fri, 08 May 2015)
Log Message:
-----------
added some debug code to ASTNode and removed a debug print in SBMLReader
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 15:42:22 UTC (rev 2284)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 15:55:31 UTC (rev 2285)
@@ -3815,6 +3815,10 @@
* the type to which this node should be set
*/
public void setType(ASTNode.Type type) {
+ if (logger.isDebugEnabled()) {
+ logger.debug("setType(Type) called - '" + type + "' " + (astnode2 != null ? astnode2.getType() : ""));
+ }
+
ASTNode2 old = astnode2;
switch (type) {
case CONSTANT_E :
@@ -4047,6 +4051,9 @@
* the type as a String.
*/
public void setType(String typeStr) {
+ if (logger.isDebugEnabled()) {
+ logger.debug("setType(String) called - '" + typeStr + "'");
+ }
Type type = Type.getTypeFor(typeStr);
setType(type);
if (type != Type.UNKNOWN) {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-08 15:42:22 UTC (rev 2284)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-08 15:55:31 UTC (rev 2285)
@@ -938,7 +938,6 @@
String type = attribute.getValue();
if (type.equalsIgnoreCase("integer")) {
- System.out.println("SBMLReader - encountered an integer in MathML !");
astNode.setType(Type.INTEGER);
} else if(type.equalsIgnoreCase("e-notation")) {
astNode.setType(Type.REAL_E);
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|
|
From: <nik...@us...> - 2015-05-08 15:42:24
|
Revision: 2284
http://sourceforge.net/p/jsbml/code/2284
Author: niko-rodrigue
Date: 2015-05-08 15:42:22 +0000 (Fri, 08 May 2015)
Log Message:
-----------
corrected the hack to set the type of 'cn' element directly in SBMLReader. Now it should work in all cases, even if the parent is a MathContainer element.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-08 14:46:57 UTC (rev 2283)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-08 15:42:22 UTC (rev 2284)
@@ -928,22 +928,35 @@
ASTNode astNode = (ASTNode) processedElement;
if (currentNode.getLocalPart().equals("cn") && hasAttributes) {
Object object = sbmlElements.peek();
- if (object != null && object instanceof ASTNode) {
- ASTNode parent = (ASTNode) object;
- if (att.next().getValue().equals("integer")) {
- astNode.setType(Type.INTEGER);
- } else if(att.next().getValue().equals("e-notation")) {
- astNode.setType(Type.REAL_E);
- } else if(att.next().getValue().equals("rational")) {
- astNode.setType(Type.RATIONAL);
- }
- // we need to remove the last child as the hierarchy of children are stored in the ASTNode2 and not directly in the ASTNode
- parent.removeChild(parent.getChildCount() - 1);
- parent.addChild(astNode);
- }
- }
+
+ while (att.hasNext()) {
+
+ Attribute attribute = att.next();
+ String attributeName = attribute.getName().getLocalPart();
+
+ if (attributeName.equals("type")) {
+ String type = attribute.getValue();
+
+ if (type.equalsIgnoreCase("integer")) {
+ System.out.println("SBMLReader - encountered an integer in MathML !");
+ astNode.setType(Type.INTEGER);
+ } else if(type.equalsIgnoreCase("e-notation")) {
+ astNode.setType(Type.REAL_E);
+ } else if(type.equalsIgnoreCase("rational")) {
+ astNode.setType(Type.RATIONAL);
+ }
+
+ if (object != null && object instanceof ASTNode) {
+ ASTNode parent = (ASTNode) object;
+
+ // we need to remove the last child as the hierarchy of children are stored in the ASTNode2 and not directly in the ASTNode
+ parent.removeChild(parent.getChildCount() - 1);
+ parent.addChild(astNode);
+ } // else the parent can be directly a MathContainer - nothing to do in this case.
+ }
+ }
+ }
}
-
sbmlElements.push(processedElement);
} else {
// It is normal to have sometimes null returned as some of the
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|
|
From: <nik...@us...> - 2015-05-08 14:46:59
|
Revision: 2283
http://sourceforge.net/p/jsbml/code/2283
Author: niko-rodrigue
Date: 2015-05-08 14:46:57 +0000 (Fri, 08 May 2015)
Log Message:
-----------
fixed the method ASTNode.isString() so that it behave as before.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 14:26:56 UTC (rev 2282)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 14:46:57 UTC (rev 2283)
@@ -3315,7 +3315,7 @@
* @see #isName()
*/
public boolean isString() {
- return isName() || isFunction();
+ return isName() || (getType() == Type.FUNCTION);
}
/**
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|
|
From: <nik...@us...> - 2015-05-08 14:26:58
|
Revision: 2282
http://sourceforge.net/p/jsbml/code/2282
Author: niko-rodrigue
Date: 2015-05-08 14:26:56 +0000 (Fri, 08 May 2015)
Log Message:
-----------
fixed the method ASTNode.getMantissa() and ASTNode.getExponent() so that they behave as before. Now they work with any type of number.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 09:09:06 UTC (rev 2281)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 14:26:56 UTC (rev 2282)
@@ -2603,6 +2603,9 @@
if (astnode2 instanceof ASTCnExponentialNode) {
return ((ASTCnExponentialNode) astnode2).getExponent();
}
+ if (isNumber()) {
+ return 1;
+ }
throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getExponent"));
}
@@ -2694,6 +2697,9 @@
if (astnode2 instanceof ASTCnExponentialNode) {
return ((ASTCnExponentialNode) toASTNode2()).getMantissa();
}
+ if (isReal()) {
+ return getReal();
+ }
throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getMantissa"));
}
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|
|
From: <nik...@us...> - 2015-05-08 09:09:09
|
Revision: 2281
http://sourceforge.net/p/jsbml/code/2281
Author: niko-rodrigue
Date: 2015-05-08 09:09:06 +0000 (Fri, 08 May 2015)
Log Message:
-----------
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-07 15:44:32 UTC (rev 2280)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-08 09:09:06 UTC (rev 2281)
@@ -4384,7 +4384,9 @@
*/
public static String astNodeToTree(ASTNode n, String tree, String indent) {
tree = tree + indent + n.getType() + " " +
- (n.isInteger() ? n.getInteger() : "") + (n.isReal() ? n.getReal() : "") + "\n";
+ (n.isInteger() ? n.getInteger() : "") + (n.isReal() ? n.getReal() : "") +
+ (n.isName() ? n.getName() : "") + ", " +
+ (n.isSetUserObjects() ? n.userObjectKeySet() : " no userObject") + "\n";
for (ASTNode child : n.getChildren()) {
tree = astNodeToTree(child, tree, indent + " ");
@@ -4392,6 +4394,54 @@
return tree;
}
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#clearUserObjects()
+ */
+ @Override
+ public void clearUserObjects() {
+ astnode2.clearUserObjects();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#containsUserObjectKey(java.lang.Object)
+ */
+ @Override
+ public boolean containsUserObjectKey(Object key) {
+ return astnode2.containsUserObjectKey(key);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#getUserObject(java.lang.Object)
+ */
+ @Override
+ public Object getUserObject(Object key) {
+ return astnode2.getUserObject(key);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#isSetUserObjects()
+ */
+ @Override
+ public boolean isSetUserObjects() {
+ return astnode2.isSetUserObjects();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#putUserObject(java.lang.Object, java.lang.Object)
+ */
+ @Override
+ public void putUserObject(Object key, Object userObject) {
+ astnode2.putUserObject(key, userObject);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#userObjectKeySet()
+ */
+ @Override
+ public Set<Object> userObjectKeySet() {
+ return astnode2.userObjectKeySet();
+ }
}
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|
|
From: <and...@us...> - 2015-05-07 15:44:34
|
Revision: 2280
http://sourceforge.net/p/jsbml/code/2280
Author: andreas-draeger
Date: 2015-05-07 15:44:32 +0000 (Thu, 07 May 2015)
Log Message:
-----------
Added more messages and removed unnecessary backslashes.
Modified Paths:
--------------
trunk/core/resources/org/sbml/jsbml/resources/Messages.xml
Modified: trunk/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- trunk/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-06 09:29:58 UTC (rev 2279)
+++ trunk/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-07 15:44:32 UTC (rev 2280)
@@ -38,7 +38,7 @@
<entry key="AbstractMathContainer.inclusion">{0} in {1}</entry>
<entry key="AbstractMathContainer.getDerivedUnitDefinition">Could not derive unit from syntax tree of {0}: {1}</entry>
- <entry key="AbstractNamedSBase.checkIdentifier">\"{0}\" is not a valid identifier for this {1}.</entry>
+ <entry key="AbstractNamedSBase.checkIdentifier">"{0}" is not a valid identifier for this {1}.</entry>
<entry key="AbstractSBase.appendNotes">There was a problem adding the given XMLNode: ''{0}'' to the ''body'' XMLNode.</entry>
<entry key="AbstractSBase.createPlugin">The package namespace or name ''{0}'' is unknown!</entry>
@@ -48,7 +48,7 @@
<entry key="AbstractSBase.registerChild1">Trying to register {0} ''{1}'', which is already registered under {2} ''{3}''.</entry>
<entry key="AbstractSBase.registerChild2">{0} ''{1}'' is associated to the different parent ''{2}''. Please remove it there before adding it to this ''{3}'' or add a clone of it to this element.</entry>
<entry key="AbstractSBase.registerChild3">Cannot register {0}.</entry>
- <entry key="AbstractSBase.setMetaId">\"{0}\" is not a valid meta-identifier for this {1}.</entry>
+ <entry key="AbstractSBase.setMetaId">"{0}" is not a valid meta-identifier for this {1}.</entry>
<entry key="AbstractSBase.setSBOTerm">Cannot set invalid SBO term {0,number,integer} because it must not be smaller than zero or larger than 9999999.</entry>
<entry key="AbstractSBase.unregisterChild1">unregister called! {0} {1}</entry>
<entry key="AbstractSBase.unregisterChild2">Cannot unregister {0}.</entry>
@@ -82,9 +82,9 @@
<entry key="ASTNode.getNumerator">getNumerator() should be called only when isRational()</entry>
<entry key="ASTNode.getReal">getReal() should be called only when isReal() returns true.</entry>
<entry key="ASTNode.getReferencedNamedSBases">Name of this node is {0} but no variable is set.</entry>
- <entry key="ASTNode.getVariable1">The name \"{0}\" represented by this node is an argument in a function call, i.e., a placeholder for some other element. No corresponding CallableSBase exists in the model</entry>
- <entry key="ASTNode.getVariable2">Cannot find any element with id \"{0}\" in the model.</entry>
- <entry key="ASTNode.getVariable3">This ASTNode is not yet linked to a model and can therefore not determine its variable \"{0}\".</entry>
+ <entry key="ASTNode.getVariable1">The name "{0}" represented by this node is an argument in a function call, i.e., a placeholder for some other element. No corresponding CallableSBase exists in the model</entry>
+ <entry key="ASTNode.getVariable2">Cannot find any element with id "{0}" in the model.</entry>
+ <entry key="ASTNode.getVariable3">This ASTNode is not yet linked to a model and can therefore not determine its variable "{0}".</entry>
<entry key="ASTNode.getVariable4">getVariable() should be called only when isVariable() == true.</entry>
<entry key="ASTNode.initDefaults">initDefaults called! type was {0}</entry>
<entry key="ASTNode.reduceToBinary1">MINUS node with {0,number,integer} children left unchanged</entry>
@@ -97,5 +97,22 @@
<entry key="ASTNode.setUnits2">Unexpected attribute {0}, only a valid unit kind or the identifier of a unit definition are allowed here.</entry>
<entry key="ASTNode.setUnits3">Cannot set unit {0} for a numbers in an ASTNode before SBML Level 3.</entry>
<entry key="ASTNode.toString">Could not compile ASTNode to formula: {0}</entry>
-
+
+ <entry key="Compartment.ERROR_MESSAGE_INVALID_DIM">Spatial dimensions must be within '{0, 3}', but {0,number} was given.</entry>
+ <entry key="Compartment.ERROR_MESSAGE_ZERO_DIM">Cannot set {0} for compartment {1} if the spatial dimensions are zero.</entry>
+ <entry key="Compartment.writeXMLAttributes">Illegal non-integer spatial dimensions {0,number}.</entry>
+
+ <entry key="Creator.setEmail">Invalid e-mail address {0}</entry>
+
+ <entry key="CVTerm.INVALID_TYPE_AND_QUALIFIER_COMBINATION_MSG">Invalid combination of type {0} with qualifier {1}.</entry>
+ <entry key="CVTerm.setBiologicalQualifierType">{0} is not a valid Biological Qualifier.</entry>
+ <entry key="CVTerm.setModelQualifierType1">Model qualifier types can only be applied if the type is set to Model Qualifier.</entry>
+ <entry key="CVTerm.setModelQualifierType2">{0} is not a valid Model Qualifier.</entry>
+ <entry key="CVTerm.setQualifierType">{0} is not a valid qualifier.</entry>
+ <entry key="CVTerm.Type.MODEL_QUALIFIER">The model</entry>
+ <entry key="CVTerm.Type.BIOLOGICAL_QUALIFIER">The biological entity</entry>
+ <entry key="CVTerm.Type.UNKNOWN_QUALIFIER">The element</entry>
+ <entry key="CVTerm.Qualifier.UNKNOWN">has something to do with</entry>
+ <entry key="CVTerm.humanReadable">{0} {1} {2}.</entry>
+
</properties>
\ No newline at end of file
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|
|
From: <nik...@us...> - 2015-05-06 09:30:00
|
Revision: 2279
http://sourceforge.net/p/jsbml/code/2279
Author: niko-rodrigue
Date: 2015-05-06 09:29:58 +0000 (Wed, 06 May 2015)
Log Message:
-----------
removed a branch not needed any more
Removed Paths:
-------------
branches/astnode2-merging/
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|
|
From: <nik...@us...> - 2015-05-06 09:28:57
|
Revision: 2278
http://sourceforge.net/p/jsbml/code/2278
Author: niko-rodrigue
Date: 2015-05-06 09:28:54 +0000 (Wed, 06 May 2015)
Log Message:
-----------
corrected the clone method of the ASTNode facade so that userObjects are copied and added a junit test for userObjects
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
Added Paths:
-----------
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/UserObjectTest.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-01 16:03:18 UTC (rev 2277)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-06 09:28:54 UTC (rev 2278)
@@ -1432,7 +1432,7 @@
* the {@link ASTNode} to be copied.
*/
public ASTNode(ASTNode astNode) {
- this();
+ super(astNode);
if (astNode.isSetASTNode2()) {
astnode2 = astNode.toASTNode2().clone();
Added: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/UserObjectTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/UserObjectTest.java (rev 0)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/UserObjectTest.java 2015-05-06 09:28:54 UTC (rev 2278)
@@ -0,0 +1,98 @@
+/*
+ * $Id$
+ * $URL$
+ *
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.test;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.Species;
+
+
+/**
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ *
+ */
+public class UserObjectTest {
+
+ private final String KEY_1 = "KEY_1";
+ private final String KEY_2 = "KEY_2";
+
+ /**
+ *
+ */
+ private static final transient Logger logger = Logger.getLogger(UserObjectTest.class);
+
+ /**
+ *
+ */
+ @Test
+ public void SpeciesTest() {
+ Species s = new Species();
+
+ assertTrue(s.isSetUserObjects() == false);
+
+ s.putUserObject(KEY_1, 3);
+ s.putUserObject(KEY_2, "userObject");
+
+ assertTrue(s.isSetUserObjects() == true);
+ assertTrue((int) s.getUserObject(KEY_1) == 3);
+ assertTrue(s.getUserObject(KEY_2) == "userObject");
+
+ Species s2 = s.clone();
+
+ assertTrue(s2.isSetUserObjects() == true);
+ assertTrue((int) s2.getUserObject(KEY_1) == 3);
+ assertTrue(s2.getUserObject(KEY_2) == "userObject");
+
+ }
+
+ /**
+ *
+ */
+ @Test
+ public void ASTNodeTest() {
+ ASTNode s = new ASTNode();
+
+ assertTrue(s.isSetUserObjects() == false);
+
+ s.putUserObject(KEY_1, 3);
+ s.putUserObject(KEY_2, "userObject");
+
+ assertTrue(s.isSetUserObjects() == true);
+ assertTrue((int) s.getUserObject(KEY_1) == 3);
+ assertTrue(s.getUserObject(KEY_2) == "userObject");
+
+ ASTNode s2 = s.clone();
+
+ assertTrue(s2.isSetUserObjects() == true);
+ assertTrue((int) s2.getUserObject(KEY_1) == 3);
+ assertTrue(s2.getUserObject(KEY_2) == "userObject");
+
+ }
+
+}
Property changes on: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/UserObjectTest.java
___________________________________________________________________
Added: svn:keywords
## -0,0 +1 ##
+Id Date Author HeadURL URL Revision
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 16:03:20
|
Revision: 2277
http://sourceforge.net/p/jsbml/code/2277
Author: niko-rodrigue
Date: 2015-05-01 16:03:18 +0000 (Fri, 01 May 2015)
Log Message:
-----------
put back the hack in SBMLReader about cn element as it is still needed for the new ASTNode facade because the children are not stored directly in the facade. Hopefully, it is a fixed version now.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 15:12:11 UTC (rev 2276)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 16:03:18 UTC (rev 2277)
@@ -140,7 +140,7 @@
}
if (attributeName.equals("type") || attributeName.equals("definitionURL")) {
- astNode.setType(value);
+ // Done in SBMLReader - astNode.setType(value);
// System.out.println("MathMLStaxParser : processAttribute : astNode Type = " + astNode.getType());
} else if (attributeName.equals("id")) {
astNode.setId(value);
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 15:12:11 UTC (rev 2276)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 16:03:18 UTC (rev 2277)
@@ -923,13 +923,13 @@
hasNamespace, sbmlElements.peek());
if (processedElement != null) {
- /* // TODO - I don't think we need this code any more!?
+ // TODO - we won't need this code any more if the list of child is stored directly in the ASTNode facade
if (processedElement instanceof ASTNode) {
ASTNode astNode = (ASTNode) processedElement;
if (currentNode.getLocalPart().equals("cn") && hasAttributes) {
- // Object object = sbmlElements.peek();
- // if (object != null && object instanceof ASTNode) {
- // ASTNode parent = (ASTNode) object;
+ Object object = sbmlElements.peek();
+ if (object != null && object instanceof ASTNode) {
+ ASTNode parent = (ASTNode) object;
if (att.next().getValue().equals("integer")) {
astNode.setType(Type.INTEGER);
} else if(att.next().getValue().equals("e-notation")) {
@@ -937,13 +937,13 @@
} else if(att.next().getValue().equals("rational")) {
astNode.setType(Type.RATIONAL);
}
- // TODO - wrong, we need to remove the last one! in fact, we don't need to remove and add it again the ASTNode as it's the same
- // parent.removeChild(0);
- // parent.addChild(astNode);
+ // we need to remove the last child as the hierarchy of children are stored in the ASTNode2 and not directly in the ASTNode
+ parent.removeChild(parent.getChildCount() - 1);
+ parent.addChild(astNode);
}
- // }
+ }
}
- */
+
sbmlElements.push(processedElement);
} else {
// It is normal to have sometimes null returned as some of the
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 15:12:11 UTC (rev 2276)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 16:03:18 UTC (rev 2277)
@@ -179,8 +179,6 @@
// testDocument.checkConsistency();
// System.out.println(XMLNode.convertXMLNodeToString(testDocument.getModel().getAnnotation().getNonRDFannotation()));
- System.out.println(ASTNode.astNodeToTree(testDocument.getModel().getReaction(0).getKineticLaw().getMath(), "", ""));
-
System.out.println("Going to check package version and namespace for all elements.");
PackageUtil.checkPackages(testDocument);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 15:12:13
|
Revision: 2276
http://sourceforge.net/p/jsbml/code/2276
Author: niko-rodrigue
Date: 2015-05-01 15:12:11 +0000 (Fri, 01 May 2015)
Log Message:
-----------
corrected a bug in SBMLReader that was removing child ASTNode when a cn element with a type attribute was not the first child. I removed the block of code as I don't think we need it any more.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode 2015-05-01 15:12:11 UTC (rev 2276)
@@ -1670,6 +1670,10 @@
* the node to add as child.
*/
public void addChild(ASTNode child) {
+ if (logger.isDebugEnabled()) {
+ logger.debug(" adding child current node: \n" + astNodeToTree(this, "", ""));
+ logger.debug(" adding child: \n" + astNodeToTree(child, "", ""));
+ }
listOfNodes.add(child);
setParentSBMLObject(child, parentSBMLObject, 0);
child.setParent(this);
@@ -3791,6 +3795,10 @@
*/
public void setType(String typeStr) {
// System.out.println("ASTNode: setType(String) called.");
+ if (logger.isDebugEnabled()) {
+ logger.debug("ASTNode: setType(String) called: " + typeStr);
+ }
+
Type type = Type.getTypeFor(typeStr);
setType(type);
if (type != Type.UNKNOWN) {
@@ -3848,7 +3856,7 @@
setValue(Maths.AVOGADRO_L3V1);
definitionURL = URI_AVOGADRO_DEFINITION;
}
- Type oldValue = getType();
+ Type oldValue = this.type;
this.type = type;
firePropertyChange(TreeNodeChangeEvent.type, oldValue, type);
}
@@ -4223,4 +4231,24 @@
}
}
+ /**
+ * Returns a simple tree view of the ASTNode internal, including mainly
+ * node type and hierarchy.
+ *
+ * @param n
+ * @param tree
+ * @param indent
+ * @return a simple tree view of the ASTNode internal
+ */
+ public static String astNodeToTree(ASTNode n, String tree, String indent) {
+ tree = tree + indent + n.getType() + " " +
+ (n.isInteger() ? n.getInteger() : "") + (n.isReal() ? n.getReal() : "") + "\n";
+
+ for (ASTNode child : n.getChildren()) {
+ tree = astNodeToTree(child, tree, indent + " ");
+ }
+
+ return tree;
+ }
+
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -126,9 +126,9 @@
ASTNode astNode = (ASTNode) contextObject;
// NOTE: By default cn ASTNodes are of type REAL
- if (value.equals("integer")) {
- astNode.setType(Type.INTEGER);
- }
+// if (value.equals("integer")) {
+// astNode.setType(Type.INTEGER);
+// }
// System.out.println("MathMLStaxParser : processAttribute called");
// System.out.println("MathMLStaxParser : processAttribute : element name = " + elementName + ", attribute name = " + attributeName +
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -923,12 +923,13 @@
hasNamespace, sbmlElements.peek());
if (processedElement != null) {
+ /* // TODO - I don't think we need this code any more!?
if (processedElement instanceof ASTNode) {
ASTNode astNode = (ASTNode) processedElement;
if (currentNode.getLocalPart().equals("cn") && hasAttributes) {
- Object object = sbmlElements.peek();
- if (object != null && object instanceof ASTNode) {
- ASTNode parent = (ASTNode) object;
+ // Object object = sbmlElements.peek();
+ // if (object != null && object instanceof ASTNode) {
+ // ASTNode parent = (ASTNode) object;
if (att.next().getValue().equals("integer")) {
astNode.setType(Type.INTEGER);
} else if(att.next().getValue().equals("e-notation")) {
@@ -936,11 +937,13 @@
} else if(att.next().getValue().equals("rational")) {
astNode.setType(Type.RATIONAL);
}
- parent.removeChild(0);
- parent.addChild(astNode);
+ // TODO - wrong, we need to remove the last one! in fact, we don't need to remove and add it again the ASTNode as it's the same
+ // parent.removeChild(0);
+ // parent.addChild(astNode);
}
- }
+ // }
}
+ */
sbmlElements.push(processedElement);
} else {
// It is normal to have sometimes null returned as some of the
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -178,7 +178,9 @@
// testDocument.checkConsistency();
// System.out.println(XMLNode.convertXMLNodeToString(testDocument.getModel().getAnnotation().getNonRDFannotation()));
-
+
+ System.out.println(ASTNode.astNodeToTree(testDocument.getModel().getReaction(0).getKineticLaw().getMath(), "", ""));
+
System.out.println("Going to check package version and namespace for all elements.");
PackageUtil.checkPackages(testDocument);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 11:41:23
|
Revision: 2275
http://sourceforge.net/p/jsbml/code/2275
Author: niko-rodrigue
Date: 2015-05-01 11:41:21 +0000 (Fri, 01 May 2015)
Log Message:
-----------
removed some unnecessary file or folder
Removed Paths:
-------------
trunk/core/resources/META-INF/
trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field-jsbml.xml
Deleted: trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field-jsbml.xml
===================================================================
--- trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field-jsbml.xml 2015-05-01 10:54:44 UTC (rev 2274)
+++ trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field-jsbml.xml 2015-05-01 11:41:21 UTC (rev 2275)
@@ -1,273 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" xmlns:req="http://www.sbml.org/sbml/level3/version1/req/version1" spatial:required="true" version="1">
- <model>
- <spatial:geometry xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <spatial:listOfAdjacentDomains>
- <spatial:adjacentDomains spatial:domain2="Cytosol0" spatial:id="Cytosol_Extracellular_membrane_Cytosol0" spatial:domain1="Cytosol_Extracellular_membrane0"/>
- <spatial:adjacentDomains spatial:domain2="Extracellular0" spatial:id="Cytosol_Extracellular_membrane_Extracellular0" spatial:domain1="Cytosol_Extracellular_membrane0"/>
- <spatial:adjacentDomains spatial:domain2="Nucleus0" spatial:id="Nucleus_Cytosol_membrane_Nucleus0" spatial:domain1="Nucleus_Cytosol_membrane0"/>
- <spatial:adjacentDomains spatial:domain2="Cytosol0" spatial:id="Nucleus_Cytosol_membrane_Cytosol0" spatial:domain1="Nucleus_Cytosol_membrane0"/>
- </spatial:listOfAdjacentDomains>
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="x" spatial:unit="um">
- </spatial:coordinateComponent>
- <spatial:coordinateComponent spatial:id="y" spatial:unit="um">
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomains>
- <spatial:domain spatial:id="Extracellular0" spatial:domainType="Extracellular"/>
- <spatial:domain spatial:id="Cytosol_Extracellular_membrane0" spatial:domainType="Cytosol_Extracellular_membrane"/>
- <spatial:domain spatial:id="Cytosol0" spatial:domainType="Cytosol"/>
- <spatial:domain spatial:id="Nucleus_Cytosol_membrane0" spatial:domainType="Nucleus_Cytosol_membrane"/>
- <spatial:domain spatial:id="Nucleus0" spatial:domainType="Nucleus"/>
- </spatial:listOfDomains>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="Extracellular" spatial:spatialDimensions="3"/>
- <spatial:domainType spatial:id="Cytosol_Extracellular_membrane" spatial:spatialDimensions="2"/>
- <spatial:domainType spatial:id="Cytosol" spatial:spatialDimensions="3"/>
- <spatial:domainType spatial:id="Nucleus_Cytosol_membrane" spatial:spatialDimensions="2"/>
- <spatial:domainType spatial:id="Nucleus" spatial:spatialDimensions="3"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfSampledFieldGeometrys>
- <spatial:sampledFieldGeometry spatial:id="mySampledField">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:minValue="0.0" spatial:maxValue="0.0" spatial:id="Extracellular" spatial:domainType="Extracellular" spatial:sampledValue="0.0"/>
- <spatial:sampledVolume spatial:minValue="0.0" spatial:maxValue="0.0" spatial:id="Cytosol" spatial:domainType="Cytosol" spatial:sampledValue="128.0"/>
- <spatial:sampledVolume spatial:minValue="0.0" spatial:maxValue="0.0" spatial:id="Nucleus" spatial:domainType="Nucleus" spatial:sampledValue="255.0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfSampledFieldGeometrys>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:samplesLength="3440" spatial:numSamples3="1" spatial:id="imgtest" spatial:numSamples1="800" spatial:numSamples2="950">120 218 237 221 193 142 27 57 12 64 193 124 122 255 185 22 216 195 30 54 240 216 238 97 83 20 89 239 154 75 183 168 2 237 96 146 249 243 71 146 36 73 146 36 73 146 36 73 26 217 117 57 3 233 181 15 64 164 215 60 248 144 248 144 238 240 224 67 226 67 226 67 138 229 193 135 196 135 196 135 196 135 148 197 131 15 137 15 137 15 137 15 41 139 7 31 18 31 18 31 82 44 15 62 36 62 36 62 164 88 30 124 72 124 72 124 72 177 60 248 144 248 144 248 144 98 121 240 33 241 33 241 33 197 242 224 67 226 67 226 67 226 67 202 226 193 135 196 135 196 135 20 203 3 16 137 15 137 15 137 15 137 15 169 0 15 62 36 62 36 31 175 36 62 36 62 164 237 62 28 136 100 125 72 124 72 124 72 124 72 124 72 133 121 240 33 241 33 241 33 241 33 101 241 224 67 226 67 186 229 3 16 137
- 15 233 14 15 62 36 62 36 62 36 62 164 52 31 128 72 175 121 240 33 241 33 241 33 241 33 101 241 224 67 250 193 7 32 18 31 18 31 82 176 15 64 164 215 60 248 144 248 144 248 144 248 144 248 144 246 243 224 67 226 67 186 229 3 16 241 193 135 196 135 20 203 131 15 241 193 135 196 135 20 236 3 16 241 193 135 116 135 7 31 226 131 15 137 15 137 15 137 15 137 15 137 15 137 15 169 27 15 62 196 7 32 18 31 18 31 82 26 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 32 18 31 82 48 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 64 196 7 31 18 31 18 31 82 26 15 62 196 7 31 210 45 31 128 8 15 62 36 62 36 62 36 62 164 253 60 248 16 31 128 72 124 72 193 60 248 16 31 124 72 124 72 177 60 248 16 31 124 72 124 72 124 72 89 60 0 17 31 124 136 15 62 164 96 30 124 136 15 62 196 7 31 18 31 82 22 15 62 196 7 31 226 131 15 41 150 7 31 226 13
- 1 15 241 193 135 20 203 131 15 241 193 135 248 224 67 138 229 193 135 248 224 67 124 240 33 197 242 224 67 124 240 33 62 248 144 98 121 240 33 62 248 16 31 124 72 124 72 89 60 248 16 31 124 136 15 62 164 88 30 124 136 15 62 196 7 30 146 245 33 241 33 241 33 241 33 29 201 131 15 241 193 135 248 224 67 138 229 193 135 248 224 67 124 240 33 197 242 224 67 124 240 33 62 248 144 240 144 248 144 248 144 10 243 224 67 124 240 33 62 240 144 172 15 137 15 137 15 169 48 15 62 196 7 31 226 3 15 201 250 144 248 144 248 144 10 243 224 67 124 240 33 60 240 144 248 144 146 120 240 33 62 248 16 31 124 72 177 60 248 16 31 124 8 15 62 36 62 36 62 164 253 60 248 16 31 124 8 15 62 36 62 36 60 36 62 164 194 60 248 16 31 124 136 15 62 164 88 30 124 136 15 62 132 7 31 18 31 18 31 210 126 30 124 136 15 64 132 7 31 226 131 15 41 141 7 31 226 3 16 241 193 135 240 224 67 226 67 42 192 3 16 241 193 135 248 224 67 120 0 34 37 250 0 68 120 0 34 62 0 17 30 128 72 153 62 0 17 31 128 8 15 62 196 7 31 82 26
- 15 62 196 7 30 194 131 15 241 129 135 132 135 196 135 84 214 135 19 22 30 120 136 15 62 132 7 30 18 31 210 102 30 124 136 15 60 132 7 31 226 131 15 9 15 137 15 169 46 15 62 196 7 31 226 131 15 225 193 135 196 135 180 159 7 31 226 131 15 225 193 135 248 224 67 202 226 193 135 248 224 67 120 240 33 62 248 144 178 120 240 33 60 248 16 31 124 8 15 62 196 7 31 210 126 30 124 136 15 62 132 7 31 226 3 16 225 193 135 196 135 84 154 7 31 226 131 15 225 193 135 248 224 67 120 240 33 241 33 85 230 193 135 248 224 67 120 240 33 62 248 16 30 124 72 124 72 149 121 240 33 60 248 16 31 124 8 15 62 196 7 31 210 126 30 124 136 15 62 132 7 31 226 131 15 225 193 135 196 135 84 153 7 31 226 131 15 225 193 135 240 0 68 124 240 33 21 224 193 135 248 224 67 120 240 33 60 248 16 31 124 72 251 121 0 34 60 248 16 31 124 8 15 62 196 7 32 194 131 15 169 54 15 62 196 7 31 194 131 15 241 193 135 240 224 67 120 240 33 241 33 157 201 131 15 225 1 136 248 224 67 120 240 33 60 248 16 31 124 72 165 121 240 33
- 60 0 17 31 124 8 15 62 132 7 31 226 131 15 169 52 15 62 132 7 31 226 131 15 225 1 136 240 224 67 124 240 33 149 230 193 135 248 224 67 120 240 33 60 248 16 31 124 8 15 64 132 7 30 210 161 62 0 17 30 124 8 15 62 132 7 31 194 131 15 225 193 135 240 224 67 58 147 7 31 194 131 15 225 193 135 248 224 67 120 0 34 62 248 16 30 124 72 135 242 224 67 124 240 33 60 0 17 31 124 8 15 62 132 7 31 226 3 16 41 135 199 250 47 62 132 199 223 46 86 52 17 83 211 209 60 214 15 241 161 209 62 214 219 0 209 76 30 235 179 248 208 60 30 235 139 248 208 40 30 235 235 248 208 16 31 235 94 124 168 59 143 245 155 0 81 39 30 255 187 217 235 247 241 161 6 60 214 147 241 161 131 121 172 199 227 67 167 242 88 41 1 162 35 125 172 85 19 136 9 106 16 143 175 133 24 161 70 241 248 18 136 25 106 183 143 149 29 31 58 133 199 218 17 32 58 130 199 218 21 31 42 207 99 109 140 15 225 193 135 78 245 177 214 9 64 12 82 3 215 199 199 64 76 82 35 121 124 8 196 40 53 147 199 103 64 204 82 67 121 0 34 60 126 11 196 56 53
- 149 199 39 64 204 83 201 62 214 58 8 136 121 106 46 143 247 64 12 84 83 63 93 1 34 60 248 16 30 143 1 49 84 77 230 241 14 136 169 42 141 71 73 31 139 15 89 31 55 129 24 171 134 243 224 67 62 93 1 34 60 248 208 161 60 10 251 88 124 104 55 15 62 132 7 31 82 51 30 63 1 49 94 101 240 56 213 7 32 202 224 81 219 135 5 34 60 248 16 30 128 200 151 143 60 32 134 44 60 248 16 30 62 96 9 15 11 68 120 88 32 194 131 15 249 155 93 64 132 7 31 194 227 84 30 126 8 75 201 58 142 226 193 135 240 0 68 120 240 161 242 60 58 249 0 68 211 121 88 32 194 195 2 81 5 30 124 8 143 86 60 252 87 213 194 3 16 225 241 128 15 64 52 155 135 223 38 37 62 44 16 225 97 129 136 15 62 132 7 31 234 227 99 241 33 60 90 250 240 5 93 120 240 33 60 248 80 57 30 189 125 0 162 223 241 56 221 135 5 34 60 248 208 22 30 221 125 0 162 223 240 224 67 120 52 230 241 206 7 32 154 204 195 2 209 99 60 38 248 0 68 147 121 188 245 1 136 238 241 224 67 120 52 231 1 136 158 225 193 135 240 104 207 227 189 15 64 116 205 245 97 129 2
- 32 1 30 131 124 0 130 199 92 30 124 40 158 71 35 31 128 40 156 7 31 194 131 15 64 240 224 131 15 133 234 152 230 3 16 60 198 250 0 68 193 58 230 249 32 4 143 161 60 62 244 1 8 30 51 125 0 162 88 30 51 125 0 130 7 31 128 232 226 131 15 61 198 99 170 15 64 240 152 199 195 2 81 40 143 185 62 0 193 131 15 62 240 224 131 15 61 195 99 176 15 64 240 224 131 15 60 248 240 1 75 143 240 224 67 124 12 226 193 135 172 15 62 132 7 31 218 202 163 163 15 63 97 130 7 31 124 232 121 30 124 8 143 89 60 248 192 131 15 255 196 86 79 235 224 67 120 240 129 7 30 120 124 11 196 117 162 131 15 62 240 224 131 15 60 248 224 67 137 58 186 242 248 16 136 75 133 7 31 124 224 193 7 31 120 224 193 135 210 116 240 33 60 248 224 3 15 60 248 192 131 15 64 148 197 131 15 215 11 15 62 248 192 3 15 62 232 224 131 15 37 241 232 237 99 241 65 7 30 124 224 193 7 31 74 214 193 7 31 120 204 229 193 7 30 124 252 18 136 171 70 199 84 30 22 8 30 124 240 65 7 30 124 40 149 7 31 124 224 193 7 31 120 224 193 7 29 124 248
- 9 69 60 248 224 67 120 240 161 186 60 248 224 3 15 62 0 161 131 15 11 4 15 62 248 192 131 15 62 180 159 7 31 128 208 193 7 31 120 240 193 7 29 124 60 230 3 16 58 70 242 224 131 14 62 248 192 131 15 95 64 232 224 131 15 21 224 193 7 32 120 240 193 7 30 124 240 129 7 31 79 250 0 4 15 62 248 160 131 143 91 62 0 193 131 15 62 232 0 228 150 15 64 240 224 131 15 58 248 224 131 14 62 130 125 0 130 7 31 124 208 193 199 45 31 128 224 193 7 31 120 240 193 7 29 128 4 251 0 4 15 62 248 160 3 16 62 240 224 131 15 58 0 225 131 14 62 10 248 0 4 143 97 64 248 160 131 15 62 232 224 131 15 60 248 216 233 3 16 60 102 1 225 131 14 62 248 160 3 144 4 31 128 224 49 10 8 31 116 240 193 7 29 128 100 248 0 132 14 62 248 192 3 144 59 60 0 161 131 15 62 232 224 227 158 15 64 240 224 131 15 58 248 184 229 3 16 60 166 0 225 131 14 62 98 121 240 129 199 16 32 23 32 116 240 193 7 29 128 240 65 7 32 21 124 0 2 199 8 32 124 176 193 7 31 112 0 194 7 29 124 212 240 1 8 29 19 128 240 65 7 32 124 208 193 71 170
- 15 64 232 232 239 227 226 3 15 64 248 160 3 144 92 31 128 224 193 7 31 116 204 5 114 241 129 7 32 207 248 0 132 142 230 64 248 192 3 16 62 232 0 36 223 7 32 120 244 6 194 7 29 128 240 129 7 32 27 124 0 66 71 107 33 124 224 1 136 15 88 116 16 2 8 29 128 240 65 7 32 190 128 224 65 72 3 31 128 208 209 152 200 197 7 29 128 240 65 7 32 59 120 0 66 71 87 32 49 239 78 135 58 10 137 122 115 58 212 208 72 220 107 211 161 126 66 248 160 3 145 4 30 67 129 184 233 173 149 240 65 7 38 41 60 46 58 212 75 72 240 75 210 161 78 64 46 62 240 0 36 139 199 36 32 238 115 123 33 23 31 120 16 146 200 227 162 67 77 128 60 243 126 116 168 5 145 139 15 60 8 225 131 14 70 170 232 104 15 196 189 29 193 228 226 131 14 70 54 240 184 232 208 225 68 158 125 21 58 244 136 144 171 131 142 166 62 220 207 41 91 228 226 131 14 64 182 241 232 7 196 181 28 35 36 229 21 232 208 153 68 146 94 128 14 157 8 228 226 131 14 66 54 235 104 3 196 53 156 4 228 226 131 13 66 10 232 56 30 136 203 55 141 200 197 7 28 128 20
- 209 113 40 16 247 109 164 144 45 207 13 135 142 0 178 235 185 233 80 113 33 91 159 26 15 85 38 178 253 153 233 80 89 35 21 30 24 14 213 52 82 227 97 217 80 45 33 255 254 121 157 103 165 67 21 132 84 125 82 58 180 153 72 237 231 132 67 58 206 135 193 8 16 58 4 8 30 226 131 14 1 130 135 248 224 67 42 9 196 52 196 7 30 2 132 15 241 193 135 248 192 67 128 240 33 241 33 157 8 196 32 196 7 31 2 132 15 241 1 136 248 224 67 128 0 34 213 246 1 136 0 33 68 124 32 34 64 0 17 31 132 8 16 64 164 51 124 0 34 64 0 17 31 128 8 16 64 196 7 32 2 4 16 201 39 44 201 2 145 44 16 201 2 145 0 225 67 124 240 33 64 248 16 31 124 8 16 64 196 7 31 210 33 64 204 67 124 0 34 64 0 17 32 124 136 15 64 4 8 31 146 5 34 89 32 146 5 34 89 32 18 32 124 136 15 62 4 8 31 226 131 15 1 130 135 248 224 67 170 15 196 40 196 7 30 2 132 15 241 129 135 0 193 67 124 224 33 21 5 98 4 226 3 15 1 66 135 248 192 67 128 240 33 109 255 6 226 252 197 7 40 2 4 17 241 193 136 0 1 69 42 236 3 21 1 194 137 248 128 73 128 16 35 62
- 40 17 32 148 72 131 129 80 34 62 72 17 32 160 136 15 70 4 8 35 226 3 18 1 194 136 248 96 68 128 136 27 64 68 137 248 96 68 128 64 34 62 24 17 32 140 136 15 68 4 8 33 226 67 110 19 32 66 5 16 65 34 62 184 17 32 140 136 15 68 4 8 34 226 131 16 1 34 66 248 16 33 128 8 16 62 4 8 32 2 68 128 148 244 193 12 31 122 33 196 158 1 68 62 137 241 33 64 0 17 32 128 168 236 119 21 183 150 15 217 40 128 8 18 64 132 8 31 2 4 16 17 2 136 0 17 31 128 8 16 66 4 8 32 226 67 132 0 34 66 0 209 195 68 200 225 67 214 11 32 66 4 16 49 194 135 16 1 68 140 0 34 68 248 16 35 2 132 17 1 34 68 0 17 35 128 136 16 64 68 8 32 34 4 16 17 194 135 8 1 68 132 0 34 68 196 135 24 1 68 136 0 34 68 0 17 34 128 136 17 64 196 8 31 98 4 16 33 2 136 16 1 68 66 4 16 33 2 136 16 1 68 132 240 33 66 0 17 33 128 136 16 62 132 8 32 98 4 16 9 23 62 196 8 32 66 132 15 33 2 136 16 225 67 132 0 34 68 248 16 32 128 72 125 133 152 169 16 225 67 132 0 34 66 248 16 34 128 8 17 62 132 8 32 66 4 16 169 35 17 19 20 34 128 8 17 64 68 8
- 32 66 132 15 33 2 136 16 1 68 58 216 136 137 9 17 64 132 8 32 66 4 16 33 2 136 48 225 67 42 111 196 124 68 8 32 66 4 16 33 194 135 16 1 68 132 0 34 149 39 98 40 34 4 16 33 194 135 8 1 68 132 0 34 68 0 145 170 11 49 10 17 2 136 8 225 67 132 240 33 66 240 144 246 11 49 0 17 130 135 8 193 67 132 240 33 66 240 144 246 10 113 228 34 132 15 1 194 135 8 1 68 132 240 33 21 16 226 168 69 8 31 34 132 15 17 2 136 148 6 196 33 139 16 62 68 8 31 34 132 15 41 75 136 195 21 32 128 136 16 62 4 8 31 82 154 16 231 42 66 0 17 33 124 136 16 62 36 64 164 10 68 156 167 8 225 67 132 0 34 5 11 113 148 66 132 15 33 2 136 20 76 196 17 10 17 62 132 8 32 82 48 17 71 39 68 248 144 248 144 98 137 56 50 17 194 135 116 71 136 227 18 34 127 131 224 67 136 88 24 210 55 68 156 138 244 210 136 3 145 94 27 113 24 210 43 37 14 65 146 36 73 146 36 73 146 36 73 146 36 73 146 36 73 146 36 73 82 195 254 1 20 164 156 86 </spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- <listOfUnitDefinitions>
- <unitDefinition id="substance">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1" kind="item"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="volume">
- <listOfUnits>
- <unit scale="0" exponent="3" multiplier="1E-6" kind="metre"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="area">
- <listOfUnits>
- <unit scale="0" exponent="2" multiplier="1E-6" kind="metre"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="molecules">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1" kind="item"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="umol_um3_litre_1">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1E-21" kind="mole"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="um3">
- <listOfUnits>
- <unit scale="0" exponent="3" multiplier="1E-6" kind="metre"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="um2">
- <listOfUnits>
- <unit scale="0" exponent="2" multiplier="1E-6" kind="metre"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="uM_um3_molecules_1">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1E-21" kind="dimensionless"/>
- <unit scale="0" exponent="-1" multiplier="1" kind="item"/>
- <unit scale="0" exponent="1" multiplier="1" kind="mole"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="molecules_um_2_s_1">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1E12" kind="dimensionless"/>
- <unit scale="0" exponent="1" multiplier="1" kind="item"/>
- <unit scale="0" exponent="-2" multiplier="1" kind="metre"/>
- <unit scale="0" exponent="-1" multiplier="1" kind="second"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="pA_um_2">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1" kind="dimensionless"/>
- <unit scale="0" exponent="1" multiplier="1" kind="ampere"/>
- <unit scale="0" exponent="-2" multiplier="1" kind="metre"/>
- </listOfUnits>
- </unitDefinition>
- <unitDefinition id="uM_um_s_1">
- <listOfUnits>
- <unit scale="0" exponent="1" multiplier="1E-9" kind="dimensionless"/>
- <unit scale="0" exponent="-2" multiplier="1" kind="metre"/>
- <unit scale="0" exponent="1" multiplier="1" kind="mole"/>
- <unit scale="0" exponent="-1" multiplier="1" kind="second"/>
- </listOfUnits>
- </unitDefinition>
- </listOfUnitDefinitions>
- <listOfCompartments>
- <compartment id="Extracellular" constant="true" spatialDimensions="3" name="Extracellular">
- </compartment>
- <compartment id="Cytosol_Extracellular_membrane" constant="true" spatialDimensions="2" name="Cytosol_Extracellular_membrane">
- </compartment>
- <compartment id="Cytosol" constant="true" spatialDimensions="3" name="Cytosol">
- </compartment>
- <compartment id="Nucleus_Cytosol_membrane" constant="true" spatialDimensions="2" name="Nucleus_Cytosol_membrane">
- </compartment>
- <compartment id="Nucleus" constant="true" spatialDimensions="3" name="Nucleus">
- </compartment>
- </listOfCompartments>
- <listOfSpecies>
- <species id="s1_nuc" spatial:isSpatial="true" initialConcentration="0" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="false" substanceUnits="molecules" compartment="Nucleus">
- <annotation>
- <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
- <vcell:VCMLSpecific>
- <vcell:Compound Name="s1_2"/>
- </vcell:VCMLSpecific>
- </vcell:VCellInfo>
- </annotation>
- </species>
- <species id="s1_cyt" spatial:isSpatial="true" initialConcentration="10" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="false" substanceUnits="molecules" compartment="Cytosol">
- <annotation>
- <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
- <vcell:VCMLSpecific>
- <vcell:Compound Name="s1_2"/>
- </vcell:VCMLSpecific>
- </vcell:VCellInfo>
- </annotation>
- </species>
- <species id="s2_nuc" spatial:isSpatial="true" initialConcentration="5" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="false" substanceUnits="molecules" compartment="Nucleus">
- <annotation>
- <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
- <vcell:VCMLSpecific>
- <vcell:Compound Name="s2_2"/>
- </vcell:VCMLSpecific>
- </vcell:VCellInfo>
- </annotation>
- </species>
- <species id="s1_EC" spatial:isSpatial="true" initialConcentration="0" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="false" substanceUnits="molecules" compartment="Extracellular">
- <annotation>
- <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
- <vcell:VCMLSpecific>
- <vcell:Compound Name="s1_2"/>
- </vcell:VCMLSpecific>
- </vcell:VCellInfo>
- </annotation>
- </species>
- </listOfSpecies>
- <listOfParameters>
- <parameter id="x" value="0">
- <spatial:spatialSymbolReference xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:spatialRef="x"/>
- </parameter>
- <parameter id="y" value="0">
- <spatial:spatialSymbolReference xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:spatialRef="y"/>
- </parameter>
- <parameter id="s1_nuc_diff" constant="true" value="10">
- <spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:variable="s1_nuc"/>
- </parameter>
- <parameter id="s1_nuc_BC_Xm" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Nucleus" spatial:coordinateBoundary="Xmin" spatial:variable="s1_nuc" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_nuc_BC_Xp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Nucleus" spatial:coordinateBoundary="Xmax" spatial:variable="s1_nuc" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_nuc_BC_Ym" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Nucleus" spatial:coordinateBoundary="Ymin" spatial:variable="s1_nuc" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_nuc_BC_Yp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Nucleus" spatial:coordinateBoundary="Ymax" spatial:variable="s1_nuc" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_cyt_diff" constant="true" value="10">
- <spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:variable="s1_cyt"/>
- </parameter>
- <parameter id="s1_cyt_BC_Xm" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Cytosol" spatial:coordinateBoundary="Xmin" spatial:variable="s1_cyt" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_cyt_BC_Xp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Cytosol" spatial:coordinateBoundary="Xmax" spatial:variable="s1_cyt" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_cyt_BC_Ym" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Cytosol" spatial:coordinateBoundary="Ymin" spatial:variable="s1_cyt" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_cyt_BC_Yp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:coordinateBoundary="Ymax" spatial:variable="s1_cyt" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_EC_diff" constant="true" value="10">
- <spatial:diffusionCoefficient xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:variable="s1_EC"/>
- </parameter>
- <parameter id="s1_EC_BC_Xm" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Extracellular" spatial:coordinateBoundary="Xmin" spatial:variable="s1_EC" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_EC_BC_Xp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Extracellular" spatial:coordinateBoundary="Xmax" spatial:variable="s1_EC" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_EC_BC_Ym" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Extracellular" spatial:coordinateBoundary="Ymin" spatial:variable="s1_EC" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="s1_EC_BC_Yp" constant="true" value="0">
- <spatial:boundaryCondition xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" spatial:boundaryDomainType="Extracellular" spatial:coordinateBoundary="Ymax" spatial:variable="s1_EC" spatial:type="DIRICHLET"/>
- </parameter>
- <parameter id="KMOLE" constant="true" value="0.00166112956810631" units="uM_um3_molecules_1"/>
- </listOfParameters>
- <listOfRules>
- <assignmentRule metaid="CDMT00006" variable="s2_nuc">
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> x </ci>
- </math>
- </assignmentRule>
- </listOfRules>
- <listOfReactions>
- <reaction id="flux1" name="flux1" reversible="true" fast="false">
- <listOfReactants>
- <speciesReference species="s1_cyt" stoichiometry="1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="s1_nuc" stoichiometry="1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <cn> 5 </cn>
- <ci> s1_cyt </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="I" value="0" units="pA_um_2"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- <reaction id="flux2" name="flux2" reversible="true" fast="false">
- <listOfReactants>
- <speciesReference species="s1_cyt" stoichiometry="1"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="s1_EC" stoichiometry="1"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <cn> 5 </cn>
- <ci> s1_cyt </ci>
- </apply>
- </math>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- </model>
-</sbml>
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 10:54:46
|
Revision: 2274
http://sourceforge.net/p/jsbml/code/2274
Author: niko-rodrigue
Date: 2015-05-01 10:54:44 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2262
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2262
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/JSBML.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
branches/astnode2-merging-alternate/dev/eclipse/JSBML_templates.xml
branches/astnode2-merging-alternate/extensions/spatial/resources/org/sbml/jsbml/ext/spatial/Messages.xml
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate 2015-05-01 10:54:44 UTC (rev 2274)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2257
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2262
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 10:54:44 UTC (rev 2274)
@@ -92,5 +92,10 @@
<entry key="ASTNode.reduceToBinary3">NOT node with {0,number,integer} children left unchanged</entry>
<entry key="ASTNode.reduceToBinary4">XOR node with {0,number,integer} children left unchanged</entry>
<entry key="ASTNode.reduceToBinary5">{0} node with {1,number,integer} children left unchanged</entry>
+ <entry key="ASTNode.setType">setType called: typeBefore={0} typeAfter={1}</entry>
+ <entry key="ASTNode.setUnits1">Unexpected attribute {0}, a unit can only be assigned to literal numbers.</entry>
+ <entry key="ASTNode.setUnits2">Unexpected attribute {0}, only a valid unit kind or the identifier of a unit definition are allowed here.</entry>
+ <entry key="ASTNode.setUnits3">Cannot set unit {0} for a numbers in an ASTNode before SBML Level 3.</entry>
+ <entry key="ASTNode.toString">Could not compile ASTNode to formula: {0}</entry>
</properties>
\ No newline at end of file
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -4064,6 +4064,12 @@
* unit definition.
*/
public void setUnits(String unitId) {
+ if (!isNumber()) {
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("ASTNode.setUnits1"),
+ unitId));
+ }
+
((ASTCnNumberNode<?>) astnode2).setUnits(unitId);
}
@@ -4322,7 +4328,6 @@
@Override
public String toString() {
String formula = "";
- String errorMsg = "Could not compile ASTNode to formula: ";
try {
formula = compile(new FormulaCompiler()).toString();
//formula = compile(new FormulaCompiler()).toString();
@@ -4331,15 +4336,15 @@
e.printStackTrace();
if (logger.isDebugEnabled()) {
- logger.error(errorMsg, e);
+ logger.error(MessageFormat.format(resourceBundle.getString("ASTNode.toString"), e.getMessage()), e);
} else {
// TODO: Do not print this message if parsing the file !!! Or remove it
- logger.warn(errorMsg + e.getMessage());
+ logger.warn(MessageFormat.format(resourceBundle.getString("ASTNode.toString"), e.getMessage()));
}
} catch (RuntimeException e) {
// added to prevent a crash when we cannot create the formula
if (logger.isDebugEnabled()) {
- logger.error(errorMsg, e);
+ logger.error(MessageFormat.format(resourceBundle.getString("ASTNode.toString"), e.getMessage()), e);
}
}
return formula;
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/JSBML.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/JSBML.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/JSBML.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -80,7 +80,7 @@
/**
* The current version number of JSBML.
*/
- private static final String jsbmlVersion = "1.0-rc1"; // TODO: replace automatically this version number with [BUILD.NUMBER]
+ private static final String jsbmlVersion = "1.1-alpha"; // TODO: replace automatically this version number with [BUILD.NUMBER]
/**
*
*/
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -356,6 +356,7 @@
* @param String units
*/
public void setUnits(String units) {
+ // TODO - add some checks on the unit, like it was done before?
String old = this.units;
this.units = units;
firePropertyChange(TreeNodeChangeEvent.units, old, this.units);
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -163,7 +163,7 @@
System.out.println(Calendar.getInstance().getTime());
String fileName = file.getAbsolutePath();
- String jsbmlWriteFileName = fileName.replaceFirst(".xml", "-jsbml.xml");
+ String jsbmlWriteFileName = fileName.replaceFirst("\\.xml", "-jsbml.xml");
System.out.printf("Reading %s and writing %s\n",
fileName, jsbmlWriteFileName);
Modified: branches/astnode2-merging-alternate/dev/eclipse/JSBML_templates.xml
===================================================================
--- branches/astnode2-merging-alternate/dev/eclipse/JSBML_templates.xml 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/dev/eclipse/JSBML_templates.xml 2015-05-01 10:54:44 UTC (rev 2274)
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?><templates><template autoinsert="true" context="java" deleted="false" description="getAllowsChildren-, getChildcount-, getChildAt- methods" enabled="true" name="JSBML_Children">${:import(java.text.MessageFormat, org.sbml.jsbml.ListOf, org.sbml.jsbml.SBase)}
@Override
-public boolean getAllowsChildren() {
+public boolean getAllowsChildren() {
return ${true_false};
}
@@ -9,7 +9,7 @@
int count = super.getChildCount();
- // TODO: the following must be implemented for each XML child variable
+ // TODO: the following must be implemented for each XML child variable
// if (isSetListOfFoos()) {
// count++;
// }
@@ -17,32 +17,33 @@
return count;
}
- public TreeNode getChildAt(int index) {
- if (index < 0) {
- throw new IndexOutOfBoundsException(index + " < 0");
- }
+ public TreeNode getChildAt(int index) {
+ if (index < 0) {
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ resourceBundle.getString("IndexSurpassesBoundsException"), index, 0));
+ }
- int count = super.getChildCount(), pos = 0;
-
- if (index < count) {
- return super.getChildAt(index);
- } else {
- index -= count;
- }
+ int count = super.getChildCount(), pos = 0;
+
+ if (index < count) {
+ return super.getChildAt(index);
+ } else {
+ index -= count;
+ }
- // TODO: the following must be implemented for each ListOf* variable
- // if (isSetListOfFoos()) {
- // if (pos == index) {
- // return getListOfFoos();
- // }
- // pos++;
- // }
+ // TODO: the following must be implemented for each ListOf* variable
+ // if (isSetListOfFoos()) {
+ // if (pos == index) {
+ // return getListOfFoos();
+ // }
+ // pos++;
+ // }
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
- index, Math.min(pos, 0)));
- }
-
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ resourceBundle.getString("IndexExceedsBoundsException"),
+ index, Math.min(pos, 0)));
+ }
+
</template>
<template autoinsert="false" context="java" deleted="false" description="Standard constructors for JSBML classes" enabled="true" name="JSBML_Constructors_id_name">/**
* Creates an ${enclosing_type} instance
@@ -105,7 +106,7 @@
public ${enclosing_type}(${enclosing_type} obj) {
super(obj);
- // TODO: copy all class attributes, e.g.:
+ // TODO: copy all class attributes, e.g.:
// bar = obj.bar;
}
@@ -204,10 +205,10 @@
listOf${Field:var}s.setSBaseListType(ListOf.Type.other);
// TODO - if the class containing this code is not of type SBasePlugin, replace the 3 lines by just "registerChild(listOf${Field:var}s);"
- if (isSetExtendedSBase()) {
- extendedSBase.registerChild(listOf${Field:var}s);
- }
+ if (isSetExtendedSBase()) {
+ extendedSBase.registerChild(listOf${Field:var}s);
}
+ }
return listOf${Field:var}s;
}
@@ -225,7 +226,7 @@
// TODO - if the class containing this code is not of type SBasePlugin, replace the 3 lines by just "registerChild(listOf${Field:var}s);"
if (isSetExtendedSBase()) {
- extendedSBase.registerChild(this.listOf${Field:var}s);
+ extendedSBase.registerChild(this.listOf${Field:var}s);
}
}
@@ -416,7 +417,7 @@
if (!isAttributeRead) {
isAttributeRead = true;
- // TODO: this must be done for each attribute
+ // TODO: this must be done for each attribute
if (attributeName.equals(${constants_class}.${field:var})) {
set${Field:var}(StringTools.parseSBMLInt(value));
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/resources/org/sbml/jsbml/ext/spatial/Messages.xml
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/resources/org/sbml/jsbml/ext/spatial/Messages.xml 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/resources/org/sbml/jsbml/ext/spatial/Messages.xml 2015-05-01 10:54:44 UTC (rev 2274)
@@ -31,5 +31,6 @@
<entry key="COMPARTMENT_MAPPING_NOT_SET">Spatial's compartmenMapping is not set for the compartment this species resides in.</entry>
<entry key="COULD_NOT_READ">Could not recognized the value {0} for the attribute {1} on the ''SpatialSpecies'' element.</entry>
+ <entry key="COULD_NOT_READ_ATTRIBUTE">Could not recognized the value {0} for the attribute {1} on the ''{2}'' element.</entry>
</properties>
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -27,9 +27,11 @@
import javax.swing.tree.TreeNode;
import javax.xml.stream.XMLStreamException;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.xml.XMLNode;
+import org.sbml.jsbml.xml.parsers.SpatialParser;
/**
@@ -86,6 +88,11 @@
/**
*
*/
+ private Logger logger = Logger.getLogger(SampledField.class);
+
+ /**
+ *
+ */
public SampledField() {
super();
}
@@ -219,7 +226,7 @@
* @param numSamples1
*/
public void setNumSamples1(int numSamples1) {
- int oldNumSamples1 = this.numSamples1;
+ Integer oldNumSamples1 = this.numSamples1;
this.numSamples1 = numSamples1;
firePropertyChange(SpatialConstants.numSamples1, oldNumSamples1, this.numSamples1);
}
@@ -233,7 +240,7 @@
*/
public boolean unsetNumSamples1() {
if (isSetNumSamples1()) {
- int oldNumSamples1 = numSamples1;
+ Integer oldNumSamples1 = numSamples1;
numSamples1 = null;
firePropertyChange(SpatialConstants.numSamples1, oldNumSamples1, numSamples1);
return true;
@@ -271,7 +278,7 @@
* @param numSamples2
*/
public void setNumSamples2(int numSamples2) {
- int oldNumSamples2 = this.numSamples2;
+ Integer oldNumSamples2 = this.numSamples2;
this.numSamples2 = numSamples2;
firePropertyChange(SpatialConstants.numSamples2, oldNumSamples2, this.numSamples2);
}
@@ -285,7 +292,7 @@
*/
public boolean unsetNumSamples2() {
if (isSetNumSamples2()) {
- int oldNumSamples2 = numSamples2;
+ Integer oldNumSamples2 = numSamples2;
numSamples2 = null;
firePropertyChange(SpatialConstants.numSamples2, oldNumSamples2, numSamples2);
return true;
@@ -324,7 +331,7 @@
* @param numSamples3
*/
public void setNumSamples3(int numSamples3) {
- int oldNumSamples3 = this.numSamples3;
+ Integer oldNumSamples3 = this.numSamples3;
this.numSamples3 = numSamples3;
firePropertyChange(SpatialConstants.numSamples3, oldNumSamples3, this.numSamples3);
}
@@ -338,7 +345,7 @@
*/
public boolean unsetNumSamples3() {
if (isSetNumSamples3()) {
- int oldNumSamples3 = numSamples3;
+ Integer oldNumSamples3 = numSamples3;
numSamples3 = null;
firePropertyChange(SpatialConstants.numSamples3, oldNumSamples3, numSamples3);
return true;
@@ -785,37 +792,29 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetNumSamples1()) {
- attributes.remove("numSamples1");
attributes.put(SpatialConstants.shortLabel + ":numSamples1", String.valueOf(getNumSamples1()));
}
-
if (isSetNumSamples2()) {
- attributes.remove("numSamples2");
attributes.put(SpatialConstants.shortLabel + ":numSamples2",
String.valueOf(getNumSamples2()));
}
if (isSetNumSamples3()) {
- attributes.remove("numSamples3");
attributes.put(SpatialConstants.shortLabel + ":numSamples3",
String.valueOf(getNumSamples3()));
}
if (isSetDataType()) {
- attributes.remove("dataType");
attributes.put(SpatialConstants.shortLabel + ":dataType",
getDataType().toString());
}
if (isSetCompression()) {
- attributes.remove("compression");
attributes.put(SpatialConstants.shortLabel + ":compression",
getCompression().toString());
}
if (isSetInterpolation()) {
- attributes.remove("interpolation");
attributes.put(SpatialConstants.shortLabel + ":interpolation",
getInterpolation().toString());
}
if (isSetSamplesLength()) {
- attributes.remove("samplesLength");
attributes.put(SpatialConstants.shortLabel + ":samplesLength",
String.valueOf(getSamplesLength()));
}
@@ -825,31 +824,28 @@
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
+ boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.numSamples1)) {
try {
setNumSamples1(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.numSamples1);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.numSamples1, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.numSamples2)) {
try {
setNumSamples2(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.numSamples2);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.numSamples2, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.numSamples3)) {
try {
setNumSamples3(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.numSamples3);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.numSamples3, getElementName()));
}
}
@@ -857,28 +853,28 @@
try {
setInterpolation(InterpolationKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.interpolation);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.interpolation, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.compression)) {
try {
setCompression(CompressionKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.compression, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.samplesLength)) {
try {
setSamplesLength(String.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.samplesLength);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.samplesLength, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(DataKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
}
}
else {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -395,7 +395,7 @@
SpatialConstants.domainType);
}
}
- if (attributeName.equals(SpatialConstants.sampledValue)) {
+ else if (attributeName.equals(SpatialConstants.sampledValue)) {
try {
setSampledValue(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
@@ -403,7 +403,7 @@
SpatialConstants.sampledValue);
}
}
- if (attributeName.equals(SpatialConstants.minValue)) {
+ else if (attributeName.equals(SpatialConstants.minValue)) {
try {
setMinValue(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
@@ -411,7 +411,7 @@
SpatialConstants.minValue);
}
}
- if (attributeName.equals(SpatialConstants.maxValue)) {
+ else if (attributeName.equals(SpatialConstants.maxValue)) {
try {
setMaxValue(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -528,6 +528,11 @@
public static final String spatialRef = "spatialRef";
/**
+ *
+ */
+ public static final Object listOfSampledFields = "listOfSampledFields";
+
+ /**
* @param level
* @param version
* @return
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 10:54:44 UTC (rev 2274)
@@ -101,11 +101,15 @@
@Override
public void processCharactersOf(String elementName, String characters,
Object contextObject) {
- if (contextObject instanceof SpatialPoints) {
+ if (contextObject instanceof SampledField) {
+ SampledField sampledField = (SampledField) contextObject;
+ sampledField.append(characters);
+ }
+ else if (contextObject instanceof SpatialPoints) {
SpatialPoints spatialPoints = (SpatialPoints) contextObject;
spatialPoints.append(characters);
}
- if (contextObject instanceof ParametricObject) {
+ else if (contextObject instanceof ParametricObject) {
ParametricObject parametricObject = (ParametricObject) contextObject;
parametricObject.append(characters);
}
@@ -114,8 +118,24 @@
@Override
public void writeCharacters(SBMLObjectForXML xmlObject,
Object sbmlElementToWrite) {
- // TODO Auto-generated method stub
- super.writeCharacters(xmlObject, sbmlElementToWrite);
+ if(sbmlElementToWrite instanceof SampledField) {
+ SampledField sampledField = (SampledField) sbmlElementToWrite;
+ if(sampledField.isSetSamples()) {
+ xmlObject.setCharacters(sampledField.getSamples());
+ }
+ }
+ else if(sbmlElementToWrite instanceof SpatialPoints) {
+ SpatialPoints spatialPoints = (SpatialPoints) sbmlElementToWrite;
+ if(spatialPoints.isSetArrayData()) {
+ xmlObject.setCharacters(spatialPoints.getArrayData());
+ }
+ }
+ else if(sbmlElementToWrite instanceof ParametricObject) {
+ ParametricObject parametricObject = (ParametricObject) sbmlElementToWrite;
+ if(parametricObject.isSetPointIndex()) {
+ xmlObject.setCharacters(parametricObject.getPointIndex());
+ }
+ }
}
/* (non-Javadoc)
@@ -191,7 +211,6 @@
public void processAttribute(String elementName, String attributeName,
String value, String uri, String prefix, boolean isLastAttribute,
Object contextObject) {
-
if (contextObject instanceof Species) {
Species species = (Species) contextObject;
SpatialSpeciesPlugin spatialSpecies = null;
@@ -302,7 +321,11 @@
} else if (elementName.equals(SpatialConstants.listOfGeometryDefinitions)) {
ListOf<GeometryDefinition> listOfGeometryDefinitions = geometry.getListOfGeometryDefinitions();
return listOfGeometryDefinitions;
+ } else if (elementName.equals(SpatialConstants.listOfSampledFields)) {
+ ListOf<SampledField> listOfSampledFields = geometry.getListOfSampledFields();
+ return listOfSampledFields;
}
+
} else if (contextObject instanceof CoordinateComponent) {
CoordinateComponent cc = (CoordinateComponent) contextObject;
if (elementName.equals(SpatialConstants.boundaryMinimum)) {
@@ -332,20 +355,7 @@
if (elementName.equals(SpatialConstants.listOfSampledVolumes)){
ListOf<SampledVolume> listOfSampledVolumes = sfg.getListOfSampledVolumes();
return listOfSampledVolumes;
- // } else if (elementName.equals(SpatialConstants.sampledField)){
- // SampledField sf = new SampledField(); // SampleField is not a child anymore in 0.88 but just a SIdRef
- // sfg.setSampledField(sf);
- // return sf;
}
- // NOTE: This has been moved in the listOf section below.
-// } else if (contextObject instanceof SampledField) {
- // SampledField sf = (SampledField) contextObject; // No more child in 0.88
- // if (elementName.equals(SpatialConstants.imageData)){
- // ImageData im = new ImageData();
- // sf.setImageData(im);
- // // sf.set
- // return im;
- // }
} else if (contextObject instanceof CSGeometry) {
CSGeometry csg = (CSGeometry) contextObject;
if (elementName.equals(SpatialConstants.listOfCSGObjects)){
Modified: branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml 2015-05-01 10:47:00 UTC (rev 2273)
+++ branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml 2015-05-01 10:54:44 UTC (rev 2274)
@@ -97,7 +97,6 @@
<req:listOfChangedMaths>
<req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
</req:listOfChangedMaths>
- <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
</species>
<species id="s1_cyt" compartment="Cytosol" initialConcentration="10" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
<annotation>
@@ -110,7 +109,6 @@
<req:listOfChangedMaths>
<req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
</req:listOfChangedMaths>
- <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
</species>
<species id="s2_nuc" compartment="Nucleus" initialConcentration="5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
<annotation>
@@ -123,7 +121,6 @@
<req:listOfChangedMaths>
<req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
</req:listOfChangedMaths>
- <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
</species>
<species id="s1_EC" compartment="Extracellular" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
<annotation>
@@ -136,7 +133,6 @@
<req:listOfChangedMaths>
<req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
</req:listOfChangedMaths>
- <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
</species>
</listOfSpecies>
<listOfParameters>
@@ -147,61 +143,49 @@
<spatial:spatialSymbolReference spatial:id="y"/>
</parameter>
<parameter id="s1_nuc_diff" value="10" constant="true">
- <spatial:diffusionCoefficient spatial:variable="s1_nuc" spatial:type="isotropic"/>
- <spatial:listOfCoordinateReferences>
- <spatial:coordinateReference spatial:coordinate="cartesianX"/>
- <spatial:coordinateReference spatial:coordinate="cartesianY"/>
- </spatial:listOfCoordinateReferences>
+ <spatial:diffusionCoefficient spatial:variable="s1_nuc" spatial:type="isotropic" spatial:coordinateReference1="cartesianX" spatial:coordinateReference2="cartesianY"/>
</parameter>
<parameter id="s1_nuc_BC_Xm" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmin" spatial:type="dirichlet" spatial:boundaryDomainType="Nucleus"/>
</parameter>
<parameter id="s1_nuc_BC_Xp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmax" spatial:type="dirichlet" spatial:boundaryDomainType="Nucleus"/>
</parameter>
<parameter id="s1_nuc_BC_Ym" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymin" spatial:type="dirichlet" spatial:boundaryDomainType="Nucleus"/>
</parameter>
<parameter id="s1_nuc_BC_Yp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymax" spatial:type="dirichlet" spatial:boundaryDomainType="Nucleus"/>
</parameter>
<parameter id="s1_cyt_diff" value="10" constant="true">
- <spatial:diffusionCoefficient spatial:variable="s1_cyt" spatial:type="isotropic"/>
- <spatial:listOfCoordinateReferences>
- <spatial:coordinateReference spatial:coordinate="cartesianX"/>
- <spatial:coordinateReference spatial:coordinate="cartesianY"/>
- </spatial:listOfCoordinateReferences>
+ <spatial:diffusionCoefficient spatial:variable="s1_cyt" spatial:type="isotropic" spatial:coordinateReference1="cartesianX" spatial:coordinateReference2="cartesianY"/>
</parameter>
<parameter id="s1_cyt_BC_Xm" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmin" spatial:type="dirichlet" spatial:boundaryDomainType="Cytosol"/>
</parameter>
<parameter id="s1_cyt_BC_Xp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmax" spatial:type="dirichlet" spatial:boundaryDomainType="Cytosol"/>
</parameter>
<parameter id="s1_cyt_BC_Ym" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymin" spatial:type="dirichlet" spatial:boundaryDomainType="Cytosol"/>
</parameter>
<parameter id="s1_cyt_BC_Yp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet"/>
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymax" spatial:type="dirichlet"/>
</parameter>
<parameter id="s1_EC_diff" value="10" constant="true">
- <spatial:diffusionCoefficient spatial:variable="s1_EC" spatial:type="isotropic"/>
- <spatial:listOfCoordinateReferences>
- <spatial:coordinateReference spatial:coordinate="cartesianX"/>
- <spatial:coordinateReference spatial:coordinate="cartesianY"/>
- </spatial:listOfCoordinateReferences>
+ <spatial:diffusionCoefficient spatial:variable="s1_EC" spatial:type="isotropic" spatial:coordinateReference1="cartesianX" spatial:coordinateReference2="cartesianY"/>
</parameter>
<parameter id="s1_EC_BC_Xm" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmin" spatial:type="dirichlet" spatial:boundaryDomainType="Extracellular"/>
</parameter>
<parameter id="s1_EC_BC_Xp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmax" spatial:type="dirichlet" spatial:boundaryDomainType="Extracellular"/>
</parameter>
<parameter id="s1_EC_BC_Ym" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymin" spatial:type="dirichlet" spatial:boundaryDomainType="Extracellular"/>
</parameter>
<parameter id="s1_EC_BC_Yp" value="0" constant="true">
- <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymax" spatial:type="dirichlet" spatial:boundaryDomainType="Extracellular"/>
</parameter>
<parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
</listOfParameters>
@@ -292,7 +276,7 @@
</spatial:sampledFieldGeometry>
</spatial:listOfGeometryDefinitions>
<spatial:listOfSampledFields>
- <spatial:sampledField spatial:id="imgtest" spatial:dataType="uint8" spatial:numSamples1="800" spatial:numSamples2="950" spatial:numSamples3="1" spatial:interpolationType="linear" spatial:compression="deflated" spatial:samplesLength="3440">120 218 237 221 193 142 27 57 12 64 193 124 122 255 185 22 216 195 30 54 240 216 238 97 83 20 89 239 154 75 183 168 2 237 96 146 249 243 71 146 36 73 146 36 73 146 36 73 26 217 117 57 3 233 181 15 64 164 215 60 248 144 248 144 238 240 224 67 226 67 226 67 138 229 193 135 196 135 196 135 196 135 148 197 131 15 137 15 137 15 137 15 41 139 7 31 18 31 18 31 82 44 15 62 36 62 36 62 164 88 30 124 72 124 72 124 72 177 60 248 144 248 144 248 144 98 121 240 33 241 33 241 33 197 242 224 67 226 67 226 67 226 67 202 226 193 135 196 135 196 135 20 203 3 16 137 15 137 15 137 15 137 15 169 0 15 62 36 62 36 31 175 36 62 36 62 164 237 62 28 136 100 125 72 124 72 124 72 124 72 124 72 133 121 240 33 241 33 241 33 241 33 101 241 224 67 226 67 186 229 3 16 137
+ <spatial:sampledField spatial:id="imgtest" spatial:dataType="uint8" spatial:numSamples1="800" spatial:numSamples2="950" spatial:numSamples3="1" spatial:interpolation="linear" spatial:compression="deflated" spatial:samplesLength="3440">120 218 237 221 193 142 27 57 12 64 193 124 122 255 185 22 216 195 30 54 240 216 238 97 83 20 89 239 154 75 183 168 2 237 96 146 249 243 71 146 36 73 146 36 73 146 36 73 26 217 117 57 3 233 181 15 64 164 215 60 248 144 248 144 238 240 224 67 226 67 226 67 138 229 193 135 196 135 196 135 196 135 148 197 131 15 137 15 137 15 137 15 41 139 7 31 18 31 18 31 82 44 15 62 36 62 36 62 164 88 30 124 72 124 72 124 72 177 60 248 144 248 144 248 144 98 121 240 33 241 33 241 33 197 242 224 67 226 67 226 67 226 67 202 226 193 135 196 135 196 135 20 203 3 16 137 15 137 15 137 15 137 15 169 0 15 62 36 62 36 31 175 36 62 36 62 164 237 62 28 136 100 125 72 124 72 124 72 124 72 124 72 133 121 240 33 241 33 241 33 241 33 101 241 224 67 226 67 186 229 3 16 137
15 233 14 15 62 36 62 36 62 36 62 164 52 31 128 72 175 121 240 33 241 33 241 33 241 33 101 241 224 67 250 193 7 32 18 31 18 31 82 176 15 64 164 215 60 248 144 248 144 248 144 248 144 248 144 246 243 224 67 226 67 186 229 3 16 241 193 135 196 135 20 203 131 15 241 193 135 196 135 20 236 3 16 241 193 135 116 135 7 31 226 131 15 137 15 137 15 137 15 137 15 137 15 137 15 169 27 15 62 196 7 32 18 31 18 31 82 26 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 62 196 7 32 18 31 82 48 15 62 196 7 31 18 31 82 44 15 62 196 7 31 18 31 82 44 15 64 196 7 31 18 31 18 31 82 26 15 62 196 7 31 210 45 31 128 8 15 62 36 62 36 62 36 62 164 253 60 248 16 31 128 72 124 72 193 60 248 16 31 124 72 124 72 177 60 248 16 31 124 72 124 72 124 72 89 60 0 17 31 124 136 15 62 164 96 30 124 136 15 62 196 7 31 18 31 82 22 15 62 196 7 31 226 131 15 41 150 7 31 226 13
1 15 241 193 135 20 203 131 15 241 193 135 248 224 67 138 229 193 135 248 224 67 124 240 33 197 242 224 67 124 240 33 62 248 144 98 121 240 33 62 248 16 31 124 72 124 72 89 60 248 16 31 124 136 15 62 164 88 30 124 136 15 62 196 7 30 146 245 33 241 33 241 33 241 33 29 201 131 15 241 193 135 248 224 67 138 229 193 135 248 224 67 124 240 33 197 242 224 67 124 240 33 62 248 144 240 144 248 144 248 144 10 243 224 67 124 240 33 62 240 144 172 15 137 15 137 15 169 48 15 62 196 7 31 226 3 15 201 250 144 248 144 248 144 10 243 224 67 124 240 33 60 240 144 248 144 146 120 240 33 62 248 16 31 124 72 177 60 248 16 31 124 8 15 62 36 62 36 62 164 253 60 248 16 31 124 8 15 62 36 62 36 60 36 62 164 194 60 248 16 31 124 136 15 62 164 88 30 124 136 15 62 132 7 31 18 31 18 31 210 126 30 124 136 15 64 132 7 31 226 131 15 41 141 7 31 226 3 16 241 193 135 240 224 67 226 67 42 192 3 16 241 193 135 248 224 67 120 0 34 37 250 0 68 120 0 34 62 0 17 30 128 72 153 62 0 17 31 128 8 15 62 196 7 31 82 26
15 62 196 7 30 194 131 15 241 129 135 132 135 196 135 84 214 135 19 22 30 120 136 15 62 132 7 30 18 31 210 102 30 124 136 15 60 132 7 31 226 131 15 9 15 137 15 169 46 15 62 196 7 31 226 131 15 225 193 135 196 135 180 159 7 31 226 131 15 225 193 135 248 224 67 202 226 193 135 248 224 67 120 240 33 62 248 144 178 120 240 33 60 248 16 31 124 8 15 62 196 7 31 210 126 30 124 136 15 62 132 7 31 226 3 16 225 193 135 196 135 84 154 7 31 226 131 15 225 193 135 248 224 67 120 240 33 241 33 85 230 193 135 248 224 67 120 240 33 62 248 16 30 124 72 124 72 149 121 240 33 60 248 16 31 124 8 15 62 196 7 31 210 126 30 124 136 15 62 132 7 31 226 131 15 225 193 135 196 135 84 153 7 31 226 131 15 225 193 135 240 0 68 124 240 33 21 224 193 135 248 224 67 120 240 33 60 248 16 31 124 72 251 121 0 34 60 248 16 31 124 8 15 62 196 7 32 194 131 15 169 54 15 62 196 7 31 194 131 15 241 193 135 240 224 67 120 240 33 241 33 157 201 131 15 225 1 136 248 224 67 120 240 33 60 248 16 31 124 72 165 121 240 33
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 10:47:03
|
Revision: 2273
http://sourceforge.net/p/jsbml/code/2273
Author: niko-rodrigue
Date: 2015-05-01 10:47:00 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2257
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2257
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractTreeNode.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Assignment.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/EventAssignment.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ExplicitRule.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/InitialAssignment.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestAnnotation.java
branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate 2015-05-01 10:47:00 UTC (rev 2273)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2254
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2257
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 10:47:00 UTC (rev 2273)
@@ -31,6 +31,8 @@
<entry key="IndexExceedsBoundsException">Index {0,number,integer} >= {1,number,integer}</entry>
<entry key="IndexExceedsBoundsException2">Node {0} has no children.</entry>
+ <entry key="IndexSurpassesBoundsException">Index {0,number,integer} < {0,number,integer}</entry>
+ <entry key="NullArgument">Argument is null.</entry>
<entry key="AbstractMathContainer.toFormula">Could not create infix formula from syntax tree.</entry>
<entry key="AbstractMathContainer.inclusion">{0} in {1}</entry>
@@ -58,5 +60,37 @@
<entry key="AbstractSBase.emptyNotes">The notes to append are empty!</entry>
<entry key="AbstractSBase.invalidNotesStructure">The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.</entry>
<entry key="AbstractSBase.problemAddingXMLNode">There was a problem adding the given XMLNode: ''{0}'' to the ''body'' XMLNode.</entry>
+
+ <entry key="Assignment.ILLEGAL_CONSTANT_VARIABLE_MSG">Cannot set the constant variable {0} as the target of this {1}.</entry>
+ <entry key="Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG">Cannot set SpeciesReference {0} as the Variable in {1} for SBML Level < 3</entry>
+ <entry key="Assignment.NO_SUCH_VARIABLE_EXCEPTION_MSG">Model {0} does not contain any variable with identifier {1}.</entry>
+
+ <entry key="ASTNode.INVALID_OPERATOR_MSG">Invalid operator {0}. The operator must be one of the following constants: PLUS, MINUS, TIMES, DIVIDE, or POWER.</entry>
+ <entry key="ASTNode.log">logarithm cannot be created for null values</entry>
+ <entry key="ASTNode.relational">Cannot create a relational node with null arguments.</entry>
+ <entry key="ASTNode1">Clone constructor: Origin type = {0}</entry>
+ <entry key="ASTNode.arithmeticOperation">Cannot divide by zero.</entry>
+ <entry key="ASTNode.compile1">Fractions must have one numerator and one denominator, here {0,number,integer} elements are given.</entry>
+ <entry key="ASTNode.compile2">ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ({0}, {1})</entry>
+ <entry key="ASTNode.compile3">ASTNode of type FUNCTION but the variable is null: ({0}, {1})! Check that your object is linked to a Model.</entry>
+ <entry key="ASTNode.compile4">getCharacter() should be called only when isOperator().</entry>
+ <entry key="ASTNode.getDenominator">getDenominator() should be called only when getType() == RATIONAL.</entry>
+ <entry key="ASTNode.getExponent">getExponent() should be called only when getType() == REAL_E or REAL</entry>
+ <entry key="ASTNode.getInteger">getInteger() should be called only when getType() == INTEGER</entry>
+ <entry key="ASTNode.getMantissa">getMantissa() should be called only when getType() == REAL or REAL_E</entry>
+ <entry key="ASTNode.getName">getName() should be called only when !isNumber() && !isOperator()</entry>
+ <entry key="ASTNode.getNumerator">getNumerator() should be called only when isRational()</entry>
+ <entry key="ASTNode.getReal">getReal() should be called only when isReal() returns true.</entry>
+ <entry key="ASTNode.getReferencedNamedSBases">Name of this node is {0} but no variable is set.</entry>
+ <entry key="ASTNode.getVariable1">The name \"{0}\" represented by this node is an argument in a function call, i.e., a placeholder for some other element. No corresponding CallableSBase exists in the model</entry>
+ <entry key="ASTNode.getVariable2">Cannot find any element with id \"{0}\" in the model.</entry>
+ <entry key="ASTNode.getVariable3">This ASTNode is not yet linked to a model and can therefore not determine its variable \"{0}\".</entry>
+ <entry key="ASTNode.getVariable4">getVariable() should be called only when isVariable() == true.</entry>
+ <entry key="ASTNode.initDefaults">initDefaults called! type was {0}</entry>
+ <entry key="ASTNode.reduceToBinary1">MINUS node with {0,number,integer} children left unchanged</entry>
+ <entry key="ASTNode.reduceToBinary2">DIVIDE node with {0,number,integer} children left unchanged</entry>
+ <entry key="ASTNode.reduceToBinary3">NOT node with {0,number,integer} children left unchanged</entry>
+ <entry key="ASTNode.reduceToBinary4">XOR node with {0,number,integer} children left unchanged</entry>
+ <entry key="ASTNode.reduceToBinary5">{0} node with {1,number,integer} children left unchanged</entry>
</properties>
\ No newline at end of file
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -619,12 +619,6 @@
}
/**
- * Message to indicate that an {@link ASTNode.Type} type has been chosen which
- * cannot be used as an operator.
- */
- public static final transient String INVALID_OPERATOR_MSG = "Invalid operator %s. The operator must be one of the following constants: PLUS, MINUS, TIMES, DIVIDE, or POWER.";
-
- /**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -1391327698196553142L;
@@ -1244,8 +1238,7 @@
private static ASTNode relational(ASTNode.Type type, ASTNode left,
ASTNode right) {
if ((left == null) || (right == null)) {
- throw new NullPointerException(
- "Cannot create a relational node with null arguments.");
+ throw new NullPointerException(resourceBundle.getString("ASTNode.relational"));
}
return new ASTNode(ASTFactory.relational(type, left.toASTNode2(),
right.toASTNode2()));
@@ -1759,12 +1752,9 @@
break;
case DIVIDE :
int childCount = getChildCount();
- if (childCount != 2) {
- throw new SBMLException(
- MessageFormat
- .format(
- "Fractions must have one numerator and one denominator, here {0,number,integer} elements are given.",
- childCount));
+ if (childCount != 2) {
+ throw new SBMLException(MessageFormat.format(
+ resourceBundle.getString("ASTNode.compile1"), childCount));
}
value = compiler.frac(getLeftChild(), getRightChild());
break;
@@ -1958,26 +1948,17 @@
value = compiler.function((FunctionDefinition) variable,
getChildren());
} else {
- logger
- .warn("ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ("
- + getName()
- + ", "
- + getParentSBMLObject().getElementName()
- + ")");
- throw new SBMLException(
- "ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ("
- + getName() + ", " + getParentSBMLObject().getElementName()
- + ")");
+ String message = MessageFormat.format(
+ resourceBundle.getString("ASTNode.compile2"),
+ getName(), getParentSBMLObject().getElementName());
+ logger.warn(message);
+ throw new SBMLException(message);
// value = compiler.compile(variable);
}
} else {
- logger
- .debug(MessageFormat
- .format(
- "ASTNode of type FUNCTION but the variable is null: ({0}, {1})! Check that your object is linked to a Model.",
- getName(), (getParentSBMLObject() != null
- ? getParentSBMLObject().getElementName()
- : null)));
+ logger.debug(MessageFormat.format(
+ resourceBundle.getString("ASTNode.compile3"),
+ getName(), (getParentSBMLObject() != null ? getParentSBMLObject().getElementName() : null)));
value = compiler.function(getName(), getChildren());
}
break;
@@ -2514,8 +2495,7 @@
break;
}
}
- throw new IllegalArgumentException(
- "getCharacter() should be called only when isOperator().");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.compile4"));
}
/**
@@ -2597,8 +2577,7 @@
if (isRational()) {
return ((ASTCnRationalNode) astnode2).getDenominator();
}
- throw new IllegalArgumentException(
- "getDenominator() should be called only when getType() == RATIONAL.");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getDenominator"));
}
/**
@@ -2613,7 +2592,7 @@
/**
* Gets the exponent value of this ASTNode. This function should be called
- * only when getType() returns REAL_E or REAL, otherwise an Exception is
+ * only when {@link #getType()} returns REAL_E or REAL, otherwise an Exception is
* thrown.
*
* @return the value of the exponent of this ASTNode.
@@ -2624,8 +2603,7 @@
if (astnode2 instanceof ASTCnExponentialNode) {
return ((ASTCnExponentialNode) astnode2).getExponent();
}
- throw new IllegalArgumentException(
- "getExponent() should be called only when getType() == REAL_E or REAL");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getExponent"));
}
/**
@@ -2649,8 +2627,7 @@
if (isInteger()) {
return ((ASTCnIntegerNode) astnode2).getInteger();
}
- throw new IllegalArgumentException(
- "getInteger() should be called only when getType() == INTEGER");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getInteger"));
}
/**
@@ -2717,8 +2694,7 @@
if (astnode2 instanceof ASTCnExponentialNode) {
return ((ASTCnExponentialNode) toASTNode2()).getMantissa();
}
- throw new IllegalArgumentException(
- "getMantissa() should be called only when getType() == REAL or REAL_E");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getMantissa"));
}
/**
@@ -2732,9 +2708,9 @@
*/
public String getName() {
if (isNumber() || isOperator()) {
- throw new IllegalArgumentException(
- "getName() should be called only when !isNumber() && !isOperator()");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getName"));
}
+
String name = null;
if (astnode2 instanceof ASTCiNumberNode) {
if (((ASTCiNumberNode)astnode2).isSetRefId()) {
@@ -2761,8 +2737,7 @@
if (isRational()) {
return ((ASTCnRationalNode) astnode2).getNumerator();
}
- throw new IllegalArgumentException(
- "getNumerator() should be called only when isRational()");
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getNumerator"));
}
/*
@@ -2818,8 +2793,8 @@
} else if (isInteger()) {
return ((ASTCnIntegerNode) astnode2).getNumber();
}
-
- return Double.NaN;
+
+ throw new IllegalArgumentException(resourceBundle.getString("ASTNode.getReal"));
}
/**
@@ -2835,6 +2810,22 @@
// TODO: Has no analogous method in the new math package.
// TODO: Is this method still necessary or is the 'testing' complete?
return null;
+/*
+ Set<NamedSBase> l = new HashSet<NamedSBase>();
+ if (isString()) {
+ if (getVariable() != null) {
+ l.add(getVariable());
+ } else {
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("ASTNode.getReferencedNamedSBases"),
+ getName()));
+ }
+ }
+ for (ASTNode child : listOfNodes) {
+ l.addAll(child.getReferencedNamedSBases());
+ }
+ return l;
+*/
}
/**
@@ -2908,13 +2899,15 @@
* if {@link #isVariable()} returns {@code false}.
*/
public CallableSBase getVariable() {
+ // TODO - this method is probably not reflecting the old behavior
+ // as the method as quite complex before.
if (astnode2 instanceof ASTCiNumberNode) {
return ((ASTCiNumberNode) astnode2).getReferenceInstance();
} else if (astnode2 instanceof ASTCiFunctionNode) {
return ((ASTCiFunctionNode) astnode2).getReferenceInstance();
- } else {
- return null;
- }
+ }
+
+ throw new RuntimeException(resourceBundle.getString("ASTNode.getVariable4"));
}
/*
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -78,7 +78,7 @@
*
*/
NotesHTML
- };
+ }
/**
* A logger for this class.
@@ -88,7 +88,7 @@
/**
* Generated serial version identifier.
*/
- private static final long serialVersionUID = 8781459818293592636L;
+ private static final long serialVersionUID = 8781459818293592636L;;
/**
* Returns {@code true} if the level and version combination is a valid one, {@code false} otherwise.
@@ -139,6 +139,11 @@
private final Map<String, String> declaredNamespaces;
/**
+ * the namespace which this SBase element belong to.
+ */
+ private String elementNamespace;
+
+ /**
* {@link Map} containing the SBML extension object of additional packages
* with the appropriate name space of the package.
*/
@@ -176,17 +181,6 @@
private XMLNode notesXMLNode;
/**
- * sbo term of the SBML component. Matches the sboTerm XML attribute of an
- * element in a SBML file.
- */
- private int sboTerm;
-
- /**
- * the namespace which this SBase element belong to.
- */
- private String elementNamespace;
-
- /**
* the name of the package which this SBase element belong to, 'core' by default.
*/
protected String packageName = "core";
@@ -197,6 +191,12 @@
private int packageVersion = 0;
/**
+ * sbo term of the SBML component. Matches the sboTerm XML attribute of an
+ * element in a SBML file.
+ */
+ private int sboTerm;
+
+ /**
* Creates an AbstractSBase instance.
*
* <p>By default, the sboTerm is -1, the
@@ -363,7 +363,6 @@
}
}
-
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#addPlugin(java.lang.String, org.sbml.jsbml.ext.SBasePlugin)
*/
@@ -372,28 +371,21 @@
addExtension(nameOrUri, sbasePlugin);
}
- /**
- * Sets the XML namespace to which this {@link SBase} belong.
- *
- * <p>This an internal method that should not be used outside of the main jsbml code
- * (core + packages). One class should always belong to the same namespace, although the namespaces can
- * have different level and version (and package version). You have to know what you are doing
- * when using this method.
- *
- * @param namespace the XML namespace to which this {@link SBase} belong.
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#appendAnnotation(java.lang.String)
*/
- public void setNamespace(String namespace) {
- if ((elementNamespace != null) && (!elementNamespace.equals(namespace))) {
- // if we implement proper conversion some days, we need to unset the namespace before changing it.
- logger.error(MessageFormat.format(
- resourceBundle.getString("AbstractSBase.setNamespaceExc"),
- elementNamespace, namespace));
- // throw new IllegalArgumentException(MessageFormat.format(resourceBundle.getString("AbstractSBase.setNamespaceExc"), elementNamespace, namespace));
- }
- String old = elementNamespace;
- elementNamespace = namespace;
+ @Override
+ public void appendAnnotation(String annotation) throws XMLStreamException {
+ getAnnotation().appendNonRDFAnnotation(annotation);
+ }
- firePropertyChange(TreeNodeChangeEvent.namespace, old, namespace);
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#appendAnnotation(org.sbml.jsbml.xml.XMLNode)
+ */
+ @Override
+ public void appendAnnotation(XMLNode annotation) {
+ getAnnotation().appendNonRDFAnnotation(annotation);
}
/* (non-Javadoc)
@@ -787,7 +779,6 @@
@Override
public abstract AbstractSBase clone();
-
/**
* Creates a new {@link History} and associates it with the annotation of
* this element. If no {@link Annotation} exists, a new such element is
@@ -801,6 +792,7 @@
return getHistory();
}
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#createPlugin(java.lang.String)
*/
@@ -856,7 +848,6 @@
}
}
-
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#equals(java.lang.Object)
*/
@@ -910,7 +901,6 @@
}
-
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier)
*/
@@ -919,22 +909,7 @@
return getAnnotation().filterCVTerms(qualifier);
}
- /* (non-Javadoc)
- * @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier, java.lang.String)
- */
- @Override
- public List<String> filterCVTerms(CVTerm.Qualifier qualifier, String pattern) {
- return filterCVTerms(qualifier, pattern, false);
- }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier, java.lang.String, boolean)
- */
- @Override
- public List<String> filterCVTerms(CVTerm.Qualifier qualifier, String pattern,
- boolean recursive) {
- return filterCVTerms(qualifier, recursive, pattern);
- }
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier, boolean, java.lang.String[])
@@ -959,6 +934,44 @@
}
/* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier, java.lang.String)
+ */
+ @Override
+ public List<String> filterCVTerms(CVTerm.Qualifier qualifier, String pattern) {
+ return filterCVTerms(qualifier, pattern, false);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#filterCVTerms(org.sbml.jsbml.CVTerm.Qualifier, java.lang.String, boolean)
+ */
+ @Override
+ public List<String> filterCVTerms(CVTerm.Qualifier qualifier, String pattern,
+ boolean recursive) {
+ return filterCVTerms(qualifier, recursive, pattern);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#fireNodeRemovedEvent()
+ */
+ @Override
+ public void fireNodeRemovedEvent() {
+
+ TreeNode parent = getParent();
+
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.fireNodeRemovedEvent"),
+ this, parent));
+ }
+
+ if ((parent != null) && (parent instanceof SBase)) {
+ ((SBase) parent).unregisterChild(this);
+ }
+
+ super.fireNodeRemovedEvent();
+ }
+
+ /* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)
*/
@Override
@@ -993,27 +1006,6 @@
}
/* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractTreeNode#fireNodeRemovedEvent()
- */
- @Override
- public void fireNodeRemovedEvent() {
-
- TreeNode parent = getParent();
-
- if (logger.isDebugEnabled()) {
- logger.debug(MessageFormat.format(
- resourceBundle.getString("AbstractSBase.fireNodeRemovedEvent"),
- this, parent));
- }
-
- if ((parent != null) && (parent instanceof SBase)) {
- ((SBase) parent).unregisterChild(this);
- }
-
- super.fireNodeRemovedEvent();
- }
-
- /* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@Override
@@ -1051,7 +1043,7 @@
@Override
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetNotes()) {
@@ -1183,7 +1175,6 @@
return 0;
}
-
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#getExtensionPackages()
*/
@@ -1192,6 +1183,7 @@
return extensions;
}
+
/**
* Return the index of the first child of type 'Element' for the given {@link XMLNode}.
*
@@ -1773,7 +1765,6 @@
return false;
}
-
/**
* Registers recursively the given {@link SBasePlugin} from the {@link Model}
* and {@link SBMLDocument}.
@@ -1811,6 +1802,7 @@
return getAnnotation().removeCVTerm(cvTerm);
}
+
/**
* Removes the {@link CVTerm} at the given index.
*
@@ -1838,19 +1830,19 @@
}
/* (non-Javadoc)
- * @see org.sbml.jsbml.SBase#setAnnotation(org.sbml.jsbml.xml.XMLNode)
+ * @see org.sbml.jsbml.SBase#setAnnotation(java.lang.String)
*/
@Override
- public void setAnnotation(XMLNode nonRDFAnnotation) {
- getAnnotation().setNonRDFAnnotation(nonRDFAnnotation);
+ public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException {
+ setAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotation)));
}
/* (non-Javadoc)
- * @see org.sbml.jsbml.SBase#setAnnotation(java.lang.String)
+ * @see org.sbml.jsbml.SBase#setAnnotation(org.sbml.jsbml.xml.XMLNode)
*/
@Override
- public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException {
- setAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotation)));
+ public void setAnnotation(XMLNode nonRDFAnnotation) {
+ getAnnotation().setNonRDFAnnotation(nonRDFAnnotation);
}
/* (non-Javadoc)
@@ -1956,6 +1948,30 @@
firePropertyChange(TreeNodeChangeEvent.metaId, oldMetaId, metaId);
}
+ /**
+ * Sets the XML namespace to which this {@link SBase} belong.
+ *
+ * <p>This an internal method that should not be used outside of the main jsbml code
+ * (core + packages). One class should always belong to the same namespace, although the namespaces can
+ * have different level and version (and package version). You have to know what you are doing
+ * when using this method.
+ *
+ * @param namespace the XML namespace to which this {@link SBase} belong.
+ */
+ public void setNamespace(String namespace) {
+ if ((elementNamespace != null) && (!elementNamespace.equals(namespace))) {
+ // if we implement proper conversion some days, we need to unset the namespace before changing it.
+ logger.error(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.setNamespaceExc"),
+ elementNamespace, namespace));
+ // throw new IllegalArgumentException(MessageFormat.format(resourceBundle.getString("AbstractSBase.setNamespaceExc"), elementNamespace, namespace));
+ }
+ String old = elementNamespace;
+ elementNamespace = namespace;
+
+ firePropertyChange(TreeNodeChangeEvent.namespace, old, namespace);
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.element.SBase#setNotes(java.lang.String)
*/
@@ -1977,6 +1993,20 @@
firePropertyChange(TreeNodeChangeEvent.notes, oldNotes, notesXMLNode);
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#setPackageVersion(int)
+ */
+ @Override
+ public void setPackageVersion(int packageVersion) {
+ int oldPackageVersion = this.packageVersion;
+
+ // TODO - add some checks to see if it agree with the package version of the parent
+ // either SBase or SBasePlugin, if the parent belong to a different package ??
+
+ this.packageVersion = packageVersion;
+ firePropertyChange(TreeNodeChangeEvent.packageVersion, oldPackageVersion, packageVersion);
+ }
+
/**
*
* @param parent
@@ -2014,20 +2044,6 @@
}
/* (non-Javadoc)
- * @see org.sbml.jsbml.SBase#setPackageVersion(int)
- */
- @Override
- public void setPackageVersion(int packageVersion) {
- int oldPackageVersion = this.packageVersion;
-
- // TODO - add some checks to see if it agree with the package version of the parent
- // either SBase or SBasePlugin, if the parent belong to a different package ??
-
- this.packageVersion = packageVersion;
- firePropertyChange(TreeNodeChangeEvent.packageVersion, oldPackageVersion, packageVersion);
- }
-
- /* (non-Javadoc)
* @see org.sbml.jsbml.SBase#setSBOTerm(int)
*/
@Override
@@ -2177,6 +2193,24 @@
}
}
+ @Override
+ public void unsetExtension(String nameOrUri) {
+
+ // use always the package name in the map
+ PackageParser packageParser = ParserManager.getManager().getPackageParser(nameOrUri);
+
+ if (packageParser != null) {
+
+ SBasePlugin sbasePlugin = extensions.remove(packageParser.getPackageName());
+ firePropertyChange(TreeNodeChangeEvent.extension, sbasePlugin, null);
+ return;
+ }
+
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.createPlugin"),
+ nameOrUri));
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#unsetHistory()
*/
@@ -2187,6 +2221,7 @@
}
}
+
/* (non-Javadoc)
* @see org.sbml.jlibsbml.SBase#unsetMetaId()
*/
@@ -2197,7 +2232,6 @@
}
}
-
/**
* Unsets the namespace that is associated to this {@link SBase}.
*
@@ -2223,24 +2257,6 @@
}
@Override
- public void unsetExtension(String nameOrUri) {
-
- // use always the package name in the map
- PackageParser packageParser = ParserManager.getManager().getPackageParser(nameOrUri);
-
- if (packageParser != null) {
-
- SBasePlugin sbasePlugin = extensions.remove(packageParser.getPackageName());
- firePropertyChange(TreeNodeChangeEvent.extension, sbasePlugin, null);
- return;
- }
-
- throw new IllegalArgumentException(MessageFormat.format(
- resourceBundle.getString("AbstractSBase.createPlugin"),
- nameOrUri));
- }
-
- @Override
public void unsetPlugin(String nameOrUri) {
unsetExtension(nameOrUri);
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractTreeNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -93,7 +93,7 @@
@SuppressWarnings("unchecked")
public static int indexOf(TreeNode parent, TreeNode child) {
if (child == null) {
- throw new IllegalArgumentException("Argument is null.");
+ throw new IllegalArgumentException(resourceBundle.getString("NullArgument"));
}
// linear search
Enumeration<TreeNode> e = parent.children();
@@ -276,7 +276,7 @@
return getChildAt(index++);
}
}
- throw new NoSuchElementException("Enumeration");
+ throw new NoSuchElementException(Enumeration.class.getSimpleName());
}
};
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -63,7 +63,7 @@
/**
* The RDF syntax name space definition URI.
*/
- public static final transient String URI_RDF_SYNTAX_NS = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+ public static final transient String URI_RDF_SYNTAX_NS = "http://www.w3.org/1999/02/22-rdf-syntax-ns#"; //$NON-NLS-1$
/**
* Returns a {@link String} which represents the given {@link Qualifier}.
@@ -231,10 +231,15 @@
* @param annotation some non RDF annotations.
* @throws XMLStreamException
*/
- public void appendNoRDFAnnotation(String annotation) throws XMLStreamException {
+ public void appendNonRDFAnnotation(String annotation) throws XMLStreamException {
+ appendNonRDFAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(annotation)));
+ }
+
+ /**
+ * @param annotationToAppend
+ */
+ public void appendNonRDFAnnotation(XMLNode annotationToAppend) {
XMLNode oldNonRDFAnnotation = null;
- XMLNode annotationToAppend = XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(annotation));
-
if (nonRDFannotation == null) {
// check if the annotation contain an annotation top level element or not
if (!annotationToAppend.getName().equals("annotation")) {
@@ -374,7 +379,9 @@
@Override
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ resourceBundle.getString("IndexSurpassesBoundsException"),
+ childIndex, 0));
}
int pos = 0;
if (isSetHistory()) {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Assignment.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Assignment.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Assignment.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -33,26 +33,6 @@
public interface Assignment extends MathContainer {
/**
- * Error message to indicate that a {@link SpeciesReference} cannot be used
- * as the {@link Variable} in this {@link Assignment} because the SBML Level
- * < 3.
- */
- public static final String ILLEGAL_VARIABLE_EXCEPTION_MSG = "Cannot set SpeciesReference {0} as the Variable in {1} for SBML Level < 3";
-
- /**
- * Error message to be displayed in case that a {@link Variable} with
- * constant property set to {@code true} is to be assigned to this
- * {@link Assignment}.
- */
- public static final String ILLEGAL_CONSTANT_VARIABLE_MSG = "Cannot set the constant variable {0} as the target of this {1}.";
-
- /**
- * Message to be displayed if no {@link Variable} can be found in the
- * associated {@link Model} that would have the desired identifier.
- */
- public static final String NO_SUCH_VARIABLE_EXCEPTION_MSG = "Model {0} does not contain any variable with identifier {1}.";
-
- /**
* Returns the variableID of this {@link Assignment}. Returns an empty
* {@link String} if it is not set.
*
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/EventAssignment.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/EventAssignment.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/EventAssignment.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -94,7 +94,7 @@
Variable nsb = getModel().findVariable(variable);
if (nsb == null) {
throw new IllegalArgumentException(MessageFormat.format(
- NO_SUCH_VARIABLE_EXCEPTION_MSG,
+ resourceBundle.getString("Assignment.NO_SUCH_VARIABLE_EXCEPTION_MSG"),
m.getId(), variable));
}
setVariable(nsb);
@@ -218,8 +218,8 @@
if (!variable.isConstant()) {
if ((getLevel() < 3) && (variable instanceof SpeciesReference)) {
throw new IllegalArgumentException(MessageFormat.format(
- ILLEGAL_VARIABLE_EXCEPTION_MSG, variable.getId(),
- getElementName()));
+ resourceBundle.getString("Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG"),
+ variable.getId(), getElementName()));
}
if (variable.isSetId()) {
setVariable(variable.getId());
@@ -228,8 +228,8 @@
}
} else {
throw new IllegalArgumentException(MessageFormat.format(
- ILLEGAL_CONSTANT_VARIABLE_MSG, variable.getId(),
- getElementName()));
+ resourceBundle.getString("Assignment.ILLEGAL_CONSTANT_VARIABLE_MSG"),
+ variable.getId(), getElementName()));
}
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ExplicitRule.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ExplicitRule.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ExplicitRule.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -501,9 +501,9 @@
public void setVariable(Variable variable) {
if (variable != null) {
if (variable.isConstant()) {
- throw new IllegalArgumentException(
- MessageFormat.format(ILLEGAL_CONSTANT_VARIABLE_MSG,
- variable.getId(), getElementName()));
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("Assignment.ILLEGAL_CONSTANT_VARIABLE_MSG"),
+ variable.getId(), getElementName()));
}
if (isSetUnits() && !(variable instanceof Parameter)) {
throw new IllegalArgumentException(MessageFormat.format(
@@ -512,8 +512,8 @@
}
if ((getLevel() < 3) && (variable instanceof SpeciesReference)) {
throw new IllegalArgumentException(MessageFormat.format(
- ILLEGAL_VARIABLE_EXCEPTION_MSG, variable.getId(),
- getElementName()));
+ resourceBundle.getString("Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG"),
+ variable.getId(), getElementName()));
}
if (variable.isSetId()) {
String oldVariable = variableID;
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/InitialAssignment.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/InitialAssignment.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/InitialAssignment.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -134,7 +134,8 @@
}
if (nsb == null) {
throw new IllegalArgumentException(MessageFormat.format(
- NO_SUCH_VARIABLE_EXCEPTION_MSG, m.getId(), variable));
+ resourceBundle.getString("Assignment.NO_SUCH_VARIABLE_EXCEPTION_MSG"),
+ m.getId(), variable));
}
setVariable(nsb.getId());
}
@@ -290,7 +291,8 @@
@Override
public void setVariable(Variable variable) {
if ((getLevel() < 3) && (variable != null) && (variable instanceof SpeciesReference)) {
- throw new IllegalArgumentException(MessageFormat.format(Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG,
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG"),
variable.getId(), getElementName()));
}
setVariable(variable != null ? variable.getId() : null);
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -157,7 +157,7 @@
*/
public void addPlugin(String nameOrUri, SBasePlugin sbasePlugin);
- /**
+ /*
* Adds an additional name space to the set of name spaces of this
* {@link SBase} if the given name space is not yet present within this
* {@link SortedSet}.
@@ -167,6 +167,55 @@
// protected void setNamespace(String namespace);
/**
+ * Appends the given annotation to the 'annotation' subelement of this object.
+ * Whereas the SBase 'notes' subelement is a container for content to be shown
+ * directly to humans, the 'annotation' element is a container for optional
+ * software-generated content not meant to be shown to humans. Every object
+ * derived from SBase can have its own value for 'annotation'. The element's
+ * content type is XML type 'any', allowing essentially arbitrary well-formed
+ * XML data content.
+ * SBML places a few restrictions on the organization of the content of
+ * annotations; these are intended to help software tools read and write the
+ * data as well as help reduce conflicts between annotations added by
+ * different tools. Please see the SBML specifications for more details.
+ * Unlike {@link SBase#setAnnotation(XMLNode)} or
+ * {@link SBase#setAnnotation(String)}, this method allows other
+ * annotations to be preserved when an application adds its own data.
+ *
+ * @param annotation
+ * an XML string that is to be copied and appended to the content of
+ * the 'annotation' subelement of this object
+ * @throws XMLStreamException
+ * thrown if the given annotation String cannot be parsed into
+ * {@link XMLNode} objects.
+ * @see #appendAnnotation(XMLNode)
+ */
+ public void appendAnnotation(String annotation) throws XMLStreamException;
+
+
+ /**
+ * Appends the given annotation to the 'annotation' subelement of this object.
+ * Whereas the SBase 'notes' subelement is a container for content to be shown
+ * directly to humans, the 'annotation' element is a container for optional
+ * software-generated content not meant to be shown to humans. Every object
+ * derived from SBase can have its own value for 'annotation'. The element's
+ * content type is XML type 'any', allowing essentially arbitrary well-formed
+ * XML data content.
+ * SBML places a few restrictions on the organization of the content of
+ * annotations; these are intended to help software tools read and write the
+ * data as well as help reduce conflicts between annotations added by
+ * different tools. Please see the SBML specifications for more details.
+ * Unlike {@link SBase#setAnnotation(XMLNode)} or
+ * {@link SBase#setAnnotation(String)}, this method allows other
+ * annotations to be preserved when an application adds its own data.
+ *
+ * @param annotation
+ * an XML structure that is to be copied and appended to the content of
+ * the 'annotation' subelement of this object
+ */
+ public void appendAnnotation(XMLNode annotation);
+
+ /**
* Appends 'notes' to the notes String of this object.
*
* @param notes
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -145,7 +145,7 @@
@Override
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
if (isSetUserObject()) {
if (userObject instanceof TreeNode) {
Modified: branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestAnnotation.java
===================================================================
--- branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestAnnotation.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestAnnotation.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -92,21 +92,21 @@
{
cvTerm.addResource("urn:miriam:kegg.compound:" + urn_id);
annotation.addCVTerm(cvTerm);
- annotation.appendNoRDFAnnotation("http://www.genome.jp/dbget-bin/www_bget?cpd:" + urn_id);
+ annotation.appendNonRDFAnnotation("http://www.genome.jp/dbget-bin/www_bget?cpd:" + urn_id);
}
if (urn_id.startsWith("G"))
{
cvTerm.addResource("urn:miriam:kegg.glycan:" + urn_id);
annotation.addCVTerm(cvTerm);
- annotation.appendNoRDFAnnotation("<myApp:xxx>http://www.genome.jp/dbget-bin/www_bget?gl:" + urn_id + "</myApp:xxx>");
+ annotation.appendNonRDFAnnotation("<myApp:xxx>http://www.genome.jp/dbget-bin/www_bget?gl:" + urn_id + "</myApp:xxx>");
}
if (urn_id.contains("."))
{
cvTerm.addResource("urn:miriam:ec-code:" + urn_id);
annotation.addCVTerm(cvTerm);
- annotation.appendNoRDFAnnotation("http://www.genome.jp/dbget-bin/www_bget?ec:" + urn_id);
+ annotation.appendNonRDFAnnotation("http://www.genome.jp/dbget-bin/www_bget?ec:" + urn_id);
}
System.out.println("The Annotation is still empty as there is no metaid defined on the species !!");
Modified: branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -625,7 +625,7 @@
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0){
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -255,7 +255,7 @@
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -583,7 +583,7 @@
@Override
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -277,7 +277,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -603,7 +603,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -173,7 +173,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -283,7 +283,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfColorDefinitions()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -145,7 +145,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfGradientStops()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -182,7 +182,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -281,7 +281,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -117,7 +117,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -209,7 +209,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -275,7 +275,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfColorDefinitions()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -97,7 +97,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfElements()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -789,7 +789,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -141,7 +141,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -677,7 +677,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfColorDefinitions()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java 2015-05-01 10:16:48 UTC (rev 2272)
+++ branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java 2015-05-01 10:47:00 UTC (rev 2273)
@@ -108,7 +108,7 @@
@Override
public SBase getChildAt(int childIndex) {
if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfLocalRenderInformation()) {
Modified: branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
===================================================================
---...
[truncated message content] |
|
From: <nik...@us...> - 2015-05-01 10:16:50
|
Revision: 2272
http://sourceforge.net/p/jsbml/code/2272
Author: niko-rodrigue
Date: 2015-05-01 10:16:48 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2254
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2254
Modified Paths:
--------------
branches/astnode2-merging-alternate/build.xml
branches/astnode2-merging-alternate/core/build.xml
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml
Removed Paths:
-------------
branches/astnode2-merging-alternate/core/resources/META-INF/
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate 2015-05-01 10:16:48 UTC (rev 2272)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2232
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2254
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/build.xml
===================================================================
--- branches/astnode2-merging-alternate/build.xml 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/build.xml 2015-05-01 10:16:48 UTC (rev 2272)
@@ -247,6 +247,7 @@
<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+ <provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
</service>
</jar>
@@ -316,6 +317,7 @@
<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+ <provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
</service>
</jar>
</target>
Modified: branches/astnode2-merging-alternate/core/build.xml
===================================================================
--- branches/astnode2-merging-alternate/core/build.xml 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/build.xml 2015-05-01 10:16:48 UTC (rev 2272)
@@ -368,6 +368,7 @@
<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+ <provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
</service>
</jar>
</target>
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -21,8 +21,10 @@
*/
package org.sbml.jsbml.xml.parsers;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.List;
import java.util.Map;
import java.util.ServiceConfigurationError;
import java.util.ServiceLoader;
@@ -66,6 +68,15 @@
*/
private Logger logger = Logger.getLogger(ParserManager.class);
+ private String[] parserDefaults =
+ {"org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader", "org.sbml.jsbml.xml.parsers.SBMLCoreParser",
+ "org.sbml.jsbml.xml.parsers.MathMLStaxParser", "org.sbml.jsbml.xml.parsers.ArraysParser", "org.sbml.jsbml.xml.parsers.CompParser",
+ "org.sbml.jsbml.xml.parsers.DistribParser", "org.sbml.jsbml.xml.parsers.DynParser", "org.sbml.jsbml.xml.parsers.FBCParser",
+ "org.sbml.jsbml.xml.parsers.GroupsParser", "org.sbml.jsbml.xml.parsers.L3LayoutParser", "org.sbml.jsbml.xml.parsers.LayoutParser",
+ "org.sbml.jsbml.xml.parsers.MultiParser", "org.sbml.jsbml.xml.parsers.QualParser", "org.sbml.jsbml.xml.parsers.RenderParser",
+ "org.sbml.jsbml.xml.parsers.ReqParser", "org.sbml.jsbml.xml.parsers.SpatialParser", "org.sbml.jsbml.xml.parsers.XMLNodeReader"};
+
+
/**
* Private constructor to make sure that we have only one {@link ParserManager} per JVM.
*/
@@ -91,7 +102,8 @@
private void init() {
// loading the ReadingParsers
Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
-
+ List<String> classNames = new ArrayList<String>();
+
// TODO - each time we add one HashMap entry, check that it was not defined already
// so that we notice problems as early as possible if two packages declared to take care of the same namespace
@@ -102,7 +114,8 @@
if (readingParser != null) {
String packageName = "core";
-
+ classNames.add(readingParser.getClass().getName());
+
if (readingParser instanceof PackageParser) {
packageName = ((PackageParser) readingParser).getPackageName();
packageParsers.put(packageName, (PackageParser) readingParser);
@@ -133,6 +146,7 @@
if (writingParser != null) {
String packageName = "core";
+ classNames.add(writingParser.getClass().getName());
if (writingParser instanceof PackageParser) {
packageName = ((PackageParser) writingParser).getPackageName();
@@ -149,7 +163,78 @@
}
}
+
+ // TODO - check the maps and add the parsers by hand if they are not present.
+ // prevent problems when developers are not setting properly eclipse, when jar
+ // files are not generated with
+
+ for (String parserClassName : parserDefaults) {
+ if (! classNames.contains(parserClassName)) {
+
+ try {
+ Object newInstance = Class.forName(parserClassName).newInstance();
+
+ if (newInstance instanceof ReadingParser) {
+ ReadingParser readingParser = (ReadingParser) newInstance;
+
+ String packageName = "core";
+
+ if (readingParser instanceof PackageParser) {
+ packageName = ((PackageParser) readingParser).getPackageName();
+ packageParsers.put(packageName, (PackageParser) readingParser);
+ }
+ for (String namespaceURI : readingParser.getNamespaces()) {
+ readingParsers.put(namespaceURI, readingParser);
+ namespaceToNameMap.put(namespaceURI, packageName);
+ }
+ if (readingParser instanceof WritingParser) {
+ for (String namespaceURI : readingParser.getNamespaces()) {
+ writingParsers.put(namespaceURI, (WritingParser) readingParser);
+ }
+ }
+ }
+
+ if (newInstance instanceof WritingParser)
+ {
+ WritingParser writingParser = (WritingParser) newInstance;
+
+ String packageName = "core";
+
+ if (writingParser instanceof PackageParser) {
+ packageName = ((PackageParser) writingParser).getPackageName();
+ packageParsers.put(packageName, (PackageParser) writingParser);
+ }
+
+ for (String namespaceURI : writingParser.getNamespaces()) {
+ writingParsers.put(namespaceURI, writingParser);
+ namespaceToNameMap.put(namespaceURI, packageName);
+ }
+ }
+ } catch (ClassNotFoundException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ }
+ }
+ catch (InstantiationException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ catch (IllegalAccessException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+
}
// <br /><dependency><br />
@@ -225,6 +310,7 @@
public Map<String, ReadingParser> getReadingParsers() {
Map<String, ReadingParser> clonedMap = new HashMap<String, ReadingParser>();
+ List<String> classNames = new ArrayList<String>();
Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
@@ -234,6 +320,8 @@
if (readingParser != null) {
+ classNames.add(readingParser.getClass().getName());
+
for (String namespaceURI : readingParser.getNamespaces()) {
clonedMap.put(namespaceURI, readingParser);
}
@@ -243,7 +331,44 @@
// No need to print the message again, it is printed once in the init() method
}
}
+
+ for (String parserClassName : parserDefaults) {
+ if (! classNames.contains(parserClassName)) {
+
+ try {
+ Object newInstance = Class.forName(parserClassName).newInstance();
+
+ if (newInstance instanceof ReadingParser) {
+ ReadingParser readingParser = (ReadingParser) newInstance;
+
+ for (String namespaceURI : readingParser.getNamespaces()) {
+ clonedMap.put(namespaceURI, readingParser);
+ }
+ }
+ } catch (ClassNotFoundException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ }
+ }
+ catch (InstantiationException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ catch (IllegalAccessException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
return clonedMap;
}
@@ -255,6 +380,7 @@
public Map<String, WritingParser> getWritingParsers() {
Map<String, WritingParser> clonedMap = new HashMap<String, WritingParser>();
+ List<String> classNames = new ArrayList<String>();
Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
@@ -264,6 +390,8 @@
if (readingParser != null && readingParser instanceof WritingParser) {
+ classNames.add(readingParser.getClass().getName());
+
for (String namespaceURI : readingParser.getNamespaces()) {
clonedMap.put(namespaceURI, (WritingParser) readingParser);
}
@@ -282,6 +410,8 @@
if (writingParser != null) {
+ classNames.add(writingParser.getClass().getName());
+
for (String namespaceURI : writingParser.getNamespaces()) {
clonedMap.put(namespaceURI, writingParser);
}
@@ -292,6 +422,41 @@
}
}
+ for (String parserClassName : parserDefaults) {
+ if (! classNames.contains(parserClassName)) {
+
+ try {
+ Object newInstance = Class.forName(parserClassName).newInstance();
+
+ if (newInstance instanceof WritingParser) {
+ WritingParser readingParser = (WritingParser) newInstance;
+
+ for (String namespaceURI : readingParser.getNamespaces()) {
+ clonedMap.put(namespaceURI, readingParser);
+ }
+ }
+ } catch (ClassNotFoundException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ }
+ }
+ catch (InstantiationException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ catch (IllegalAccessException e)
+ {
+ if (logger.isDebugEnabled()) {
+ logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+ e.printStackTrace();
+ }
+ }
+ }
+ }
return clonedMap;
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -1249,8 +1249,7 @@
@Override
public void writeCharacters(SBMLObjectForXML xmlObject,
Object sbmlElementToWrite) {
- // The method should never be called !
- log4jLogger.warn("The SBML core XML element should not have any content, everything should be stored as attribute.");
+ // The SBML core XML element should not have any content, everything should be stored as attribute.
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -695,7 +695,7 @@
if (!characters.isWhiteSpace()) {
isText = true; // the characters are not only 'white spaces'
}
- if ((sbmlElements.peek() instanceof XMLNode) || isInsideNotes || isInsideAnnotation) {
+ if ((!sbmlElements.isEmpty() && (sbmlElements.peek() instanceof XMLNode)) || isInsideNotes || isInsideAnnotation) {
isText = true; // We want to keep the whitespace/formatting when reading html block
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -1025,6 +1025,7 @@
childParser.writeElement(childXmlObject, nextObjectToWrite);
childParser.writeNamespaces(childXmlObject, nextObjectToWrite);
childParser.writeAttributes(childXmlObject, nextObjectToWrite);
+ childParser.writeCharacters(childXmlObject, nextObjectToWrite);
if (!childXmlObject.isSetName()) {
logger.error("XML name not set, element ignored!");
@@ -1062,6 +1063,11 @@
indent + indentCount, false);
elementIsNested = isClosedAnnotation = true;
}
+
+ if (childXmlObject.getCharacters() != null && childXmlObject.getCharacters().trim().length() != 0) {
+ newOutPutElement.addCharacters(childXmlObject.getCharacters());
+ }
+
if (s.getChildCount() > 0) {
// make sure that we'll have line breaks if an element has any sub elements.
elementIsNested = true;
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -231,7 +231,7 @@
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value)) && (SpatialConstants.shortLabel == prefix);
+ boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.spatialId)) {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -329,6 +329,7 @@
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.type)) {
+ // TODO: In the specs v0.90, the type name begins with capital letter.
if (!Pattern.matches("[a-z]*", value)) {
throw new SBMLException("The value is not all lower-case.");
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -269,8 +269,7 @@
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
+ boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.domainType)) {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -23,8 +23,10 @@
import java.text.MessageFormat;
import java.util.Map;
+import java.util.regex.Pattern;
import org.sbml.jsbml.AbstractSBase;
+import org.sbml.jsbml.SBMLException;
@@ -111,6 +113,15 @@
return coordinate != null;
}
+ /**
+ * @param coordinate
+ */
+ public void setCoordinate(String coordinate) {
+ if (!Pattern.matches("[a-z]*", coordinate)) {
+ throw new SBMLException("The value is not all lower-case.");
+ }
+ setCoordinate(CoordinateKind.valueOf(coordinate.toUpperCase()));
+ }
/**
* @param coordinate the coordinate to set
@@ -151,7 +162,7 @@
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.coordinate)) {
try {
- setCoordinate(CoordinateKind.valueOf(value));
+ setCoordinate(value);
} catch (Exception e) {
MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -52,6 +52,10 @@
/**
*
*/
+ private String pointIndex;
+ /**
+ *
+ */
private Integer pointIndexLength;
/**
*
@@ -85,6 +89,9 @@
if (po.isSetCompression()) {
setCompression(po.getCompression());
}
+ if (po.isSetPointIndex()) {
+ setPointIndex(po.getPointIndex());
+ }
if (po.isSetPointIndexLength()) {
setPointIndexLength(po.getPointIndexLength());
}
@@ -138,6 +145,10 @@
if (equal && isSetCompression()) {
equal &= po.getCompression().equals(getCompression());
}
+ equal &= po.isSetPointIndex() == isSetPointIndex();
+ if (equal && isSetPointIndex()) {
+ equal &= po.getPointIndex() == getPointIndex();
+ }
equal &= po.isSetPointIndexLength() == isSetPointIndexLength();
if (equal && isSetPointIndexLength()) {
equal &= po.getPointIndexLength() == getPointIndexLength();
@@ -323,13 +334,81 @@
/**
+ * Returns the value of {@link #pointIndex}.
+ *
+ * @return the value of {@link #pointIndex}.
+ */
+ public String getPointIndex() {
+ if (isSetPointIndex()) {
+ return pointIndex;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.pointIndex, this);
+ }
+
+
+ /**
+ * Returns whether {@link #pointIndex} is set.
+ *
+ * @return whether {@link #pointIndex} is set.
+ */
+ public boolean isSetPointIndex() {
+ return this.pointIndex != null;
+ }
+
+
+ /**
+ * Sets the value of pointIndex
+ *
+ * @param pointIndex the value of pointIndex to be set.
+ */
+ public void setPointIndex(String pointIndex) {
+ String oldPointIndex = this.pointIndex;
+ this.pointIndex = pointIndex;
+ firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+ }
+
+
+ /**
+ * Unsets the variable pointIndex.
+ *
+ * @return {@code true} if pointIndex was set before, otherwise {@code false}.
+ */
+ public boolean unsetPointIndex() {
+ if (isSetPointIndex()) {
+ String oldPointIndex = this.pointIndex;
+ this.pointIndex = null;
+ this.pointIndexLength = null;
+ firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Appends the variable data to pointIndex.
+ * @return {@code true} if data was appended to pointIndex, otherwise {@code false}.
+ */
+ public boolean append(String data) {
+ if (data == null) { return false; }
+ if (isSetPointIndex()) {
+ String oldPointIndex = this.pointIndex;
+ this.pointIndex = this.pointIndex + data;
+ firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+ } else {
+ setPointIndex(data);
+ }
+ return true;
+ }
+
+ /**
* Returns the value of pointIndexLength.
*
* @return the value of pointIndexLength.
*/
public int getPointIndexLength() {
if (isSetPointIndexLength()) {
- return pointIndexLength.intValue();
+ return pointIndexLength;
}
// This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
throw new PropertyUndefinedError(SpatialConstants.pointIndexLength, this);
@@ -447,6 +526,9 @@
if (isSetCompression()) {
hashCode += prime * getCompression().hashCode();
}
+ if (isSetPointIndex()) {
+ hashCode += prime * getPointIndex().hashCode();
+ }
if (isSetPointIndexLength()) {
hashCode += prime * getPointIndexLength();
}
@@ -514,21 +596,21 @@
try {
setCompression(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
}
}
else if (attributeName.equals(SpatialConstants.pointIndexLength)) {
try {
setPointIndexLength(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.pointIndexLength);
}
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
}
}
else {
@@ -551,6 +633,8 @@
builder.append(domainType);
builder.append(", compression=");
builder.append(compression);
+ builder.append(", pointIndex=");
+ builder.append(pointIndex);
builder.append(", pointIndexLength=");
builder.append(pointIndexLength);
builder.append(", dataType=");
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -69,6 +69,10 @@
/**
*
*/
+ private String samples;
+ /**
+ *
+ */
private Integer samplesLength;
/**
*
@@ -106,14 +110,15 @@
if (sf.isSetCompression()) {
setCompression(sf.getCompression());
}
+ if (sf.isSetSamples()) {
+ setSamples(sf.getSamples());
+ }
if (sf.isSetSamplesLength()) {
setSamplesLength(sf.getSamplesLength());
}
if (sf.isSetInterpolation()) {
setInterpolation(sf.getInterpolation());
}
-
- // TODO - data ?
}
/**
@@ -172,6 +177,10 @@
if (equal && isSetSamplesLength()) {
equal &= sf.getSamplesLength() == getSamplesLength();
}
+ equal &= sf.isSetSamples() == isSetSamples();
+ if (equal && isSetSamples()) {
+ equal &= sf.getSamples() == getSamples();
+ }
equal &= sf.isSetDataType() == isSetDataType();
if (equal && isSetDataType()) {
equal &= sf.getDataType().equals(getDataType());
@@ -491,7 +500,75 @@
return false;
}
+
+ /**
+ * Returns the value of {@link #samples}.
+ *
+ * @return the value of {@link #samples}.
+ */
+ public String getSamples() {
+ if (isSetSamples()) {
+ return samples;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.samples, this);
+ }
+
+ /**
+ * Returns whether {@link #samples} is set.
+ *
+ * @return whether {@link #samples} is set.
+ */
+ public boolean isSetSamples() {
+ return this.samples != null;
+ }
+
+
+ /**
+ * Sets the value of samples
+ *
+ * @param samples the value of samples to be set.
+ */
+ public void setSamples(String samples) {
+ String oldSamples = this.samples;
+ this.samples = samples;
+ firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+ }
+
+
+ /**
+ * Unsets the variable samples.
+ *
+ * @return {@code true} if samples was set before, otherwise {@code false}.
+ */
+ public boolean unsetSamples() {
+ if (isSetSamples()) {
+ String oldSamples = this.samples;
+ this.samples = null;
+ this.samplesLength = null;
+ firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Appends the variable data to samples.
+ * @return {@code true} if data was appended to samples, otherwise {@code false}.
+ */
+ public boolean append(String data) {
+ if (data == null) { return false; }
+ if (isSetSamples()) {
+ String oldSamples = this.samples;
+ this.samples = this.samples + data;
+ firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+ } else {
+ setSamples(data);
+ }
+ return true;
+ }
+
/**
* Returns the value of {@link #samplesLength}.
*
@@ -689,6 +766,10 @@
hashCode += prime * getCompression().hashCode();
}
+ if (isSetSamples()) {
+ hashCode += prime * getSamples().hashCode();
+ }
+
if (isSetSamplesLength()) {
hashCode += prime * getSamplesLength();
}
@@ -733,6 +814,11 @@
attributes.put(SpatialConstants.shortLabel + ":interpolation",
getInterpolation().toString());
}
+ if (isSetSamplesLength()) {
+ attributes.remove("samplesLength");
+ attributes.put(SpatialConstants.shortLabel + ":samplesLength",
+ String.valueOf(getSamplesLength()));
+ }
return attributes;
}
@@ -823,6 +909,8 @@
builder.append(compression);
builder.append(", samplesLength=");
builder.append(samplesLength);
+ builder.append(", samples=");
+ builder.append(samples);
builder.append(", data=");
builder.append(data);
builder.append("]");
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -151,7 +151,7 @@
/**
*
*/
- public static final String spatialId = "spatialId";
+ public static final String spatialId = "id";
/**
*
*/
@@ -515,9 +515,19 @@
/**
*
*/
+ public static final String arrayData = "arrayData";
+
+ /**
+ *
+ */
public static final String arrayDataLength = "arrayDataLength";
/**
+ *
+ */
+ public static final String spatialRef = "spatialRef";
+
+ /**
* @param level
* @param version
* @return
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -54,7 +54,10 @@
*
*/
private DataKind dataType;
-
+ /**
+ *
+ */
+ private String arrayData;
@@ -91,6 +94,9 @@
if (sp.isSetDataType()) {
setDataType(sp.getDataType());
}
+ if (sp.isSetArrayData()) {
+ setArrayData(sp.getArrayData());
+ }
}
@@ -111,6 +117,10 @@
if (equal && isSetCompression()) {
equal &= sp.getCompression().equals(getCompression());
}
+ equal &= sp.isSetArrayData() == isSetArrayData();
+ if (equal && isSetArrayData()) {
+ equal &= sp.getArrayData() == getArrayData();
+ }
equal &= sp.isSetArrayDataLength() == isSetArrayDataLength();
if (equal && isSetArrayDataLength()) {
equal &= sp.getArrayDataLength() == getArrayDataLength();
@@ -192,13 +202,81 @@
/**
+ * Returns the value of {@link #arrayData}.
+ *
+ * @return the value of {@link #arrayData}.
+ */
+ public String getArrayData() {
+ if (isSetArrayData()) {
+ return arrayData;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.arrayData, this);
+ }
+
+
+ /**
+ * Returns whether {@link #arrayData} is set.
+ *
+ * @return whether {@link #arrayData} is set.
+ */
+ public boolean isSetArrayData() {
+ return this.arrayData != null;
+ }
+
+
+ /**
+ * Sets the value of arrayData
+ *
+ * @param arrayData the value of arrayData to be set.
+ */
+ public void setArrayData(String arrayData) {
+ String oldArrayData = this.arrayData;
+ this.arrayData = arrayData;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ }
+
+
+ /**
+ * Unsets the variable arrayData.
+ *
+ * @return {@code true} if arrayData was set before, otherwise {@code false}.
+ */
+ public boolean unsetArrayData() {
+ if (isSetArrayData()) {
+ String oldArrayData = this.arrayData;
+ this.arrayData = null;
+ this.arrayDataLength = null;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Appends the variable data to arrayData.
+ * @return {@code true} if data was appended to arrayData, otherwise {@code false}.
+ */
+ public boolean append(String data) {
+ if (data == null) { return false; }
+ if (isSetArrayData()) {
+ String oldArrayData = this.arrayData;
+ this.arrayData = this.arrayData + data;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ } else {
+ setArrayData(data);
+ }
+ return true;
+ }
+
+ /**
* Returns the value of arrayDataLength.
*
* @return the value of arrayDataLength.
*/
public int getArrayDataLength() {
if (isSetArrayDataLength()) {
- return arrayDataLength.intValue();
+ return arrayDataLength;
}
// This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
throw new PropertyUndefinedError(SpatialConstants.arrayDataLength, this);
@@ -313,6 +391,9 @@
if (isSetArrayDataLength()) {
hashCode += prime * getArrayDataLength();
}
+ if (isSetArrayData()) {
+ hashCode += prime * getArrayData().hashCode();
+ }
if (isSetDataType()) {
hashCode += prime * getDataType().hashCode();
}
@@ -350,21 +431,21 @@
try {
setCompression(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
}
}
else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
try {
setArrayDataLength(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.arrayDataLength);
}
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
}
}
else {
@@ -382,6 +463,8 @@
StringBuilder builder = new StringBuilder();
builder.append("ParametricObject [compression=");
builder.append(compression);
+ builder.append(", arrayData=");
+ builder.append(arrayData);
builder.append(", arrayDataLength=");
builder.append(arrayDataLength);
builder.append(", dataType=");
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -21,6 +21,10 @@
*/
package org.sbml.jsbml.ext.spatial;
+import java.util.Map;
+
+import org.sbml.jsbml.PropertyUndefinedError;
+
/**
* @author Alex Thomas
* @author Andreas Dräger
@@ -37,15 +41,23 @@
/**
*
*/
+ private String spatialRef;
+
+ /**
+ *
+ */
public SpatialSymbolReference() {
super();
}
/**
- * @param classvar
+ * @param ssr
*/
- public SpatialSymbolReference(SpatialSymbolReference classvar) {
- super(classvar);
+ public SpatialSymbolReference(SpatialSymbolReference ssr) {
+ super(ssr);
+ if (ssr.isSetSpatialRef()) {
+ setSpatialRef(ssr.getSpatialRef());
+ }
}
/**
@@ -71,5 +83,84 @@
public boolean equals(Object object) {
return super.equals(object);
}
-
+
+
+ /**
+ * Returns the value of {@link #spatialRef}.
+ *
+ * @return the value of {@link #spatialRef}.
+ */
+ public String getSpatialRef() {
+ //TODO: if variable is boolean, create an additional "isVar"
+ //TODO: return primitive data type if possible (e.g., int instead of Integer)
+ if (isSetSpatialRef()) {
+ return spatialRef;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.spatialRef, this);
+ }
+
+
+ /**
+ * Returns whether {@link #spatialRef} is set.
+ *
+ * @return whether {@link #spatialRef} is set.
+ */
+ public boolean isSetSpatialRef() {
+ return this.spatialRef != null;
+ }
+
+
+ /**
+ * Sets the value of spatialRef
+ *
+ * @param spatialRef the value of spatialRef to be set.
+ */
+ public void setSpatialRef(String spatialRef) {
+ String oldSpatialRef = this.spatialRef;
+ this.spatialRef = spatialRef;
+ firePropertyChange(SpatialConstants.spatialRef, oldSpatialRef, this.spatialRef);
+ }
+
+
+ /**
+ * Unsets the variable spatialRef.
+ *
+ * @return {@code true} if spatialRef was set before, otherwise {@code false}.
+ */
+ public boolean unsetSpatialRef() {
+ if (isSetSpatialRef()) {
+ String oldSpatialRef = this.spatialRef;
+ this.spatialRef = null;
+ firePropertyChange(SpatialConstants.spatialRef, oldSpatialRef, this.spatialRef);
+ return true;
+ }
+ return false;
+ }
+
+
+ public Map<String, String> writeXMLAttributes() {
+ Map<String, String> attributes = super.writeXMLAttributes();
+ if (isSetSpatialRef()) {
+ attributes.remove(SpatialConstants.spatialRef);
+ attributes.put(SpatialConstants.shortLabel + ":" + SpatialConstants.spatialRef, getSpatialRef());
+ }
+ return attributes;
+ }
+
+
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
+ if (!isAttributeRead) {
+ isAttributeRead = true;
+ System.out.println("SpatialSymbolReference: debug attribute name: " + attributeName);
+ if (attributeName.equals(SpatialConstants.spatialRef)) {
+ setSpatialRef(value);
+ }
+ else {
+ isAttributeRead = false;
+ }
+ }
+ return isAttributeRead;
+ }
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 10:16:48 UTC (rev 2272)
@@ -84,7 +84,7 @@
@ProviderFor(ReadingParser.class)
public class SpatialParser extends AbstractReaderWriter implements PackageParser {
- // TODO - check that it is properly updated to the 0.88 draft specs
+ // TODO - check that it is properly updated to the 0.90 draft specs
/**
* A {@link Logger} for this class.
@@ -96,6 +96,28 @@
*/
public static final String namespaceURIrequired = "http://www.sbml.org/sbml/level3/version1/req/version1";
+
+
+ @Override
+ public void processCharactersOf(String elementName, String characters,
+ Object contextObject) {
+ if (contextObject instanceof SpatialPoints) {
+ SpatialPoints spatialPoints = (SpatialPoints) contextObject;
+ spatialPoints.append(characters);
+ }
+ if (contextObject instanceof ParametricObject) {
+ ParametricObject parametricObject = (ParametricObject) contextObject;
+ parametricObject.append(characters);
+ }
+ }
+
+ @Override
+ public void writeCharacters(SBMLObjectForXML xmlObject,
+ Object sbmlElementToWrite) {
+ // TODO Auto-generated method stub
+ super.writeCharacters(xmlObject, sbmlElementToWrite);
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getShortLabel()
*/
@@ -245,6 +267,7 @@
param.addExtension(SpatialConstants.namespaceURI, spatialParam);
}
+ // TODO: CHECK create method. this might be the source of the problem.
if (elementName.equals(SpatialConstants.spatialSymbolReference)) {
SpatialSymbolReference ssr = new SpatialSymbolReference();
spatialParam.setParamType(ssr);
@@ -314,14 +337,15 @@
// sfg.setSampledField(sf);
// return sf;
}
- } else if (contextObject instanceof SampledField) {
+ // NOTE: This has been moved in the listOf section below.
+// } else if (contextObject instanceof SampledField) {
// SampledField sf = (SampledField) contextObject; // No more child in 0.88
// if (elementName.equals(SpatialConstants.imageData)){
// ImageData im = new ImageData();
// sf.setImageData(im);
// // sf.set
// return im;
- // }
+ // }
} else if (contextObject instanceof CSGeometry) {
CSGeometry csg = (CSGeometry) contextObject;
if (elementName.equals(SpatialConstants.listOfCSGObjects)){
@@ -379,24 +403,14 @@
} else if (contextObject instanceof ParametricGeometry) {
ParametricGeometry pg = (ParametricGeometry) contextObject;
if (elementName.equals(SpatialConstants.spatialPoints)){
- SpatialPoints spatialPoints = pg.getSpatialPoints();
- return spatialPoints;
+ SpatialPoints sp = new SpatialPoints();
+ pg.setSpatialPoints(sp);
+ return sp;
} else if (elementName.equals(SpatialConstants.listOfParametricObjects)){
ListOf<ParametricObject> listOfParametricObjects = pg.getListOfParametricObjects();
return listOfParametricObjects;
}
- } else if (contextObject instanceof ParametricObject) {
- ParametricObject po = (ParametricObject) contextObject;
- if (elementName.equals(SpatialConstants.imageData)){
- // TODO: THIS NEEDS to be updated with the details provided in the spatial package v0.90,
- // See ArrayData text child and PointIndex text child
- //PolygonObject polygonObject = new PolygonObject();
- //po.setPolygonObject(polygonObject);
- //return polygonObject;
- }
- }
-
- else if (contextObject instanceof ListOf<?>) {
+ } else if (contextObject instanceof ListOf<?>) {
ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
if (elementName.equals(SpatialConstants.coordinateComponent)) {
@@ -459,6 +473,11 @@
SampledVolume elem = new SampledVolume();
sfg.addSampledVolume(elem);
return elem;
+ } else if (elementName.equals(SpatialConstants.sampledField)) {
+ Geometry g = (Geometry) listOf.getParentSBMLObject();
+ SampledField elem = new SampledField();
+ g.addSampledField(elem);
+ return elem;
} else if (elementName.equals(SpatialConstants.csgPrimitive)) {
CSGSetOperator csgso = (CSGSetOperator) listOf.getParentSBMLObject();
CSGPrimitive elem = new CSGPrimitive();
Copied: branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml (from rev 2240, trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml 2015-05-01 10:16:48 UTC (rev 2272)
@@ -0,0 +1,311 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/req/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="area">
+ <listOfUnits>
+ <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="molecules">
+ <listOfUnits>
+ <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="umol_um3_litre_1">
+ <listOfUnits>
+ <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="um3">
+ <listOfUnits>
+ <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="um2">
+ <listOfUnits>
+ <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="uM_um3_molecules_1">
+ <listOfUnits>
+ <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
+ <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+ <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="molecules_um_2_s_1">
+ <listOfUnits>
+ <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000000000"/>
+ <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="pA_um_2">
+ <listOfUnits>
+ <unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="ampere" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="uM_um_s_1">
+ <listOfUnits>
+ <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-09"/>
+ <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+ <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="Extracellular" name="Extracellular" spatialDimensions="3" constant="true">
+ <spatial:compartmentMapping spatial:id="ExtracellularExtracellular" spatial:domainType="Extracellular" spatial:unitSize="1"/>
+ </compartment>
+ <compartment id="Cytosol_Extracellular_membrane" name="Cytosol_Extracellular_membrane" spatialDimensions="2" constant="true">
+ <spatial:compartmentMapping spatial:id="Cytosol_Extracellular_membraneCytosol_Extracellular_membrane" spatial:domainType="Cytosol_Extracellular_membrane" spatial:unitSize="1"/>
+ </compartment>
+ <compartment id="Cytosol" name="Cytosol" spatialDimensions="3" constant="true">
+ <spatial:compartmentMapping spatial:id="CytosolCytosol" spatial:domainType="Cytosol" spatial:unitSize="1"/>
+ </compartment>
+ <compartment id="Nucleus_Cytosol_membrane" name="Nucleus_Cytosol_membrane" spatialDimensions="2" constant="true">
+ <spatial:compartmentMapping spatial:id="Nucleus_Cytosol_membraneNucleus_Cytosol_membrane" spatial:domainType="Nucleus_Cytosol_membrane" spatial:unitSize="1"/>
+ </compartment>
+ <compartment id="Nucleus" name="Nucleus" spatialDimensions="3" constant="true">
+ <spatial:compartmentMapping spatial:id="NucleusNucleus" spatial:domainType="Nucleus" spatial:unitSize="1"/>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="s1_nuc" compartment="Nucleus" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+ <annotation>
+ <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+ <vcell:VCMLSpecific>
+ <vcell:Compound Name="s1_2"/>
+ </vcell:VCMLSpecific>
+ </vcell:VCellInfo>
+ </annotation>
+ <req:listOfChangedMaths>
+ <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+ </req:listOfChangedMaths>
+ <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+ </species>
+ <species id="s1_cyt" compartment="Cytosol" initialConcentration="10" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+ <annotation>
+ <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+ <vcell:VCMLSpecific>
+ <vcell:Compound Name="s1_2"/>
+ </vcell:VCMLSpecific>
+ </vcell:VCellInfo>
+ </annotation>
+ <req:listOfChangedMaths>
+ <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+ </req:listOfChangedMaths>
+ <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+ </species>
+ <species id="s2_nuc" compartment="Nucleus" initialConcentration="5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+ <annotation>
+ <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+ <vcell:VCMLSpecific>
+ <vcell:Compound Name="s2_2"/>
+ </vcell:VCMLSpecific>
+ </vcell:VCellInfo>
+ </annotation>
+ <req:listOfChangedMaths>
+ <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+ </req:listOfChangedMaths>
+ <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+ </species>
+ <species id="s1_EC" compartment="Extracellular" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+ <annotation>
+ <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+ <vcell:VCMLSpecific>
+ <vcell:Compound Name="s1_2"/>
+ </vcell:VCMLSpecific>
+ </vcell:VCellInfo>
+ </annotation>
+ <req:listOfChangedMaths>
+ <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+ </req:listOfChangedMaths>
+ <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+ </species>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="x" value="0">
+ <spatial:spatialSymbolReference spatial:id="x"/>
+ </parameter>
+ <parameter id="y" value="0">
+ <spatial:spatialSymbolReference spatial:id="y"/>
+ </parameter>
+ <parameter id="s1_nuc_diff" value="10" constant="true">
+ <spatial:diffusionCoefficient spatial:variable="s1_nuc" spatial:type="isotropic"/>
+ <spatial:listOfCoordinateReferences>
+ <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+ <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+ </spatial:listOfCoordinateReferences>
+ </parameter>
+ <parameter id="s1_nuc_BC_Xm" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ </parameter>
+ <parameter id="s1_nuc_BC_Xp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ </parameter>
+ <parameter id="s1_nuc_BC_Ym" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ </parameter>
+ <parameter id="s1_nuc_BC_Yp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+ </parameter>
+ <parameter id="s1_cyt_diff" value="10" constant="true">
+ <spatial:diffusionCoefficient spatial:variable="s1_cyt" spatial:type="isotropic"/>
+ <spatial:listOfCoordinateReferences>
+ <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+ <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+ </spatial:listOfCoordinateReferences>
+ </parameter>
+ <parameter id="s1_cyt_BC_Xm" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ </parameter>
+ <parameter id="s1_cyt_BC_Xp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ </parameter>
+ <parameter id="s1_cyt_BC_Ym" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+ </parameter>
+ <parameter id="s1_cyt_BC_Yp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet"/>
+ </parameter>
+ <parameter id="s1_EC_diff" value="10" constant="true">
+ <spatial:diffusionCoefficient spatial:variable="s1_EC" spatial:type="isotropic"/>
+ <spatial:listOfCoordinateReferences>
+ <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+ <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+ </spatial:listOfCoordinateReferences>
+ </parameter>
+ <parameter id="s1_EC_BC_Xm" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ </parameter>
+ <parameter id="s1_EC_BC_Xp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ </parameter>
+ <parameter id="s1_EC_BC_Ym" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ </parameter>
+ <parameter id="s1_EC_BC_Yp" value="0" constant="true">
+ <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+ </parameter>
+ <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true">
+ <listOfReactants>
+ <speciesReference species="s1_cyt" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s1_nuc" stoichiometry="1"/>
+ ...
[truncated message content] |
|
From: <nik...@us...> - 2015-05-01 10:01:35
|
Revision: 2271
http://sourceforge.net/p/jsbml/code/2271
Author: niko-rodrigue
Date: 2015-05-01 10:01:31 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2232
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2232
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
branches/astnode2-merging-alternate/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialParameterPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate 2015-05-01 10:01:31 UTC (rev 2271)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2227
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2232
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-05-01 10:01:31 UTC (rev 2271)
@@ -31,8 +31,6 @@
<entry key="IndexExceedsBoundsException">Index {0,number,integer} >= {1,number,integer}</entry>
<entry key="IndexExceedsBoundsException2">Node {0} has no children.</entry>
- <entry key="IndexSurpassesBoundsException">Index {0,number,integer} < {0,number,integer}</entry>
- <entry key="NullArgument">Argument is null.</entry>
<entry key="AbstractMathContainer.toFormula">Could not create infix formula from syntax tree.</entry>
<entry key="AbstractMathContainer.inclusion">{0} in {1}</entry>
@@ -60,42 +58,5 @@
<entry key="AbstractSBase.emptyNotes">The notes to append are empty!</entry>
<entry key="AbstractSBase.invalidNotesStructure">The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.</entry>
<entry key="AbstractSBase.problemAddingXMLNode">There was a problem adding the given XMLNode: ''{0}'' to the ''body'' XMLNode.</entry>
-
- <entry key="Assignment.ILLEGAL_CONSTANT_VARIABLE_MSG">Cannot set the constant variable {0} as the target of this {1}.</entry>
- <entry key="Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG">Cannot set SpeciesReference {0} as the Variable in {1} for SBML Level < 3</entry>
- <entry key="Assignment.NO_SUCH_VARIABLE_EXCEPTION_MSG">Model {0} does not contain any variable with identifier {1}.</entry>
-
- <entry key="ASTNode.INVALID_OPERATOR_MSG">Invalid operator {0}. The operator must be one of the following constants: PLUS, MINUS, TIMES, DIVIDE, or POWER.</entry>
- <entry key="ASTNode.log">logarithm cannot be created for null values</entry>
- <entry key="ASTNode.relational">Cannot create a relational node with null arguments.</entry>
- <entry key="ASTNode1">Clone constructor: Origin type = {0}</entry>
- <entry key="ASTNode.arithmeticOperation">Cannot divide by zero.</entry>
- <entry key="ASTNode.compile1">Fractions must have one numerator and one denominator, here {0,number,integer} elements are given.</entry>
- <entry key="ASTNode.compile2">ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ({0}, {1})</entry>
- <entry key="ASTNode.compile3">ASTNode of type FUNCTION but the variable is null: ({0}, {1})! Check that your object is linked to a Model.</entry>
- <entry key="ASTNode.compile4">getCharacter() should be called only when isOperator().</entry>
- <entry key="ASTNode.getDenominator">getDenominator() should be called only when getType() == RATIONAL.</entry>
- <entry key="ASTNode.getExponent">getExponent() should be called only when getType() == REAL_E or REAL</entry>
- <entry key="ASTNode.getInteger">getInteger() should be called only when getType() == INTEGER</entry>
- <entry key="ASTNode.getMantissa">getMantissa() should be called only when getType() == REAL or REAL_E</entry>
- <entry key="ASTNode.getName">getName() should be called only when !isNumber() && !isOperator()</entry>
- <entry key="ASTNode.getNumerator">getNumerator() should be called only when isRational()</entry>
- <entry key="ASTNode.getReal">getReal() should be called only when isReal() returns true.</entry>
- <entry key="ASTNode.getReferencedNamedSBases">Name of this node is {0} but no variable is set.</entry>
- <entry key="ASTNode.getVariable1">The name \"{0}\" represented by this node is an argument in a function call, i.e., a placeholder for some other element. No corresponding CallableSBase exists in the model</entry>
- <entry key="ASTNode.getVariable2">Cannot find any element with id \"{0}\" in the model.</entry>
- <entry key="ASTNode.getVariable3">This ASTNode is not yet linked to a model and can therefore not determine its variable \"{0}\".</entry>
- <entry key="ASTNode.getVariable4">getVariable() should be called only when isVariable() == true.</entry>
- <entry key="ASTNode.initDefaults">initDefaults called! type was {0}</entry>
- <entry key="ASTNode.reduceToBinary1">MINUS node with {0,number,integer} children left unchanged</entry>
- <entry key="ASTNode.reduceToBinary2">DIVIDE node with {0,number,integer} children left unchanged</entry>
- <entry key="ASTNode.reduceToBinary3">NOT node with {0,number,integer} children left unchanged</entry>
- <entry key="ASTNode.reduceToBinary4">XOR node with {0,number,integer} children left unchanged</entry>
- <entry key="ASTNode.reduceToBinary5">{0} node with {1,number,integer} children left unchanged</entry>
- <entry key="ASTNode.setType">setType called: typeBefore={0} typeAfter={1}</entry>
- <entry key="ASTNode.setUnits1">Unexpected attribute {0}, a unit can only be assigned to literal numbers.</entry>
- <entry key="ASTNode.setUnits2">Unexpected attribute {0}, only a valid unit kind or the identifier of a unit definition are allowed here.</entry>
- <entry key="ASTNode.setUnits3">Cannot set unit {0} for a numbers in an ASTNode before SBML Level 3.</entry>
- <entry key="ASTNode.toString">Could not compile ASTNode to formula: {0}</entry>
</properties>
\ No newline at end of file
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -150,7 +150,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
@@ -180,12 +180,14 @@
name = getElementName();
SBase parent = getParentSBMLObject();
if ((parent != null) && (parent instanceof NamedSBase)) {
- name += " in " + parent.toString();
+ name = MessageFormat.format(
+ resourceBundle.getString("AbstractMathContainer.inclusion"),
+ name, parent.toString());
}
}
logger.warn(MessageFormat.format(
- "Could not derive unit from syntax tree of {0}: {1}", name,
- exc.getLocalizedMessage()));
+ resourceBundle.getString("AbstractMathContainer.getDerivedUnitDefinition"),
+ name, exc.getLocalizedMessage()));
logger.debug(exc.getLocalizedMessage(), exc);
}
}
@@ -233,8 +235,8 @@
public String getFormula() {
try {
return isSetMath() ? getMath().toFormula() : "";
- } catch (Throwable e) {
- logger.warn("Could not create infix formula from syntax tree.", e);
+ } catch (Throwable exc) {
+ logger.warn(resourceBundle.getString("AbstractMathContainer.toFormula"), exc);
return "invalid";
}
}
@@ -352,4 +354,5 @@
}
return attributes;
}
+
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -162,7 +162,8 @@
boolean checkIdentifier(String sID) {
if ((sID == null) || !SyntaxChecker.isValidId(sID, getLevel(), getVersion())) {
throw new IllegalArgumentException(MessageFormat.format(
- "\"{0}\" is not a valid identifier for this {1}.", sID, getElementName()));
+ resourceBundle.getString("AbstractNamedSBase.checkIdentifier"),
+ sID, getElementName()));
}
return true;
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -689,7 +689,9 @@
for (i=0; i < addedNotes.getChildCount(); i++)
{
if (curBody.addChild(addedNotes.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.appendNotes"),
+ SBMLtools.toXML(addedNotes.getChildAt(i))));
return;
}
}
@@ -731,7 +733,9 @@
for (i = 0; i < addedNotes.getChildCount(); i++)
{
if (curNotes.addChild(addedNotes.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.appendNotes"),
+ SBMLtools.toXML(addedNotes.getChildAt(i))));
return;
}
}
@@ -760,7 +764,7 @@
* Level/Version combination than this current {@link SBase}, an
* {@link LevelVersionError} is thrown. This method is only
* package-wide visible because it is not intended to be a
- * "real" check, rather than to indicate potential errors.
+ * <i>real</i> check, rather than to indicate potential errors.
*/
protected boolean checkLevelAndVersionCompatibility(SBase sbase) {
if (sbase.getLevelAndVersion().equals(getLevelAndVersion())) {
@@ -812,7 +816,7 @@
}
throw new IllegalArgumentException(MessageFormat.format(
- "The package namespace or name ''{0}'' is unknown!",
+ resourceBundle.getString("AbstractSBase.createPlugin"),
nameOrUri));
}
@@ -843,13 +847,12 @@
*/
@Override
public void enablePackage(String packageURIOrName, boolean enabled) {
-
SBMLDocument doc = getSBMLDocument();
if (doc != null) {
doc.enablePackage(packageURIOrName, enabled);
- } else {
- logger.debug("Package not enabled, could not find the SBMLDocument.");
+ } else if (logger.isDebugEnabled()) {
+ logger.debug(resourceBundle.getString("AbstractSBase.enablePackage"));
}
}
@@ -998,7 +1001,9 @@
TreeNode parent = getParent();
if (logger.isDebugEnabled()) {
- logger.debug("fireNodeRemovedEvent called on " + this + " (parent = " + parent + ")");
+ logger.debug(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.fireNodeRemovedEvent"),
+ this, parent));
}
if ((parent != null) && (parent instanceof SBase)) {
@@ -1076,10 +1081,10 @@
}
}
- throw new IndexOutOfBoundsException(isLeaf() ? MessageFormat.format(
- "Node {0} has no children.", getElementName()) : MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
- childIndex, Math.min(pos, 0)));
+ throw new IndexOutOfBoundsException(isLeaf() ?
+ MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException2"), getElementName()) :
+ MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
@@ -1111,7 +1116,7 @@
return annotation.getCVTerm(index);
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "No such controlled vocabulary term with index {0,number,integer}.", index));
+ resourceBundle.getString("AbstractSBase.getCVTerm"), index));
}
/* (non-Javadoc)
@@ -1154,16 +1159,15 @@
*/
@Override
public SBasePlugin getExtension(String nameOrUri) {
-
// use always the package name in the map
PackageParser packageParser = ParserManager.getManager().getPackageParser(nameOrUri);
if (packageParser != null) {
-
return extensions.get(packageParser.getPackageName());
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
}
/* (non-Javadoc)
@@ -1383,7 +1387,8 @@
}
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
}
/* (non-Javadoc)
@@ -1616,7 +1621,8 @@
// return false;
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
}
/* (non-Javadoc)
@@ -1691,11 +1697,11 @@
if ((sbase != null) && (sbase.getParent() != null)) {
if (sbase.getParent() == this) {
logger.warn(MessageFormat.format(
- "Trying to register {0} ''{1}'', which is already registered under {2} ''{3}''.",
+ resourceBundle.getString("AbstractSBase.registerChild1"),
sbase.getElementName(), sbase, getElementName(), this));
} else {
logger.warn(MessageFormat.format(
- "{0} ''{1}'' is associated to the different parent ''{2}''. Please remove it there before adding it to this ''{3}'' or add a clone of it to this element.",
+ resourceBundle.getString("AbstractSBase.registerChild2"),
sbase.getClass().getSimpleName(), sbase, sbase.getParent(), this));
}
return false;
@@ -1743,7 +1749,8 @@
sbase.addAllChangeListeners(listeners);
throw new IllegalArgumentException(MessageFormat.format(
- "Cannot register {0}.", sbase.getElementName()));
+ resourceBundle.getString("AbstractSBase.registerChild3"),
+ sbase.getElementName()));
}
// TODO - set package version and namespace if needed
@@ -1918,7 +1925,7 @@
throw new PropertyNotAvailableException(TreeNodeChangeEvent.metaId, this);
} else if (!SyntaxChecker.isValidMetaId(metaId)) {
throw new IllegalArgumentException(MessageFormat.format(
- "\"{0}\" is not a valid meta-identifier for this {1}.",
+ resourceBundle.getString("AbstractSBase.setMetaId"),
metaId, getElementName()));
}
}
@@ -2031,7 +2038,7 @@
}
if (!SBO.checkTerm(term)) {
throw new IllegalArgumentException(MessageFormat.format(
- "Cannot set invalid SBO term {0,number,integer} because it must not be smaller than zero or larger than 9999999.",
+ resourceBundle.getString("AbstractSBase.setSBOTerm"),
term));
}
Integer oldTerm = Integer.valueOf(sboTerm);
@@ -2086,8 +2093,10 @@
public void unregisterChild(SBase sbase) {
if (logger.isDebugEnabled()) {
- logger.debug("unregister called! " + sbase.getElementName() + " "
- + (sbase instanceof NamedSBase ? ((NamedSBase) sbase).getId() : ""));
+ logger.debug(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.unregisterChild1"),
+ sbase.getElementName(),
+ (sbase instanceof NamedSBase ? ((NamedSBase) sbase).getId() : "")));
}
if ((sbase != null)) {
@@ -2103,7 +2112,8 @@
// If possible, recursively unregister all ids of the SBase in our model:
if ((idManager != null)
&& !idManager.unregister(sbase)) {
- throw new IllegalArgumentException(MessageFormat.format("Cannot unregister {0}.",
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.unregisterChild2"),
sbase.getElementName()));
}
@@ -2125,7 +2135,9 @@
private void unregisterChild(SBasePlugin sbasePlugin) {
if (logger.isDebugEnabled()) {
- logger.debug("AbstractSBase - #unregisterChild(SBasePlugin) - called on '" + sbasePlugin + "'");
+ logger.debug(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.unregisterChild3"),
+ sbasePlugin));
}
int childCount = sbasePlugin.getChildCount();
@@ -2223,7 +2235,9 @@
return;
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.createPlugin"),
+ nameOrUri));
}
@Override
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -399,7 +399,7 @@
// pos++;
// }
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -125,7 +125,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -404,7 +404,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -184,7 +184,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -288,7 +288,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -1876,7 +1876,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -511,7 +511,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -662,7 +662,7 @@
return getModel();
}
}
- throw new IndexOutOfBoundsException(MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+ throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -279,7 +279,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -697,7 +697,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
+ Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -176,7 +176,7 @@
}
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, getChildCount()));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -272,7 +272,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -600,7 +600,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -535,7 +535,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -485,7 +485,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -615,7 +615,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -177,7 +177,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -185,7 +185,7 @@
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -479,7 +479,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
+ resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -1,262 +1,262 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2014 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.distrib;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import javax.swing.tree.TreeNode;
-
-import org.sbml.jsbml.AbstractNamedSBase;
-import org.sbml.jsbml.xml.XMLNode;
-
-/**
- *
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.1
- * @date 26.03.2015
- */
-public class Uncertainty extends AbstractNamedSBase {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -904719821379100471L;
- /**
- *
- */
- private XMLNode uncertML;
-
- /**
- * Creates an Uncertainty instance
- */
- public Uncertainty() {
- super();
- initDefaults();
- }
-
-
- /**
- * Creates a Uncertainty instance with an id.
- *
- * @param id the identifier for the new element.
- */
- public Uncertainty(String id) {
- super(id);
- initDefaults();
- }
-
-
- /**
- * Creates a Uncertainty instance with a level and version.
- *
- * @param level SBML Level
- * @param version SBML Version
- */
- public Uncertainty(int level, int version) {
- this(null, null, level, version);
- }
-
-
- /**
- * Creates a Uncertainty instance with an id, level, and version.
- *
- * @param id the identifier for this element.
- * @param level the SBML Level
- * @param version the SBML Version
- */
- public Uncertainty(String id, int level, int version) {
- this(id, null, level, version);
- }
-
-
- /**
- * Creates a Uncertainty instance with an id, name, level, and version.
- *
- * @param id the identifier for this element.
- * @param name a human-readable name for this element that can be used for display purposes.
- * @param level the SBML Level
- * @param version the SBML Version
- */
- public Uncertainty(String id, String name, int level, int version) {
- super(id, name, level, version);
- initDefaults();
- }
-
-
- /**
- * Clone constructor
- * @param obj
- */
- public Uncertainty(Uncertainty obj) {
- super(obj);
- }
-
- /**
- * Initializes the default values using the namespace.
- */
- public void initDefaults() {
- setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- setPackageVersion(-1);
- packageName = DistribConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
- */
- @Override
- public boolean isIdMandatory() {
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#clone()
- */
- @Override
- public Uncertainty clone() {
- return new Uncertainty(this);
- }
-
-
- /**
- * Returns the value of {@link #uncertML}.
- *
- * @return the value of {@link #uncertML}.
- */
- public XMLNode getUncertML() {
- if (isSetUncertML()) {
- return uncertML;
- }
-
- return null;
- }
-
-
- /**
- * Returns whether {@link #uncertML} is set.
- *
- * @return whether {@link #uncertML} is set.
- */
- public boolean isSetUncertML() {
- return uncertML != null;
- }
-
-
- /**
- * Sets the value of uncertML
- *
- * @param uncertML the value of uncertML to be set.
- */
- public void setUncertML(XMLNode uncertML) {
- XMLNode oldUncertML = this.uncertML;
- this.uncertML = uncertML;
- this.uncertML.setParent(this);
- firePropertyChange(DistribConstants.uncertML, oldUncertML, this.uncertML);
- }
-
-
- /**
- * Unsets the variable uncertML.
- *
- * @return {@code true} if uncertML was set before, otherwise {@code false}.
- */
- public boolean unsetUncertML() {
- if (isSetUncertML()) {
- XMLNode oldUncertML = uncertML;
- uncertML = null;
- firePropertyChange(DistribConstants.uncertML, oldUncertML, uncertML);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#getAllowsChildren()
- */
- @Override
- public boolean getAllowsChildren() {
- return true;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#getChildCount()
- */
- @Override
- public int getChildCount() {
- int count = super.getChildCount();
-
- if (isSetUncertML()) {
- count++;
- }
-
- return count;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
- */
- @Override
- public TreeNode getChildAt(int index) {
- if (index < 0) {
- throw new IndexOutOfBoundsException(index + " < 0");
- }
- int count = super.getChildCount(), pos = 0;
-
- if (index < count) {
- return super.getChildAt(index);
- } else {
- index -= count;
- }
-
- if (isSetUncertML()) {
- if (pos == index) {
- return getUncertML();
- }
- pos++;
- }
-
- throw new IndexOutOfBoundsException(
- MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
- index, Math.min(pos, 0)));
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
-
- if (isSetId()) {
- attributes.remove("id");
- attributes.put(DistribConstants.shortLabel + ":id", getId());
- }
- if (isSetName()) {
- attributes.remove("name");
- attributes.put(DistribConstants.shortLabel + ":name", getId());
- }
-
- return attributes;
- }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.distrib;
+
+import java.text.MessageFormat;
+import java.util.Map;
+
+import javax.swing.tree.TreeNode;
+
+import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.xml.XMLNode;
+
+/**
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ * @date 26.03.2015
+ */
+public class Uncertainty extends AbstractNamedSBase {
+
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -904719821379100471L;
+ /**
+ *
+ */
+ private XMLNode uncertML;
+
+ /**
+ * Creates an Uncertainty instance
+ */
+ public Uncertainty() {
+ super();
+ initDefaults();
+ }
+
+
+ /**
+ * Creates a Uncertainty instance with an id.
+ *
+ * @param id the identifier for the new element.
+ */
+ public Uncertainty(String id) {
+ super(id);
+ initDefaults();
+ }
+
+
+ /**
+ * Creates a Uncertainty instance with a level and version.
+ *
+ * @param level SBML Level
+ * @param version SBML Version
+ */
+ public Uncertainty(int level, int version) {
+ this(null, null, level, version);
+ }
+
+
+ /**
+ * Creates a Uncertainty instance with an id, level, and version.
+ *
+ * @param id the identifier for this element.
+ * @param level the SBML Level
+ * @param version the SBML Version
+ */
+ public Uncertainty(String id, int level, int version) {
+ this(id, null, level, version);
+ }
+
+
+ /**
+ * Creates a Uncertainty instance with an id, name, level, and version.
+ *
+ * @param id the identifier for this element.
+ * @param name a human-readable name for this element that can be used for display purposes.
+ * @param level the SBML Level
+ * @param version the SBML Version
+ */
+ public Uncertainty(String id, String name, int level, int version) {
+ super(id, name, level, version);
+ initDefaults();
+ }
+
+
+ /**
+ * Clone constructor
+ * @param obj
+ */
+ public Uncertainty(Uncertainty obj) {
+ super(obj);
+ }
+
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ setPackageVersion(-1);
+ packageName = DistribConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
+ */
+ @Override
+ public boolean isIdMandatory() {
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#clone()
+ */
+ @Override
+ public Uncertainty clone() {
+ return new Uncertainty(this);
+ }
+
+
+ /**
+ * Returns the value of {@link #uncertML}.
+ *
+ * @return the value of {@link #uncertML}.
+ */
+ public XMLNode getUncertML() {
+ if (isSetUncertML()) {
+ return uncertML;
+ }
+
+ return null;
+ }
+
+
+ /**
+ * Returns whether {@link #uncertML} is set.
+ *
+ * @return whether {@link #uncertML} is set.
+ */
+ public boolean isSetUncertML() {
+ return uncertML != null;
+ }
+
+
+ /**
+ * Sets the value of uncertML
+ *
+ * @param uncertML the value of uncertML to be set.
+ */
+ public void setUncertML(XMLNode uncertML) {
+ XMLNode oldUncertML = this.uncertML;
+ this.uncertML = uncertML;
+ this.uncertML.setParent(this);
+ firePropertyChange(DistribConstants.uncertML, oldUncertML, this.uncertML);
+ }
+
+
+ /**
+ * Unsets the variable uncertML.
+ *
+ * @return {@code true} if uncertML was set before, otherwise {@code false}.
+ */
+ public boolean unsetUncertML() {
+ if (isSetUncertML()) {
+ XMLNode oldUncertML = uncertML;
+ uncertML = null;
+ firePropertyChange(DistribConstants.uncertML, oldUncertML, uncertML);
+ return true;
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#getAllowsChildren()
+ */
+ @Override
+ public boolean getAllowsChildren() {
+ return true;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#getChildCount()
+ */
+ @Override
+ public int getChildCount() {
+ int count = super.getChildCount();
+
+ if (isSetUncertML()) {
+ count++;
+ }
+
+ return count;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
+ */
+ @Override
+ public TreeNode getChildAt(int index) {
+ if (index < 0) {
+ throw new IndexOutOfBoundsException(index + " < 0");
+ }
+ int count = super.getChildCount(), pos = 0;
+
+ if (index < count) {
+ return super.getChildAt(index);
+ } else {
+ index -= count;
+ }
+
+ if (isSetUncertML()) {
+ if (pos == index) {
+ return getUncertML();
+ }
+ pos++;
+ }
+
+ throw new IndexOutOfBoundsException(
+ MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
+ index, Math.min(pos, 0)));
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
+ */
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ Map<String, String> attributes = super.writeXMLAttributes();
+
+ if (isSetId()) {
+ attributes.remove("id");
+ attributes.put(DistribConstants.shortLabel + ":id", getId());
+ }
+ if (isSetName()) {
+ attributes.remove("name");
+ attributes.put(DistribConstants.shortLabel + ":name", getId());
+ }
+
+ return attributes;
+ }
+
+}
Modified: branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -267,7 +267,7 @@
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0 || childIndex >= 1) {
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, +Math.min(getChildCount(), 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -293,7 +293,7 @@
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0 || childIndex >= 1) {
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, +Math.min(getChildCount(), 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -259,7 +259,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -179,7 +179,7 @@
}
throw new IndexOutOfBoundsException(
- MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+ MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -166,7 +166,7 @@
}
int pos = 0;
throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
+ resourceBundle.getString("IndexExceedsBoundsException"),
index, + Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java 2015-05-01 10:01:31 UTC (rev 2271)
@@ -158,7 +158,7 @@
pos++;
}
throw new IndexOutOfBoundsException(
- MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+ MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java 2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOpera...
[truncated message content] |
|
From: <nik...@us...> - 2015-05-01 09:56:21
|
Revision: 2270
http://sourceforge.net/p/jsbml/code/2270
Author: niko-rodrigue
Date: 2015-05-01 09:56:17 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2227
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2227
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
branches/astnode2-merging-alternate/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
branches/astnode2-merging-alternate/modules/celldesigner/src/org/sbml/jsbml/celldesigner/SBMLLayoutVisualizer.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate 2015-05-01 09:56:17 UTC (rev 2270)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2226
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2227
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -151,7 +151,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -397,7 +397,7 @@
}
/* (non-Javadoc)
- * @see org.sbml.jlibsbml.SBase#appendNotes(java.lang.String)
+ * @see org.sbml.jsbml.SBase#appendNotes(java.lang.String)
*/
@Override
public void appendNotes(String notes) throws XMLStreamException {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -577,6 +577,14 @@
return getNonRDFannotation();
}
+ /**
+ *
+ * @param nonRDFannotation
+ */
+ public void setXMLNode(XMLNode nonRDFannotation) {
+ setNonRDFAnnotation(nonRDFannotation);
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#hashCode()
*/
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -29,7 +29,6 @@
import java.util.regex.Pattern;
import javax.swing.tree.TreeNode;
-import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.util.TreeNodeAdapter;
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -126,7 +126,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -405,7 +405,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -289,7 +289,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1877,7 +1877,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -512,7 +512,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -663,7 +663,7 @@
}
}
throw new IndexOutOfBoundsException(MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -280,7 +280,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -114,6 +114,25 @@
}
/**
+ *
+ * @param indent
+ * @throws XMLStreamException
+ */
+ public MathMLXMLStreamCompiler(String indent) throws XMLStreamException {
+ SMOutputFactory smFactory = new SMOutputFactory(XMLOutputFactory.newInstance());
+ writer = smFactory.createStax2Writer(new StringWriter());
+ this.indent = indent;
+ }
+
+ /**
+ * @throws XMLStreamException
+ *
+ */
+ public MathMLXMLStreamCompiler() throws XMLStreamException {
+ this("");
+ }
+
+ /**
* Writes an {@link ASTNode} the mathML.
*
* @param astNode the {@link ASTNode} to serialize as mathML
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -273,7 +273,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -601,7 +601,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -536,7 +536,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -486,7 +486,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -616,7 +616,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -178,7 +178,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
@Override
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,208 +1,208 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2014 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.distrib;
-
-import java.text.MessageFormat;
-
-import javax.swing.tree.TreeNode;
-
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.1
- * @date 26.03.2015
- */
-public class DistribSBasePlugin extends AbstractSBasePlugin {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -1732369832900356125L;
- /**
- *
- */
- private Uncertainty uncertainty;
-
- /**
- * Creates a new {@link DistribSBasePlugin} instance.
- *
- * @param sbase the {@link SBase} to be extended.
- */
- public DistribSBasePlugin(SBase sbase) {
- super(sbase);
- setPackageVersion(-1);
- }
-
- /**
- * Creates a new {@link DistribSBasePlugin} instance, cloned from
- * the input parameter.
- *
- * @param obj the {@link DistribSBasePlugin} to clone
- */
- public DistribSBasePlugin(DistribSBasePlugin obj) {
- super(obj);
-
- if (obj.isSetUncertainty()) {
- setUncertainty(obj.getUncertainty().clone());
- }
- }
-
-
- /**
- * Creates and Sets a new {@link Uncertainty} instance.
- *
- * @return the newly created {@link Uncertainty} instance.
- */
- public Uncertainty createUncertainty() {
- Uncertainty uncert = new Uncertainty();
- setUncertainty(uncert);
- return uncert;
- }
-
-
- /**
- * Returns the value of {@link #uncertainty}.
- *
- * @return the value of {@link #uncertainty}.
- */
- public Uncertainty getUncertainty() {
- if (isSetUncertainty()) {
- return uncertainty;
- }
-
- return null;
- }
-
-
- /**
- * Returns whether {@link #uncertainty} is set.
- *
- * @return whether {@link #uncertainty} is set.
- */
- public boolean isSetUncertainty() {
- return uncertainty != null;
- }
-
-
- /**
- * Sets the value of uncertainty
- *
- * @param uncertainty the value of uncertainty to be set.
- */
- public void setUncertainty(Uncertainty uncertainty) {
- Uncertainty oldUncertainty = this.uncertainty;
- this.uncertainty = uncertainty;
- if (getExtendedSBase() != null) {
- getExtendedSBase().registerChild(uncertainty);
- }
- firePropertyChange(DistribConstants.uncertainty, oldUncertainty, this.uncertainty);
- }
-
-
- /**
- * Unsets the variable uncertainty.
- *
- * @return {@code true} if uncertainty was set before, otherwise {@code false}.
- */
- public boolean unsetUncertainty() {
- if (isSetUncertainty()) {
- Uncertainty oldUncertainty = uncertainty;
- uncertainty = null;
- firePropertyChange(DistribConstants.uncertainty, oldUncertainty, uncertainty);
- return true;
- }
- return false;
- }
-
-
- @Override
- public String getElementNamespace() {
- return DistribConstants.namespaceURI_L3V1V1; // TODO - change to return a String attribute that can be changed
- }
-
- @Override
- public String getPackageName() {
- return DistribConstants.shortLabel;
- }
-
- @Override
- public String getPrefix() {
- return DistribConstants.shortLabel;
- }
-
- @Override
- public String getURI() {
- return DistribConstants.namespaceURI; // TODO - change to return a String attribute that can be changed
- }
-
-
- @Override
- public int getChildCount() {
- int count = 0;
-
- if (isSetUncertainty()) {
- count++;
- }
-
- return count;
- }
-
-
- @Override
- public TreeNode getChildAt(int index) {
- if (index < 0) {
- throw new IndexOutOfBoundsException(index + " < 0");
- }
- int pos = 0;
-
- if (isSetUncertainty()) {
- if (pos == index) {
- return getUncertainty();
- }
- pos++;
- }
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
- }
-
- @Override
- public boolean getAllowsChildren() {
- return true;
- }
-
- @Override
- public AbstractSBasePlugin clone() {
- return new DistribSBasePlugin(this);
- }
-
- @Override
- public boolean readAttribute(String attributeName, String prefix,
- String value) {
- return false;
- }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.distrib;
+
+import java.text.MessageFormat;
+
+import javax.swing.tree.TreeNode;
+
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+
+/**
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ * @date 26.03.2015
+ */
+public class DistribSBasePlugin extends AbstractSBasePlugin {
+
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -1732369832900356125L;
+ /**
+ *
+ */
+ private Uncertainty uncertainty;
+
+ /**
+ * Creates a new {@link DistribSBasePlugin} instance.
+ *
+ * @param sbase the {@link SBase} to be extended.
+ */
+ public DistribSBasePlugin(SBase sbase) {
+ super(sbase);
+ setPackageVersion(-1);
+ }
+
+ /**
+ * Creates a new {@link DistribSBasePlugin} instance, cloned from
+ * the input parameter.
+ *
+ * @param obj the {@link DistribSBasePlugin} to clone
+ */
+ public DistribSBasePlugin(DistribSBasePlugin obj) {
+ super(obj);
+
+ if (obj.isSetUncertainty()) {
+ setUncertainty(obj.getUncertainty().clone());
+ }
+ }
+
+
+ /**
+ * Creates and Sets a new {@link Uncertainty} instance.
+ *
+ * @return the newly created {@link Uncertainty} instance.
+ */
+ public Uncertainty createUncertainty() {
+ Uncertainty uncert = new Uncertainty();
+ setUncertainty(uncert);
+ return uncert;
+ }
+
+
+ /**
+ * Returns the value of {@link #uncertainty}.
+ *
+ * @return the value of {@link #uncertainty}.
+ */
+ public Uncertainty getUncertainty() {
+ if (isSetUncertainty()) {
+ return uncertainty;
+ }
+
+ return null;
+ }
+
+
+ /**
+ * Returns whether {@link #uncertainty} is set.
+ *
+ * @return whether {@link #uncertainty} is set.
+ */
+ public boolean isSetUncertainty() {
+ return uncertainty != null;
+ }
+
+
+ /**
+ * Sets the value of uncertainty
+ *
+ * @param uncertainty the value of uncertainty to be set.
+ */
+ public void setUncertainty(Uncertainty uncertainty) {
+ Uncertainty oldUncertainty = this.uncertainty;
+ this.uncertainty = uncertainty;
+ if (getExtendedSBase() != null) {
+ getExtendedSBase().registerChild(uncertainty);
+ }
+ firePropertyChange(DistribConstants.uncertainty, oldUncertainty, this.uncertainty);
+ }
+
+
+ /**
+ * Unsets the variable uncertainty.
+ *
+ * @return {@code true} if uncertainty was set before, otherwise {@code false}.
+ */
+ public boolean unsetUncertainty() {
+ if (isSetUncertainty()) {
+ Uncertainty oldUncertainty = uncertainty;
+ uncertainty = null;
+ firePropertyChange(DistribConstants.uncertainty, oldUncertainty, uncertainty);
+ return true;
+ }
+ return false;
+ }
+
+
+ @Override
+ public String getElementNamespace() {
+ return DistribConstants.namespaceURI_L3V1V1; // TODO - change to return a String attribute that can be changed
+ }
+
+ @Override
+ public String getPackageName() {
+ return DistribConstants.shortLabel;
+ }
+
+ @Override
+ public String getPrefix() {
+ return DistribConstants.shortLabel;
+ }
+
+ @Override
+ public String getURI() {
+ return DistribConstants.namespaceURI; // TODO - change to return a String attribute that can be changed
+ }
+
+
+ @Override
+ public int getChildCount() {
+ int count = 0;
+
+ if (isSetUncertainty()) {
+ count++;
+ }
+
+ return count;
+ }
+
+
+ @Override
+ public TreeNode getChildAt(int index) {
+ if (index < 0) {
+ throw new IndexOutOfBoundsException(index + " < 0");
+ }
+ int pos = 0;
+
+ if (isSetUncertainty()) {
+ if (pos == index) {
+ return getUncertainty();
+ }
+ pos++;
+ }
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ "Index {0,number,integer} >= {1,number,integer}", index,
+ Math.min(pos, 0)));
+ }
+
+ @Override
+ public boolean getAllowsChildren() {
+ return true;
+ }
+
+ @Override
+ public AbstractSBasePlugin clone() {
+ return new DistribSBasePlugin(this);
+ }
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix,
+ String value) {
+ return false;
+ }
+
+}
Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -480,7 +480,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -230,7 +230,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -238,7 +238,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -172,7 +172,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -526,7 +526,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -250,7 +250,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -623,7 +623,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -219,7 +219,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -228,7 +228,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -180,7 +180,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -179,7 +179,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,321 +1,321 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.multi;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-import org.sbml.jsbml.util.filters.NameFilter;
-
-/**
- * In order to encode the structures needed to define and use multistate and multi-component
- * complexes, the element model is extended to be linked to a list of {@link SpeciesType}s.
- *
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.0
- */
-public class MultiModelPlugin extends AbstractSBasePlugin {
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return MultiConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return MultiConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractTreeNode#getParent()
- */
- @Override
- public SBMLDocument getParent() {
- return (SBMLDocument) getExtendedSBase().getParent();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
- */
- @Override
- public SBMLDocument getParentSBMLObject() {
- return getParent();
- }
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -2875299722787282885L;
- /**
- *
- */
- ListOf<SpeciesType> listOfSpeciesTypes;
-
- /**
- *
- * @param model
- */
- public MultiModelPlugin(Model model) {
- super(model);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- }
-
- /**
- *
- * @param multiModel
- */
- public MultiModelPlugin(MultiModelPlugin multiModel) {
- super(multiModel);
-
- if (multiModel == null) {
- return;
- }
- if (multiModel.isSetListOfSpeciesTypes()) {
- setListOfSpeciesTypes(multiModel.getListOfSpeciesTypes().clone());
- }
- }
-
- @Override
- public MultiModelPlugin clone() {
- return new MultiModelPlugin(this);
- }
-
- /**
- * Returns the {@link Model}
- *
- * @return the {@link Model}
- */
- public Model getModel() {
- return (Model) extendedSBase;
- }
-
-
- /**
- * Returns the listOfSpeciesTypes.
- *
- * @return the listOfSpeciesTypes
- */
- public ListOf<SpeciesType> getListOfSpeciesTypes() {
- if (listOfSpeciesTypes == null) {
- listOfSpeciesTypes = new ListOf<SpeciesType>();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- listOfSpeciesTypes.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'multi'
- listOfSpeciesTypes.setPackageName(null);
- listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
- listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
-
- if (isSetExtendedSBase()) {
- extendedSBase.registerChild(listOfSpeciesTypes);
- }
- }
-
- return listOfSpeciesTypes;
- }
-
- /**
- * Adds a {@link SpeciesType}.
- *
- * @param speciesType the speciesType to add
- * @return
- */
- public boolean addSpeciesType(SpeciesType speciesType) {
- return getListOfSpeciesTypes().add(speciesType);
- }
-
- /**
- * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
- * <p>
- *
- * @return the {@link SpeciesType} object created
- * <p>
- * @see #addSpeciesType(SpeciesType r)
- */
- public SpeciesType createSpeciesType() {
- return createSpeciesType(null);
- }
-
- /**
- * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
- *
- * @param id
- * the id of the new element to create
- * @return the {@link SpeciesType} object created
- */
- public SpeciesType createSpeciesType(String id) {
- SpeciesType speciesType = new SpeciesType();
- speciesType.setId(id);
- addSpeciesType(speciesType);
-
- return speciesType;
- }
-
- /**
- * Gets the ith {@link SpeciesType}.
- *
- * @param i
- *
- * @return the ith {@link SpeciesType}
- * @throws IndexOutOfBoundsException if the index is invalid.
- */
- public SpeciesType getSpeciesType(int i) {
- return getListOfSpeciesTypes().get(i);
- }
-
- /**
- * Gets the {@link SpeciesType} that has the given id.
- *
- * @param id
- * @return the {@link SpeciesType} that has the given id or null if
- * no {@link SpeciesType} are found that match {@code id}.
- */
- public SpeciesType getSpeciesType(String id) {
- if (isSetListOfSpeciesTypes()) {
- return listOfSpeciesTypes.firstHit(new NameFilter(id));
- }
- return null;
- }
-
- /**
- * Returns {@code true} if the listOfSpeciesType is set.
- *
- * @return {@code true} if the listOfSpeciesType is set.
- */
- public boolean isSetListOfSpeciesTypes() {
- return listOfSpeciesTypes != null;
- }
-
- /**
- * Sets the listOfSpeciesTypes. If there was already some elements defined
- * on listOfSpeciesTypes, they will be unset beforehand.
- *
- * @param listOfSpeciesTypes
- */
- public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes) {
- unsetListOfSpeciesTypes();
- this.listOfSpeciesTypes = listOfSpeciesTypes;
-
- if (listOfSpeciesTypes != null) {
- listOfSpeciesTypes.unsetNamespace();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- listOfSpeciesTypes.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'multi'
- listOfSpeciesTypes.setPackageName(null);
- listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
- listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
- }
- if (extendedSBase != null) {
- extendedSBase.registerChild(this.listOfSpeciesTypes);
- }
- }
-
-
- /**
- * Sets the listOfSpeciesTypes to null
- *
- * @return {@code true} is successful
- */
- public boolean unsetListOfSpeciesTypes() {
- if (isSetListOfSpeciesTypes()) {
- ListOf<SpeciesType> oldSpeciesTypeElements = listOfSpeciesTypes;
- listOfSpeciesTypes = null;
- oldSpeciesTypeElements.fireNodeRemovedEvent();
- return true;
- }
- return false;
- }
-
-
-
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- // no attribute to read
- return false;
- }
-
- /* (non-Javadoc)
- * @see javax.swing.tree.TreeNode#getChildAt(int)
- */
- @Override
- public SBase getChildAt(int childIndex) {
- if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
- }
-
- int pos = 0;
- if (isSetListOfSpeciesTypes()) {
- if (pos == childIndex) {
- return getListOfSpeciesTypes();
- }
- pos++;
- }
-
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
- }
-
- /* (non-Javadoc)
- * @see javax.swing.tree.TreeNode#getChildCount()
- */
- @Override
- public int getChildCount() {
- int count = 0;
- if (isSetListOfSpeciesTypes()) {
- count++;
- }
-
- return count;
- }
-
- @Override
- public boolean getAllowsChildren() {
- return true;
- }
-
- @Override
- public Map<String, String> writeXMLAttributes() {
- // no attribute to write
- return null;
- }
-
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.multi;
+
+import java.text.MessageFormat;
+import java.util.Map;
+
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+import org.sbml.jsbml.util.filters.NameFilter;
+
+/**
+ * In order to encode the structures needed to define and use multistate and multi-component
+ * complexes, the element model is extended to be linked to a list of {@link SpeciesType}s.
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.0
+ */
+public class MultiModelPlugin extends AbstractSBasePlugin {
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
+ */
+ @Override
+ public String getPackageName() {
+ return MultiConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
+ */
+ @Override
+ public String getPrefix() {
+ return MultiConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
+ */
+ @Override
+ public String getURI() {
+ return getElementNamespace();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#getParent()
+ */
+ @Override
+ public SBMLDocument getParent() {
+ return (SBMLDocument) getExtendedSBase().getParent();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
+ */
+ @Override
+ public SBMLDocument getParentSBMLObject() {
+ return getParent();
+ }
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -2875299722787282885L;
+ /**
+ *
+ */
+ ListOf<SpeciesType> listOfSpeciesTypes;
+
+ /**
+ *
+ * @param model
+ */
+ public MultiModelPlugin(Model model) {
+ super(model);
+ setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ }
+
+ /**
+ *
+ * @param multiModel
+ */
+ public MultiModelPlugin(MultiModelPlugin multiModel) {
+ super(multiModel);
+
+ if (multiModel == null) {
+ return;
+ }
+ if (multiModel.isSetListOfSpeciesTypes()) {
+ setListOfSpeciesTypes(multiModel.getListOfSpeciesTypes().clone());
+ }
+ }
+
+ @Override
+ public MultiModelPlugin clone() {
+ return new MultiModelPlugin(this);
+ }
+
+ /**
+ * Returns the {@link Model}
+ *
+ * @return the {@link Model}
+ */
+ public Model getModel() {
+ return (Model) extendedSBase;
+ }
+
+
+ /**
+ * Returns the listOfSpeciesTypes.
+ *
+ * @return the listOfSpeciesTypes
+ */
+ public ListOf<SpeciesType> getListOfSpeciesTypes() {
+ if (listOfSpeciesTypes == null) {
+ listOfSpeciesTypes = new ListOf<SpeciesType>();
+ listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ listOfSpeciesTypes.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'multi'
+ listOfSpeciesTypes.setPackageName(null);
+ listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
+ listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
+
+ if (isSetExtendedSBase()) {
+ extendedSBase.registerChild(listOfSpeciesTypes);
+ }
+ }
+
+ return listOfSpeciesTypes;
+ }
+
+ /**
+ * Adds a {@link SpeciesType}.
+ *
+ * @param speciesType the speciesType to add
+ * @return
+ */
+ public boolean addSpeciesType(SpeciesType speciesType) {
+ return getListOfSpeciesTypes().add(speciesType);
+ }
+
+ /**
+ * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
+ * <p>
+ *
+ * @return the {@link SpeciesType} object created
+ * <p>
+ * @see #addSpeciesType(SpeciesType r)
+ */
+ public SpeciesType createSpeciesType() {
+ return createSpeciesType(null);
+ }
+
+ /**
+ * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
+ *
+ * @param id
+ * the id of the new element to create
+ * @return the {@link SpeciesType} object created
+ */
+ public SpeciesType createSpeciesType(String id) {
+ SpeciesType speciesType = new SpeciesType();
+ speciesType.setId(id);
+ addSpeciesType(speciesType);
+
+ return speciesType;
+ }
+
+ /**
+ * Gets the ith {@link SpeciesType}.
+ *
+ * @param i
+ *
+ * @return the ith {@link SpeciesType}
+ * @throws IndexOutOfBoundsException if the index is invalid.
+ */
+ public SpeciesType getSpeciesType(int i) {
+ return getListOfSpeciesTypes().get(i);
+ }
+
+ /**
+ * Gets the {@link SpeciesType} that has the given id.
+ *
+ * @param id
+ * @return the {@link SpeciesType} that has the given id or null if
+ * no {@link SpeciesType} are found that match {@code id}.
+ */
+ public SpeciesType getSpeciesType(String id) {
+ if (isSetListOfSpeciesTypes()) {
+ return listOfSpeciesTypes.firstHit(new NameFilter(id));
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@code true} if the listOfSpeciesType is set.
+ *
+ * @return {@code true} if the listOfSpeciesType is set.
+ */
+ public boolean isSetListOfSpeciesTypes() {
+ return listOfSpeciesTypes != null;
+ }
+
+ /**
+ * Sets the listOfSpeciesTypes. If there was already some elements defined
+ * on listOfSpeciesTypes, they will be unset beforehand.
+ *
+ * @param listOfSpeciesTypes
+ */
+ public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes) {
+ unsetListOfSpeciesTypes();
+ this.listOfSpeciesTypes = listOfSpeciesTypes;
+
+ if (listOfSpeciesTypes != null) {
+ listOfSpeciesTypes.unsetNamespace();
+ listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ listOfSpeciesTypes.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'multi'
+ listOfSpeciesTypes.setPackageName(null);
+ listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
+ listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
+ }
+ if (extendedSBase != null) {
+ extendedSBase.registerChild(this.listOfSpeciesTypes);
+ }
+ }
+
+
+ /**
+ * Sets the listOfSpeciesTypes to null
+ *
+ * @return {@code true} is successful
+ */
+ public boolean unsetListOfSpeciesTypes() {
+ if (isSetListOfSpeciesTypes()) {
+ ListOf<SpeciesType> oldSpeciesTypeElements = listOfSpeciesTypes;
+ listOfSpeciesTypes = null;
+ oldSpeciesTypeElements.fireNodeRemovedEvent();
+ return true;
+ }
+ return false;
+ }
+
+
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ // no attribute to read
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.tree.TreeNode#getChildAt(int)
+ */
+ @Override
+ public SBase getChildAt(int childIndex) {
+ if (childIndex < 0) {
+ throw new IndexOutOfBoundsException(childIndex + " < 0");
+ }
+
+ int pos = 0;
+ if (isSetListOfSpeciesTypes()) {
+ if (pos == childIndex) {
+ return getListOfSpeciesTypes();
+ }
+ pos++;
+ }
+
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ "Index {0,number,integer} >= {1,number,integer}",
+ childIndex, Math.min(pos, 0)));
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.tree.TreeNode#getChildCount()
+ */
+ @Override
+ public int getChildCount() {
+ int count = 0;
+ if (isSetListOfSpeciesTypes()) {
+ count++;
+ }
+
+ return count;
+ }
+
+ @Override
+ public boolean getAllowsChildren() {
+ return true;
+ }
+
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ // no attribute to write
+ return null;
+ }
+
+
+}
Modified: branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,672 +1,672 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.multi;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.Species;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Nicolas Rodriguez
- * @author Marine Dumousseau
- * @since 1.0
- * @version $Rev$
- */
-public class MultiSpeciesPlugin extends AbstractSBasePlugin {
-
- // TODO - implements IdManager: SpeciesFeature are id unique within one Species
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return MultiConstants.shortLabel;
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return MultiConstants.shortLabel;
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -5396837209115412420L;
-
- /**
- *
- */
- private ListOf<OutwardBindingSite> listOfOutwardBindingSites;
-
- /**
- *
- */
- private ListOf<SpeciesFeature> listOfSpeciesFeatures;
-
- /**
- *
- */
- private String speciesType;
-
- /**
- *
- * @param species
- */
- public MultiSpeciesPlugin(Species species) {
- super(species);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- }
-
-
- /**
- * @param multiSpecies
- */
- public MultiSpeciesPlugin(MultiSpeciesPlugin multiSpecies) {
- super(multiSpecies);
-
- // c...
[truncated message content] |
|
From: <nik...@us...> - 2015-05-01 09:53:15
|
Revision: 2269
http://sourceforge.net/p/jsbml/code/2269
Author: niko-rodrigue
Date: 2015-05-01 09:53:13 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2226
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2226
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate 2015-05-01 09:53:13 UTC (rev 2269)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2217
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2226
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -318,10 +318,9 @@
*/
@Override
public void addDeclaredNamespace(String prefix, String namespace) {
-
if ((!prefix.startsWith("xmlns:")) && (!prefix.equals("xmlns"))) {
if (prefix.indexOf(":") != -1) {
- throw new IllegalArgumentException("The only allowed prefix for a namespace is 'xmlns:'.");
+ throw new IllegalArgumentException(resourceBundle.getString("AbstractSBase.addDeclaredNamespace"));
}
prefix = "xmlns:" + prefix;
}
@@ -360,7 +359,7 @@
firePropertyChange(TreeNodeChangeEvent.addExtension, null, sbasePlugin);
} else {
throw new IllegalArgumentException(MessageFormat.format(
- "The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ resourceBundle.getString("AbstractSBase.addExtensionExc"), nameOrUri));
}
}
@@ -384,12 +383,12 @@
* @param namespace the XML namespace to which this {@link SBase} belong.
*/
public void setNamespace(String namespace) {
-
if ((elementNamespace != null) && (!elementNamespace.equals(namespace))) {
// if we implement proper conversion some days, we need to unset the namespace before changing it.
- logger.error(MessageFormat.format("An SBase element cannot belong to two different namespaces! Current namespace = ''{0}'', new namespace = ''{1}''", elementNamespace, namespace));
- // throw new IllegalArgumentException(MessageFormat.format("An SBase element cannot belong to two different namespaces ! "
- // + "Current namespace = '{0}', new namespace = '{1}' ", elementNamespace, namespace));
+ logger.error(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.setNamespaceExc"),
+ elementNamespace, namespace));
+ // throw new IllegalArgumentException(MessageFormat.format(resourceBundle.getString("AbstractSBase.setNamespaceExc"), elementNamespace, namespace));
}
String old = elementNamespace;
elementNamespace = namespace;
@@ -496,7 +495,7 @@
else
{
// the given notes is empty
- logger.info("The notes to append are empty !!");
+ logger.info(resourceBundle.getString("AbstractSBase.emptyNotes"));
return;
}
}
@@ -533,7 +532,7 @@
// The given notes node needs to be added to a parent node
// if the node is neither "html" nor "body" element because the
// children of addedNotes will be added to the current notes later if the
- // node is neither "html" nor "body" (i.e. any XHTML element that
+ // node is neither "html" nor "body" (i.e., any XHTML element that
// would be permitted within a "body" element)
addedNotes.addChild(notes);
addedNotesType = NOTES_TYPE.NotesAny;
@@ -569,7 +568,7 @@
if (!headFound || !bodyFound || otherElementFound)
{
// TODO - throw an exception as well
- logger.warn("The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.");
+ logger.warn(resourceBundle.getString("AbstractSBase.invalidNotesStructure"));
return;
}
}
@@ -639,7 +638,9 @@
for (i=0; i < addedBody.getChildCount(); i++)
{
if (curBody.addChild(addedBody.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedBody.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.problemAddingXMLNode"),
+ SBMLtools.toXML(addedBody.getChildAt(i))));
return;
}
}
@@ -650,10 +651,12 @@
// adds the given body or other tag (permitted in the body) to the current
// html tag
- for (i=0; i < addedNotes.getChildCount(); i++)
+ for (i = 0; i < addedNotes.getChildCount(); i++)
{
if (curBody.addChild(addedNotes.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.problemAddingXMLNode"),
+ SBMLtools.toXML(addedNotes.getChildAt(i))));
return;
}
}
@@ -1775,7 +1778,7 @@
// Could/Should be used by the method #firePropertyChange
// TODO - set package version and namespace if needed
-
+
int childCount = sbasePlugin.getChildCount();
if (childCount > 0) {
@@ -1828,6 +1831,22 @@
}
/* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#setAnnotation(org.sbml.jsbml.xml.XMLNode)
+ */
+ @Override
+ public void setAnnotation(XMLNode nonRDFAnnotation) {
+ getAnnotation().setNonRDFAnnotation(nonRDFAnnotation);
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#setAnnotation(java.lang.String)
+ */
+ @Override
+ public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException {
+ setAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotation)));
+ }
+
+ /* (non-Javadoc)
* @see org.sbml.jsbml.SBase#setHistory(org.sbml.jsbml.History)
*/
@Override
@@ -2204,7 +2223,7 @@
return;
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
}
@Override
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -29,10 +29,13 @@
import java.util.regex.Pattern;
import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.util.TreeNodeAdapter;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
+import org.sbml.jsbml.xml.XMLAttributes;
+import org.sbml.jsbml.xml.XMLNode;
/**
* Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
@@ -507,6 +510,42 @@
}
/**
+ *
+ * @param miriam
+ */
+ public CVTerm(XMLNode miriam) {
+ this();
+ if (miriam.getName().equals("annotation")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("RDF")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("Description")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getURI().equals("http://biomodels.net/biology-qualifiers/")) {
+ if (miriam.getPrefix().equals("bqbiol")) {
+ setQualifier(Qualifier.getBiologicalQualifierFor(miriam.getName()));
+ } else {
+ setQualifier(Qualifier.getModelQualifierFor(miriam.getName()));
+ }
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("Bag")) {
+ for (int j = 0; j < miriam.getChildCount(); j++) {
+ XMLNode child = miriam.getChildAt(j);
+ if (child.getName().equals("li")) {
+ XMLAttributes attributes = child.getAttributes();
+ for (int i = 0; i < attributes.size(); i++) {
+ addResource(attributes.getValue(i));
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Creates a {@link CVTerm} instance from a given {@link CVTerm}.
*
* @param term the {@link CVTerm} to clone
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -503,15 +503,15 @@
public int getCVTermCount();
/**
- * Returns the name of the SBML Level 3 package in which this element is defined, as
+ * Returns the name of the SBML Level 3 package in which this element is defined, as
* defined in <a href="http://sbml.org/Community/Wiki"> the sbml.org community wiki</a>.
*
- * <p> For example, the string "core" will be returned if this element is defined in SBML Level 3 Core.
+ * <p> For example, the string "core" will be returned if this element is defined in SBML Level 3 Core.
*
* @return the name of the SBML Level 3 package in which this element is defined.
*/
public String getPackageName();
-
+
/**
* Returns the version of the SBML Level 3 package to which this element belongs.
*
@@ -522,7 +522,7 @@
* @return the version of the SBML Level 3 package to which this element belongs.
*/
public int getPackageVersion();
-
+
/**
* Returns the parent of this {@link SBase}.
*
@@ -584,16 +584,16 @@
/**
* Returns the namespace to which this {@link SBase} belong to. Same as {@link #getNamespace()}.
*
- * <p>For example, all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core
+ * <p>For example, all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core
* must have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
* <p>The elements that belong to SBML core might return null.
*
* @return the namespace to which this {@link SBase} belong to.
* @see SBase#getNamespace()
- * @libsbml.deprecated
+ * @libsbml.deprecated
*/
public String getURI();
-
+
/**
* Returns the Version within the SBML Level of the overall SBML document.
* Return -1 if it is not set.
@@ -858,6 +858,19 @@
public void setAnnotation(Annotation annotation);
/**
+ *
+ * @param nonRDFAnnotation
+ */
+ public void setAnnotation(XMLNode nonRDFAnnotation);
+
+ /**
+ *
+ * @param nonRDFAnnotation
+ * @throws XMLStreamException
+ */
+ public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException;
+
+ /**
* Sets the history.
*
* @param history the history of this {@link SBase}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -510,11 +510,18 @@
* @return the number of attributes in this {@link XMLAttributes} set.
*/
public int getLength() {
+ return attributeNames.size();
+ }
+ /**
+ *
+ * @return
+ * @see #getLength()
+ */
+ public int size() {
return attributeNames.size();
}
-
/**
* Returns the local name of an attribute in this {@link XMLAttributes} set (by position).
* <p>
Copied: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java (from rev 2226, trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -0,0 +1,44 @@
+/*
+ * $Id: CompressionKind.java 2206 2015-04-23 09:57:59Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java $
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+/**
+ * This enum type was created following the specifications defined in Spatial Package v0.90.
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date 23 Apr 2015
+ */
+public enum CompressionKind {
+ /**
+ * If no compression is used
+ */
+ UNCOMPRESSED,
+ /**
+ * If the deflation algorithm was used to compress the text version of the data
+ */
+ DEFLATED,
+ /**
+ * If the base 64 algorithm was used to transform the binary form of the actual members into text
+ */
+ BASE64;
+}
\ No newline at end of file
Copied: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java (from rev 2226, trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -0,0 +1,53 @@
+/*
+ * $Id: DataKind.java 2206 2015-04-23 09:57:59Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java $
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+
+/**
+ * This enum type was created following the specifications defined in Spatial Package v0.90.
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date 23 Apr 2015
+ */
+public enum DataKind {
+ /**
+ * To indicate 8-bit unsigned integer
+ */
+ UINT8,
+ /**
+ * To indicate 16-bit unsigned integer
+ */
+ UINT16,
+ /**
+ * To indicate 32-bit unsigned integer
+ */
+ UINT32,
+ /**
+ * To indicate single-precision (32-bit) floating point values
+ */
+ FLOAT,
+ /**
+ * To indicate double-precision (64-bit) floating point values
+ */
+ DOUBLE;
+}
\ No newline at end of file
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -28,6 +28,7 @@
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.PropertyUndefinedError;
/**
* @author Alex Thomas
@@ -41,7 +42,7 @@
/**
*
*/
- ListOf<SpatialPoints> listOfSpatialPoints;
+ SpatialPoints spatialPoints;
/**
*
*/
@@ -69,8 +70,8 @@
setListOfParametricObjects(pg.getListOfParametricObjects().clone());
}
- if (pg.isSetListOfSpatialPoints()) {
- setListOfSpatialPoints(pg.getListOfSpatialPoints().clone());
+ if (pg.isSetSpatialPoints()) {
+ setSpatialPoints(pg.getSpatialPoints().clone());
}
}
@@ -113,9 +114,9 @@
equal &= pg.getListOfParametricObjects().equals(getListOfParametricObjects());
}
- equal &= pg.isSetListOfSpatialPoints() == isSetListOfSpatialPoints();
- if (equal && isSetListOfSpatialPoints()) {
- equal &= pg.getListOfSpatialPoints().equals(getListOfSpatialPoints());
+ equal &= pg.isSetSpatialPoints() == isSetSpatialPoints();
+ if (equal && isSetSpatialPoints()) {
+ equal &= pg.getSpatialPoints().equals(getSpatialPoints());
}
}
@@ -129,8 +130,8 @@
if (isSetListOfParametricObjects()) {
hashCode += prime * getListOfParametricObjects().hashCode();
}
- if (isSetListOfSpatialPoints()) {
- hashCode += prime * getListOfSpatialPoints().hashCode();
+ if (isSetSpatialPoints()) {
+ hashCode += prime * getSpatialPoints().hashCode();
}
return hashCode;
}
@@ -251,7 +252,7 @@
//}
/**
* Creates a new ParametricObject element and adds it to the ListOfParametricObjects list
- * @return
+ * @return a new {@link ParametricObject} element
*/
public ParametricObject createParametricObject() {
return createParametricObject(null);
@@ -270,146 +271,60 @@
return parametricObject;
}
- /**
- *
- */
-
+
/**
- * Returns {@code true}, if listOfSpatialPoints contains at least one element.
+ * Returns the value of {@link #spatialPoints}.
*
- * @return {@code true}, if listOfSpatialPoints contains at least one element,
- * otherwise {@code false}
+ * @return the value of {@link #spatialPoints}.
*/
- public boolean isSetListOfSpatialPoints() {
- if ((listOfSpatialPoints == null) || listOfSpatialPoints.isEmpty()) {
- return false;
+ public SpatialPoints getSpatialPoints() {
+ if (isSetSpatialPoints()) {
+ return spatialPoints;
}
- return true;
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.spatialPoints, this);
}
/**
- * Returns the listOfSpatialPoints. Creates it if it is not already existing.
+ * Returns whether {@link #spatialPoints} is set.
*
- * @return the listOfSpatialPoints
+ * @return whether {@link #spatialPoints} is set.
*/
- public ListOf<SpatialPoints> getListOfSpatialPoints() {
- if (!isSetListOfSpatialPoints()) {
- listOfSpatialPoints = new ListOf<SpatialPoints>(getLevel(),
- getVersion());
- listOfSpatialPoints.setNamespace(SpatialConstants.namespaceURI);
- listOfSpatialPoints.setSBaseListType(ListOf.Type.other);
- registerChild(listOfSpatialPoints);
- }
- return listOfSpatialPoints;
+ public boolean isSetSpatialPoints() {
+ return this.spatialPoints != null;
}
/**
- * Sets the given {@code ListOf<SpatialPoint>}. If listOfSpatialPoints
- * was defined before and contains some elements, they are all unset.
+ * Sets the value of spatialPoints
*
- * @param listOfSpatialPoints
+ * @param spatialPoints the value of spatialPoints to be set.
*/
- public void setListOfSpatialPoints(ListOf<SpatialPoints> listOfSpatialPoints) {
- unsetListOfSpatialPoints();
- this.listOfSpatialPoints = listOfSpatialPoints;
- registerChild(this.listOfSpatialPoints);
+ public void setSpatialPoints(SpatialPoints spatialPoints) {
+ SpatialPoints oldSpatialPoints = this.spatialPoints;
+ this.spatialPoints = spatialPoints;
+ firePropertyChange(SpatialConstants.spatialPoints, oldSpatialPoints, this.spatialPoints);
}
/**
- * Returns {@code true}, if listOfSpatialPoints contain at least one element,
- * otherwise {@code false}
+ * Unsets the variable spatialPoints.
*
- * @return {@code true}, if listOfSpatialPoints contain at least one element,
- * otherwise {@code false}
+ * @return {@code true} if spatialPoints was set before, otherwise {@code false}.
*/
- public boolean unsetListOfSpatialPoints() {
- if (isSetListOfSpatialPoints()) {
- ListOf<SpatialPoints> oldSpatialPoints = listOfSpatialPoints;
- listOfSpatialPoints = null;
- oldSpatialPoints.fireNodeRemovedEvent();
+ public boolean unsetSpatialPoints() {
+ if (isSetSpatialPoints()) {
+ SpatialPoints oldSpatialPoints = this.spatialPoints;
+ this.spatialPoints = null;
+ firePropertyChange(SpatialConstants.spatialPoints, oldSpatialPoints, this.spatialPoints);
return true;
}
return false;
}
- /**
- * Adds a new {@link SpatialPoints} to the listOfSpatialPoints.
- * <p>The listOfSpatialPoints is initialized if necessary.
- *
- * @param spatialPoints the element to add to the list
- * @return true (as specified by {@link Collection#add})
- */
- public boolean addSpatialPoints(SpatialPoints spatialPoints) {
- return getListOfSpatialPoints().add(spatialPoints);
- }
-
-
- /**
- * Removes an element from the listOfSpatialPoints.
- *
- * @param spatialPoints the element to be removed from the list
- * @return true if the list contained the specified element
- * @see List#remove(Object)
- */
- public boolean removeSpatialPoints(SpatialPoints spatialPoints) {
- if (isSetListOfSpatialPoints()) {
- return getListOfSpatialPoints().remove(spatialPoints);
- }
- return false;
- }
-
-
- /**
- * Removes an element from the listOfSpatialPoints at the given index.
- *
- * @param i the index where to remove the {@link SpatialPoint}
- * @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
- */
- public void removeSpatialPoints(int i) {
- if (!isSetListOfSpatialPoints()) {
- throw new IndexOutOfBoundsException(Integer.toString(i));
- }
- // if (getListOfSpatialPoints().size() == 1) {
- // throw new SBMLException("There must be at least one SpatialPoint defined for this list");
- // }
- getListOfSpatialPoints().remove(i);
- }
-
-
- /*
- * TODO: if the ID is mandatory for SpatialPoints objects,
- * one should also add this methods
- */
- //public void removeSpatialPoints(String id) {
- // getListOfSpatialPoints().removeFirst(new NameFilter(id));
- //}
- /**
- * Creates a new SpatialPoints element and adds it to the ListOfSpatialPoints list
- * @return
- */
- public SpatialPoints createSpatialPoints() {
- return createSpatialPoints(null);
- }
-
-
- /**
- * Creates a new {@link SpatialPoints} element and adds it to the ListOfSpatialPoints list
- * @param id
- *
- * @return a new {@link SpatialPoints} element
- */
- public SpatialPoints createSpatialPoints(String id) {
- SpatialPoints spatialPoints = new SpatialPoints(getLevel(), getVersion());
- addSpatialPoints(spatialPoints);
- return spatialPoints;
- }
-
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#getAllowsChildren()
*/
@@ -427,7 +342,7 @@
if (isSetListOfParametricObjects()) {
count++;
}
- if (isSetListOfSpatialPoints()) {
+ if (isSetSpatialPoints()) {
count++;
}
return count;
@@ -453,9 +368,9 @@
}
pos++;
}
- if (isSetListOfSpatialPoints()) {
+ if (isSetSpatialPoints()) {
if (pos == index) {
- return getListOfSpatialPoints();
+ return getSpatialPoints();
}
pos++;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -330,5 +330,34 @@
return success;
}
+
+ /*
+ * (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#hashCode()
+ */
+ @Override
+ public int hashCode() {
+ final int prime = 2039;
+ int hashCode = super.hashCode();
+ if (isSetGeometry()) {
+ hashCode += prime * getGeometry().hashCode();
+ }
+ return hashCode;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("SpatialModelPlugin [geometry=");
+ builder.append(geometry);
+ builder.append(", spatialIdMap=");
+ builder.append(spatialIdMap);
+ builder.append("]");
+ return builder.toString();
+ }
+
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -197,7 +197,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 2039;
int hashCode = super.hashCode();
if (isSetIsLocal()) {
hashCode += prime * isLocal.hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -29,7 +29,6 @@
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
-import org.sbml.jsbml.util.TreeNodeChangeEvent;
/**
* @author Alex Thomas
@@ -112,6 +111,9 @@
if (equal && isSetComponents()) {
equal &= tc.getComponents().equals(getComponents());
}
+ if (equal && isSetComponentsLength()) {
+ equal &= tc.getComponentsLength() == getComponentsLength();
+ }
}
return equal;
}
@@ -178,7 +180,7 @@
*/
public int getComponentsLength() {
if (isSetComponentsLength()) {
- return componentsLength;
+ return componentsLength.intValue();
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.componentsLength, this);
@@ -204,6 +206,9 @@
if (isSetComponents()) {
hashCode += prime * getComponents().hashCode();
}
+ if (isSetComponentsLength()) {
+ hashCode += prime * getComponentsLength();
+ }
return hashCode;
}
@@ -223,15 +228,6 @@
attributes.put(SpatialConstants.shortLabel + ":componentsLength",
String.valueOf(getComponentsLength()));
}
-
- if (isSetSBOTerm()) {
- attributes.remove(TreeNodeChangeEvent.sboTerm);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.sboTerm, getSBOTermID());
- }
- if (isSetMetaId()) {
- attributes.remove(TreeNodeChangeEvent.metaId);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.metaId, getMetaId());
- }
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -378,9 +378,9 @@
}
} else if (contextObject instanceof ParametricGeometry) {
ParametricGeometry pg = (ParametricGeometry) contextObject;
- if (elementName.equals(SpatialConstants.listOfSpatialPoints)){
- ListOf<SpatialPoints> listOfSpatialPoints = pg.getListOfSpatialPoints();
- return listOfSpatialPoints;
+ if (elementName.equals(SpatialConstants.spatialPoints)){
+ SpatialPoints spatialPoints = pg.getSpatialPoints();
+ return spatialPoints;
} else if (elementName.equals(SpatialConstants.listOfParametricObjects)){
ListOf<ParametricObject> listOfParametricObjects = pg.getListOfParametricObjects();
return listOfParametricObjects;
@@ -497,7 +497,7 @@
} else if (elementName.equals(SpatialConstants.spatialPoints)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
SpatialPoints elem = new SpatialPoints();
- pg.addSpatialPoints(elem);
+ pg.setSpatialPoints(elem);
return elem;
} else if (elementName.equals(SpatialConstants.parametricObject)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 09:46:02
|
Revision: 2268
http://sourceforge.net/p/jsbml/code/2268
Author: niko-rodrigue
Date: 2015-05-01 09:46:00 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2217
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2217
Removed Paths:
-------------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
Deleted: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-05-01 09:44:19 UTC (rev 2267)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-05-01 09:46:00 UTC (rev 2268)
@@ -1,358 +0,0 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.spatial;
-
-import java.text.MessageFormat;
-import java.util.Arrays;
-import java.util.Map;
-import java.util.StringTokenizer;
-
-import org.sbml.jsbml.AbstractSBase;
-import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.StringTools;
-
-/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @since 1.0
- * @version $Rev$
- */
-public class ImageData extends AbstractSBase {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = 1872012239027099782L;
-
- /**
- *
- */
- private Integer samplesLength;
- /**
- *
- */
- private Integer samples[];
-
- /**
- *
- */
- private String dataType;
-
- /**
- *
- */
- public ImageData() {
- super();
- initDefaults();
- }
-
- /**
- * @param im
- */
- public ImageData(ImageData im) {
- super(im);
- if (im.isSetSamples()) {
- samples = im.getSamples().clone();
- samplesLength = samples.length;
- }
- if (im.isSetDataType()) {
- dataType = new String(im.getDataType());
- }
- }
-
- /**
- * @param level
- * @param version
- */
- public ImageData(int level, int version) {
- super(level, version);
- initDefaults();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#clone()
- */
- @Override
- public ImageData clone() {
- return new ImageData(this);
- }
-
- /**
- * Initializes the default values using the namespace.
- */
- public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- setPackageVersion(-1);
- packageName = SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#equals(java.lang.Object)
- */
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- ImageData im = (ImageData) object;
-
- equal &= im.isSetSamples() == isSetSamples();
- if (equal && isSetSamples()) {
- equal &= im.getSamples().equals(getSamples());
- }
-
- equal &= im.isSetDataType() == isSetDataType();
- if (equal && isSetDataType()) {
- equal &= im.getDataType().equals(getDataType());
- }
-
- }
- return equal;
- }
-
-
- /**
- * Returns the value of samples
- *
- * @return the value of samples
- */
- public Integer[] getSamples() {
- if (isSetSamples()) {
- return samples;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samples, this);
- }
-
-
- /**
- * Returns whether samples is set
- *
- * @return whether samples is set
- */
- public boolean isSetSamples() {
- return samples != null;
- }
-
- /**
- * Sets the value of samples
- * @param samples
- */
- public void setSamples(Integer... samples) {
- Integer[] oldSamples = this.samples;
- this.samples = samples;
- samplesLength = samples.length;
- firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
- firePropertyChange(SpatialConstants.samples, oldSamples.length, samplesLength);
- }
-
- /**
- * Unsets the variable samples
- *
- * @return {@code true}, if samples was set before,
- * otherwise {@code false}
- */
- public boolean unsetSamples() {
- if (isSetSamples()) {
- Integer[] oldSamples = samples;
- samples = null;
- samplesLength = null;
- firePropertyChange(SpatialConstants.samples, oldSamples, samples);
- firePropertyChange(SpatialConstants.samplesLength, oldSamples.length, samplesLength);
- return true;
- }
- return false;
- }
-
-
- /**
- * Returns the value of samplesLength
- *
- * @return the value of samplesLength
- */
- public int getSamplesLength() {
- if (isSetSamplesLength()) {
- return samplesLength;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samplesLength, this);
- }
-
-
- /**
- * Returns whether samplesLength is set
- *
- * @return whether samplesLength is set
- */
- public boolean isSetSamplesLength() {
- return samplesLength != null;
- }
-
-
- /**
- * Returns the value of dataType
- *
- * @return the value of dataType
- */
- public String getDataType() {
- if (isSetDataType()) {
- return dataType;
- }
- return null;
- }
-
-
- /**
- * Returns whether dataType is set
- *
- * @return whether dataType is set
- */
- public boolean isSetDataType() {
- return dataType != null;
- }
-
- /**
- * Sets the value of dataType
- * @param dataType
- */
- public void setDataType(String dataType) {
- String oldDataType = this.dataType;
- this.dataType = dataType;
- firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
- }
-
- /**
- * Unsets the variable dataType
- *
- * @return {@code true}, if dataType was set before,
- * otherwise {@code false}
- */
- public boolean unsetDataType() {
- if (isSetDataType()) {
- String oldDataType = dataType;
- dataType = null;
- firePropertyChange(SpatialConstants.dataType, oldDataType, dataType);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetSamples()) {
- hashCode += prime * getSamples().hashCode();
- }
- if (isSetDataType()) {
- hashCode += prime * getDataType().hashCode();
- }
-
- return hashCode;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetSamples()) {
- attributes.remove("samples");
- attributes.put(SpatialConstants.shortLabel + ":samples", Arrays.toString(getSamples()));
- }
-
- if (isSetSamplesLength()) {
- attributes.remove("samplesLength");
- attributes.put(SpatialConstants.shortLabel + ":samplesLength",
- String.valueOf(getSamplesLength()));
- }
-
- if (isSetDataType()) {
- attributes.remove("dataType");
- attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType());
- }
- return attributes;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
- */
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
- if (!isAttributeRead) {
- isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.samples)) {
- StringTokenizer test = new StringTokenizer(value);
- Integer[] samplesTemp = new Integer[test.countTokens()];
- int i = 0;
- while(test.hasMoreTokens()) {
- try {
- samplesTemp[i] = StringTools.parseSBMLInt(test.nextToken());
- i++;
- } catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.pointIndex);
- }
- }
- if (samplesTemp.length > 0) {
- unsetSamples();
- setSamples(samplesTemp);
- }
- }
- else if (attributeName.equals(SpatialConstants.dataType)) {
- try {
- setDataType(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("ImageData [samplesLength=");
- builder.append(samplesLength);
- builder.append(", dataType=");
- builder.append(dataType);
- builder.append(", samples=");
- builder.append(Arrays.toString(samples)); // TODO - Should we really print the whole content of the array here?
- builder.append("]");
- return builder.toString();
- }
-
-}
Deleted: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-05-01 09:44:19 UTC (rev 2267)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-05-01 09:46:00 UTC (rev 2268)
@@ -1,468 +0,0 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.spatial;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.StringTools;
-
-/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @since 1.0
- * @version $Rev$
- */
-public class SpatialPoint extends AbstractSpatialNamedSBase {
-
- /**
- *
- */
- private String domain;
-
- /**
- *
- */
- private Double coord1;
- /**
- *
- */
- private Double coord2;
- /**
- *
- */
- private Double coord3;
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -1171421071571874086L;
-
- /**
- *
- */
- public SpatialPoint() {
- super();
- }
-
- /**
- * @param sp
- */
- public SpatialPoint(SpatialPoint sp) {
- super(sp);
-
-
- if (sp.isSetDomain()) {
- domain = new String(sp.getDomain());
- }
-
- if (sp.isSetCoord1()) {
- coord1 = new Double(sp.getCoord1());
- }
-
- if (sp.isSetCoord2()) {
- coord2 = new Double(sp.getCoord2());
- }
-
- if (sp.isSetCoord3()) {
- coord3 = new Double(sp.getCoord3());
- }
- }
-
-
- /**
- * @param level
- * @param version
- */
- public SpatialPoint(int level, int version) {
- super(level, version);
- }
-
-
- /**
- *
- * @param id
- * @param level
- * @param version
- */
- public SpatialPoint(String id, int level, int version) {
- super(id, level, version);
- }
-
-
- @Override
- public SpatialPoint clone() {
- return new SpatialPoint(this);
- }
-
-
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- SpatialPoint sp = (SpatialPoint) object;
-
- equal &= sp.isSetDomain() == isSetDomain();
- if (equal && isSetDomain()) {
- equal &= sp.getDomain().equals(getDomain());
- }
-
- equal &= sp.isSetCoord1() == isSetCoord1();
- if (equal && isSetCoord1()) {
- equal &= sp.getCoord1() == getCoord1();
- }
-
- equal &= sp.isSetCoord2() == isSetCoord2();
- if (equal && isSetCoord2()) {
- equal &= sp.getCoord2() == getCoord2();
- }
-
- equal &= sp.isSetCoord3() == isSetCoord3();
- if (equal && isSetCoord3()) {
- equal &= sp.getCoord3() == getCoord3();
- }
- //TODO: add equal statements for each attribute and class
- }
- return equal;
- }
-
- /**
- * Returns the value of coord1
- *
- * @return the value of coord1
- */
- public double getCoord1() {
- if (isSetCoord1()) {
- return coord1;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord1, this);
- }
-
-
- /**
- * Returns whether coord1 is set
- *
- * @return whether coord1 is set
- */
- public boolean isSetCoord1() {
- return coord1 != null;
- }
-
- /**
- * Sets the value of coord1
- * @param coord1
- */
- public void setCoord1(double coord1) {
- double oldCoord1 = this.coord1;
- this.coord1 = coord1;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, this.coord1);
- }
-
-
- /**
- * Unsets the variable coord1
- *
- * @return {@code true}, if coord1 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord1() {
- if (isSetCoord1()) {
- double oldCoord1 = coord1;
- coord1 = null;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, coord1);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord2
- *
- * @return the value of coord2
- */
- public double getCoord2() {
- if (isSetCoord2()) {
- return coord2;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord2, this);
- }
-
-
- /**
- * Returns whether coord2 is set
- *
- * @return whether coord2 is set
- */
- public boolean isSetCoord2() {
- return coord2 != null;
- }
-
- /**
- * Sets the value of coord2
- * @param coord2
- */
- public void setCoord2(double coord2) {
- double oldCoord2 = this.coord2;
- this.coord2 = coord2;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, this.coord2);
- }
-
-
- /**
- * Unsets the variable coord2
- *
- * @return {@code true}, if coord2 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord2() {
- if (isSetCoord2()) {
- double oldCoord2 = coord2;
- coord2 = null;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, coord2);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord3
- *
- * @return the value of coord3
- */
- public double getCoord3() {
- if (isSetCoord3()) {
- return coord3;
- }
- // TODO:This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord3, this);
- }
-
-
- /**
- * Returns whether coord3 is set
- *
- * @return whether coord3 is set
- */
- public boolean isSetCoord3() {
- return coord3 != null;
- }
-
- /**
- * Sets the value of coord3
- * @param coord3
- */
- public void setCoord3(double coord3) {
- double oldCoord3 = this.coord3;
- this.coord3 = coord3;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, this.coord3);
- }
-
-
- /**
- * Unsets the variable coord3
- *
- * @return {@code true}, if coord3 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord3() {
- if (isSetCoord3()) {
- double oldCoord3 = coord3;
- coord3 = null;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, coord3);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of domain
- *
- * @return the value of domain
- */
- public String getDomain() {
- if (isSetDomain()) {
- return domain;
- }
- // TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.domain, this);
- }
-
-
- /**
- * Returns whether domain is set
- *
- * @return whether domain is set
- */
- public boolean isSetDomain() {
- return domain != null;
- }
-
- /**
- * Sets the value of domain
- * @param domain
- */
- public void setDomain(String domain) {
- String oldDomain = this.domain;
- this.domain = domain;
- firePropertyChange(SpatialConstants.domain, oldDomain, this.domain);
- }
-
- /**
- * Unsets the variable domain
- *
- * @return {@code true}, if domain was set before,
- * otherwise {@code false}
- */
- public boolean unsetDomain() {
- if (isSetDomain()) {
- String oldDomain = domain;
- domain = null;
- firePropertyChange(SpatialConstants.domain, oldDomain, domain);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetDomain()) {
- hashCode += prime * getDomain().hashCode();
- }
-
- if (isSetCoord1()) {
- hashCode += prime * getCoord1();
- }
-
- if (isSetCoord2()) {
- hashCode += prime * getCoord2();
- }
-
- if (isSetCoord3()) {
- hashCode += prime * getCoord3();
- }
- return hashCode;
- }
-
-
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetDomain()) {
- attributes.remove("domain");
- attributes.put(SpatialConstants.shortLabel + ":domain", getDomain());
- }
-
- if (isSetCoord1()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord1()));
- }
-
- if (isSetCoord2()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord2()));
- }
-
- if (isSetCoord3()) {
- attributes.remove("coord3");
- attributes.put(SpatialConstants.shortLabel + ":coord3",
- String.valueOf(getCoord3()));
- }
- return attributes;
- }
-
-
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
- if (!isAttributeRead) {
- isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.domain)) {
- try {
- setDomain(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domain);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord1)) {
- try {
- setCoord1(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord1);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord2)) {
- try {
- setCoord2(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord2);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord3)) {
- try {
- setCoord3(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord3);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("SpatialPoint [domain=");
- builder.append(domain);
- builder.append(", coord1=");
- builder.append(coord1);
- builder.append(", coord2=");
- builder.append(coord2);
- builder.append(", coord3=");
- builder.append(coord3);
- builder.append("]");
- return builder.toString();
- }
-
-
-
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-05-01 09:44:23
|
Revision: 2267
http://sourceforge.net/p/jsbml/code/2267
Author: niko-rodrigue
Date: 2015-05-01 09:44:19 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2217
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2217
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
branches/astnode2-merging-alternate/src/
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate 2015-05-01 09:44:19 UTC (rev 2267)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Added: svn:mergeinfo
## -0,0 +1 ##
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2217
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -1743,6 +1743,8 @@
"Cannot register {0}.", sbase.getElementName()));
}
+ // TODO - set package version and namespace if needed
+
/*
* Now, we can add all previous listeners. The next change will
* be fired after registering all ids.
@@ -1772,6 +1774,8 @@
private void registerChild(SBasePlugin sbasePlugin) {
// Could/Should be used by the method #firePropertyChange
+ // TODO - set package version and namespace if needed
+
int childCount = sbasePlugin.getChildCount();
if (childCount > 0) {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -157,9 +157,8 @@
*
*/
public Annotation(String annotation) throws XMLStreamException {
- this();
// parse the String as an XMLNode
- nonRDFannotation = XMLNode.convertStringToXMLNode(annotation);
+ this(XMLNode.convertStringToXMLNode(annotation));
}
/**
@@ -182,6 +181,15 @@
}
/**
+ *
+ * @param annotation
+ */
+ public Annotation(XMLNode annotation) {
+ this();
+ nonRDFannotation = annotation;
+ }
+
+ /**
* Adds a {@link CVTerm}.
*
* @param cvTerm
@@ -201,6 +209,23 @@
}
/**
+ * Adds an additional namespace to the set of declared namespaces of this
+ * {@link SBase}.
+ *
+ * @param prefix the prefix of the namespace to add
+ * @param uri the namespace uri
+ *
+ */
+ public void addDeclaredNamespace(String prefix, String uri)
+ {
+ if (!isSetNonRDFannotation()) {
+ nonRDFannotation = new XMLNode(new XMLTriple("annotation", null, null), new XMLAttributes());
+ }
+
+ nonRDFannotation.addNamespace(uri, prefix);
+ }
+
+ /**
* Appends some 'annotation' to the non RDF annotation {@link XMLNode} of this object.
*
* @param annotation some non RDF annotations.
@@ -246,6 +271,18 @@
return new Annotation(this);
}
+ /**
+ * @see org.sbml.jsbml.SBase#getHistory()
+ * @return
+ */
+ private History createHistory() {
+ history = new History();
+ history.parent = this;
+ history.addAllChangeListeners(getListOfTreeNodeChangeListeners());
+
+ return history;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#equals(java.lang.Object)
*/
@@ -301,6 +338,7 @@
return l;
}
+
/**
* Returns the about String of this object.
*
@@ -310,6 +348,7 @@
return about == null ? "" : about;
}
+
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@@ -318,7 +357,6 @@
return true;
}
-
/**
* Returns the {@link XMLNode} representing non RDF annotations.
*
@@ -330,58 +368,6 @@
return nonRDFannotation;
}
-
- /**
- *
- *
- * @return
- */
- public XMLNode getFullAnnotation() {
-
- XMLNode nonRdfAnnotationClone = null;
-
- if (isSetNonRDFannotation()) {
- nonRdfAnnotationClone = nonRDFannotation.clone();
- }
-
- // TODO - get the list of AnnotationWriter from the manager
- List<AnnotationWriter> annotationParsers = new ArrayList<AnnotationWriter>();
- // hack to delete
- annotationParsers.add(new SBMLRDFAnnotationParser());
-
- // calling the annotation parsers so that they update the XMLNode before returning it to the user
- for (AnnotationWriter annoWriter : annotationParsers) {
- nonRdfAnnotationClone = annoWriter.writeAnnotation((SBase) getParent(), nonRdfAnnotationClone);
- }
-
- return nonRdfAnnotationClone;
- }
-
- /**
- *
- *
- * @return
- */
- public String getFullAnnotationString() {
-
- XMLNode fullAnnotation = getFullAnnotation();
-
- // System.out.println("getFullAnnotationString - " + fullAnnotation);
-
- if (fullAnnotation != null) {
- try {
- return fullAnnotation.toXMLString();
- } catch (XMLStreamException e) {
- Logger logger = Logger.getLogger(Annotation.class);
- if (logger.isDebugEnabled()) {
- e.printStackTrace();
- }
- }
- }
-
- return "";
- }
-
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getChildAt(int)
*/
@@ -414,7 +400,7 @@
// }
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
@@ -447,27 +433,84 @@
/**
- * Returns the {@link History} of the Annotation.
+ * Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
- * @return the {@link History} of the Annotation.
+ * @return the number of controlled vocabulary terms in this {@link Annotation}.
*/
- public History getHistory() {
- if (!isSetHistory()) {
- createHistory();
+ public int getCVTermCount() {
+ return isSetListOfCVTerms() ? listOfCVTerms.size() : 0;
+ }
+
+ /**
+ *
+ * @return
+ */
+ public XMLNamespaces getDeclaredNamespaces() {
+ return isSetNonRDFannotation() ? nonRDFannotation.getNamespaces() : null;
+ }
+
+ /**
+ *
+ *
+ * @return
+ */
+ public XMLNode getFullAnnotation() {
+
+ XMLNode nonRdfAnnotationClone = null;
+
+ if (isSetNonRDFannotation()) {
+ nonRdfAnnotationClone = nonRDFannotation.clone();
}
- return history;
+ // TODO - get the list of AnnotationWriter from the manager
+ List<AnnotationWriter> annotationParsers = new ArrayList<AnnotationWriter>();
+ // hack to delete
+ annotationParsers.add(new SBMLRDFAnnotationParser());
+
+ // calling the annotation parsers so that they update the XMLNode before returning it to the user
+ for (AnnotationWriter annoWriter : annotationParsers) {
+ nonRdfAnnotationClone = annoWriter.writeAnnotation((SBase) getParent(), nonRdfAnnotationClone);
+ }
+
+ return nonRdfAnnotationClone;
}
+
/**
- * @see org.sbml.jsbml.SBase#getHistory()
+ *
+ *
* @return
*/
- private History createHistory() {
- history = new History();
- history.parent = this;
- history.addAllChangeListeners(getListOfTreeNodeChangeListeners());
+ public String getFullAnnotationString() {
+ XMLNode fullAnnotation = getFullAnnotation();
+
+ // System.out.println("getFullAnnotationString - " + fullAnnotation);
+
+ if (fullAnnotation != null) {
+ try {
+ return fullAnnotation.toXMLString();
+ } catch (XMLStreamException e) {
+ Logger logger = Logger.getLogger(Annotation.class);
+ if (logger.isDebugEnabled()) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ return "";
+ }
+
+ /**
+ * Returns the {@link History} of the Annotation.
+ *
+ * @return the {@link History} of the Annotation.
+ */
+ public History getHistory() {
+ if (!isSetHistory()) {
+ createHistory();
+ }
+
return history;
}
@@ -483,6 +526,19 @@
return listOfCVTerms;
}
+ /**
+ * Returns the {@link XMLNode} containing annotations other than
+ * the official RDF annotation, as defined in the SBML specifications.
+ *
+ * @return the {@link XMLNode} containing annotations other than RDF
+ * annotation. Return null if there are none.
+ */
+ public XMLNode getNonRDFannotation() {
+ if (nonRDFannotation != null) {
+ return nonRDFannotation;
+ }
+ return null;
+ }
/**
* Returns the String containing annotations other than RDF
@@ -503,21 +559,6 @@
}
/**
- * Returns the {@link XMLNode} containing annotations other than
- * the official RDF annotation, as defined in the SBML specifications.
- *
- * @return the {@link XMLNode} containing annotations other than RDF
- * annotation. Return null if there are none.
- */
- public XMLNode getNonRDFannotation() {
- if (nonRDFannotation != null) {
- return nonRDFannotation;
- }
- return null;
- }
-
-
- /**
* Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
* @return the number of controlled vocabulary terms in this {@link Annotation}.
@@ -527,13 +568,13 @@
return getCVTermCount();
}
+
/**
- * Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
- * @return the number of controlled vocabulary terms in this {@link Annotation}.
+ * @return
*/
- public int getCVTermCount() {
- return isSetListOfCVTerms() ? listOfCVTerms.size() : 0;
+ public XMLNode getXMLNode() {
+ return getNonRDFannotation();
}
/* (non-Javadoc)
@@ -552,7 +593,6 @@
return hashCode;
}
-
/**
*
* @return
@@ -572,6 +612,7 @@
return about != null;
}
+
/**
* Checks if the {@link Annotation} is initialized.
*
@@ -613,7 +654,6 @@
return history != null && !history.isEmpty();
}
-
/**
* Checks if the list of {@link CVTerm} is not empty.
*
@@ -653,6 +693,7 @@
return isSetNonRDFannotation();
}
+
/**
* Checks if the RDF part of the Annotation is initialized.
*
@@ -699,7 +740,6 @@
return false;
}
-
/**
* Removes the given {@link CVTerm}.
*
@@ -718,6 +758,8 @@
return success;
}
+
+
/**
* Removes the {@link CVTerm} at the given index.
*
@@ -748,8 +790,6 @@
firePropertyChange(TreeNodeChangeEvent.about, oldAbout, this.about);
}
-
-
/**
* Changes the {@link History} instance to 'history'
*
@@ -766,6 +806,18 @@
/**
* Sets the value of the non RDF annotations
*
+ * @param nonRDFAnnotationStr
+ * @throws XMLStreamException
+ */
+ public void setNonRDFAnnotation(String nonRDFAnnotationStr) throws XMLStreamException {
+ if (nonRDFAnnotationStr != null) {
+ setNonRDFAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotationStr)));
+ }
+ }
+
+ /**
+ * Sets the value of the non RDF annotations
+ *
* @param nonRDFAnnotation
*/
public void setNonRDFAnnotation(XMLNode nonRDFAnnotation) {
@@ -791,18 +843,6 @@
}
/**
- * Sets the value of the non RDF annotations
- *
- * @param nonRDFAnnotationStr
- * @throws XMLStreamException
- */
- public void setNonRDFAnnotation(String nonRDFAnnotationStr) throws XMLStreamException {
- if (nonRDFAnnotationStr != null) {
- setNonRDFAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotationStr)));
- }
- }
-
- /**
* Clears the {@link List} of {@link CVTerm}s.
*/
public void unsetCVTerms() {
@@ -841,29 +881,4 @@
}
}
- /**
- * Adds an additional namespace to the set of declared namespaces of this
- * {@link SBase}.
- *
- * @param prefix the prefix of the namespace to add
- * @param uri the namespace uri
- *
- */
- public void addDeclaredNamespace(String prefix, String uri)
- {
- if (!isSetNonRDFannotation()) {
- nonRDFannotation = new XMLNode(new XMLTriple("annotation", null, null), new XMLAttributes());
- }
-
- nonRDFannotation.addNamespace(uri, prefix);
- }
-
- /**
- *
- * @return
- */
- public XMLNamespaces getDeclaredNamespaces() {
- return isSetNonRDFannotation() ? nonRDFannotation.getNamespaces() : null;
- }
-
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -332,6 +332,18 @@
return t;
}
+ /**
+ * Creates a new {@link Trigger} instance and sets it to this {@link Event}.
+ *
+ * @param math math the math expression for the new {@link Trigger}
+ * @return the new {@link Trigger} instance.
+ */
+ public Trigger createTrigger(ASTNode math) {
+ Trigger t = createTrigger();
+ t.setMath(math);
+ return t;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBaseWithUnit#equals(java.lang.Object)
*/
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -131,6 +131,8 @@
*/
public SBMLError(String message) {
super(message);
+ this.message = new Message();
+ this.message.setMessage(message);
}
/**
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -198,6 +198,20 @@
return isSetStoichiometry() ? false : true;
}
+ /**
+ *
+ * @param math
+ * @return
+ * @deprecated since SBML Level 3 this should not be used anymore.
+ */
+ @Deprecated
+ public StoichiometryMath createStoichiometryMath(ASTNode math) {
+ StoichiometryMath sm = new StoichiometryMath(getLevel(), getVersion());
+ sm.setMath(math);
+ setStoichiometryMath(sm);
+ return sm;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SimpleSpeciesReference#equals(java.lang.Object)
*/
@@ -345,8 +359,8 @@
/**
*
- * @return the stoichiometryMath of this SpeciesReference. Can be null if
- * the stoichiometryMath is not set.
+ * @return the stoichiometryMath of this SpeciesReference. Can be {@code null}
+ * if the stoichiometryMath is not set.
* @deprecated since SBML Level 3 this should not be used anymore.
*/
@Deprecated
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -178,6 +178,36 @@
*/
public static final String or = "or";
+ /**
+ * Introduced to FBC in version 2.
+ */
+ public static final String associatedSpecies = "associatedSpecies";
+
+ /**
+ *
+ */
+ public static final String fluxObjective = "fluxObjective";
+
+ /**
+ *
+ */
+ public static final String objective = "objective";
+
+ /**
+ *
+ */
+ public static final String fluxBound = "fluxBound";
+
+ /**
+ *
+ */
+ public static final String listOfFluxObjectives = "listOfFluxObjectives";
+
+ /**
+ *
+ */
+ public static final String listOfFluxes = "listOfFluxes";
+
static {
namespaces = new ArrayList<String>();
namespaces.add(namespaceURI_L3V1V1);
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -23,6 +23,7 @@
import java.util.Map;
import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.UniqueNamedSBase;
/**
@@ -48,6 +49,65 @@
/**
*
*/
+ private String associatedSpecies;
+
+
+ /**
+ * Returns the value of {@link #associatedSpecies}.
+ *
+ * @return the value of {@link #associatedSpecies}.
+ */
+ public String getAssociatedSpecies() {
+ //TODO: if variable is boolean, create an additional "isVar"
+ //TODO: return primitive data type if possible (e.g., int instead of Integer)
+ if (isSetAssociatedSpecies()) {
+ return associatedSpecies;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(FBCConstants.associatedSpecies, this);
+ }
+
+
+ /**
+ * Returns whether {@link #associatedSpecies} is set.
+ *
+ * @return whether {@link #associatedSpecies} is set.
+ */
+ public boolean isSetAssociatedSpecies() {
+ return associatedSpecies != null;
+ }
+
+
+ /**
+ * Sets the value of associatedSpecies
+ *
+ * @param associatedSpecies the value of associatedSpecies to be set.
+ */
+ public void setAssociatedSpecies(String associatedSpecies) {
+ String oldAssociatedSpecies = this.associatedSpecies;
+ this.associatedSpecies = associatedSpecies;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, this.associatedSpecies);
+ }
+
+
+ /**
+ * Unsets the variable associatedSpecies.
+ *
+ * @return {@code true} if associatedSpecies was set before, otherwise {@code false}.
+ */
+ public boolean unsetAssociatedSpecies() {
+ if (isSetAssociatedSpecies()) {
+ String oldAssociatedSpecies = associatedSpecies;
+ associatedSpecies = null;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, associatedSpecies);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ */
public GeneProduct() {
super();
initDefaults();
@@ -186,6 +246,8 @@
if (attributeName.equals(FBCConstants.geneProductIdentifier) || attributeName.equals(FBCConstants.label)) {
setLabel(value);
+ } else if (attributeName.equals(FBCConstants.associatedSpecies)) {
+ setAssociatedSpecies(value);
} else {
isAttributeRead = false;
}
@@ -260,6 +322,9 @@
if (isSetLabel()) {
attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.label, getLabel());
}
+ if (isSetAssociatedSpecies()) {
+ attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.associatedSpecies, getAssociatedSpecies());
+ }
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -313,7 +313,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -69,6 +69,7 @@
* @since 1.0
* @version $Rev$
*/
+@SuppressWarnings("deprecation")
@ProviderFor(ReadingParser.class)
public class FBCParser extends AbstractReaderWriter implements PackageParser {
@@ -191,7 +192,7 @@
*/
// Create the proper object and link it to his parent.
@Override
- @SuppressWarnings({"unchecked", "deprecation"})
+ @SuppressWarnings({"unchecked"})
public Object processStartElement(String elementName, String uri, String prefix,
boolean hasAttributes, boolean hasNamespaces, Object contextObject)
{
@@ -226,7 +227,7 @@
} else if (contextObject instanceof Objective) {
Objective objective = (Objective) contextObject;
- if (elementName.equals("listOfFluxObjectives") || elementName.equals("listOfFluxes")) {
+ if (elementName.equals(FBCConstants.listOfFluxObjectives) || elementName.equals(FBCConstants.listOfFluxes)) {
// listOfFluxes was the first name of listOfFluxObjectives in the preliminary specifications
ListOf<FluxObjective> listOfFluxObjectives = objective.getListOfFluxObjectives();
groupList = FBCList.listOfFluxObjectives;
@@ -285,7 +286,7 @@
else if (contextObject instanceof ListOf<?>) {
ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
- if (elementName.equals("fluxBound")
+ if (elementName.equals(FBCConstants.fluxBound)
&& groupList.equals(FBCList.listOfFluxBounds)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -294,7 +295,7 @@
extendeModel.addFluxBound(fluxBound);
return fluxBound;
- } else if (elementName.equals("objective")
+ } else if (elementName.equals(FBCConstants.objective)
&& groupList.equals(FBCList.listOfObjectives)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -303,7 +304,7 @@
extendeModel.addObjective(objective);
return objective;
- } else if (elementName.equals("fluxObjective")
+ } else if (elementName.equals(FBCConstants.fluxObjective)
&& groupList.equals(FBCList.listOfFluxObjectives)) {
Objective objective = (Objective) listOf.getParentSBMLObject();
@@ -311,7 +312,7 @@
objective.addFluxObjective(fluxObjective);
return fluxObjective;
- } else if (elementName.equals("geneProduct")
+ } else if (elementName.equals(FBCConstants.geneProduct)
&& groupList.equals(FBCList.listOfGeneProducts)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -329,12 +330,13 @@
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.WritingParser#writeElement(org.sbml.jsbml.xml.stax.SBMLObjectForXML, java.lang.Object)
*/
- @SuppressWarnings("deprecation")
@Override
public void writeElement(SBMLObjectForXML xmlObject,
Object sbmlElementToWrite) {
- logger.debug("FBCParser: writeElement");
+ if (logger.isDebugEnabled()) {
+ logger.debug("FBCParser: writeElement");
+ }
if (sbmlElementToWrite instanceof SBase) {
SBase sbase = (SBase) sbmlElementToWrite;
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -33,7 +33,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -103,6 +104,9 @@
this.spatialId = spatialId;
}
+ @Override
+ public abstract AbstractSpatialNamedSBase clone();
+
/**
* Initializes the default values using the namespace.
*/
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -1,143 +1,152 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.spatial;
-
-import java.util.Map;
-
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Alex Thomas
- * @version $Rev$
- * @since 1.0
- * @date Jan 22, 2014
- */
-public abstract class AbstractSpatialSBasePlugin extends AbstractSBasePlugin {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -75143209163226722L;
-
- /**
- *
- */
- public AbstractSpatialSBasePlugin() {
- super();
- initDefaults();
- }
-
- /**
- * @param plugin
- */
- public AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin plugin) {
- super(plugin);
- }
-
- /**
- * @param extendedSBase
- */
- public AbstractSpatialSBasePlugin(SBase extendedSBase) {
- super(extendedSBase);
- initDefaults();
- }
-
- /**
- * Initializes the default values using the namespace.
- */
- public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractTreeNode#getParent()
- */
- @Override
- public SBase getParent() {
- if (isSetExtendedSBase()) {
- return (SBase) getExtendedSBase().getParent();
- }
-
- return null;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
- */
- @Override
- public SBase getParentSBMLObject() {
- return getParent();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
- */
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- return super.writeXMLAttributes();
- }
-
- /**
- * @return
- */
- public Model getModel() {
- SBMLDocument doc = getSBMLDocument();
- return doc != null ? doc.getModel() : null;
- }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+import java.util.Map;
+
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+
+/**
+ *
+ * @author Alex Thomas
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date Jan 22, 2014
+ */
+public abstract class AbstractSpatialSBasePlugin extends AbstractSBasePlugin {
+
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -75143209163226722L;
+
+ /**
+ *
+ */
+ public AbstractSpatialSBasePlugin() {
+ super();
+ initDefaults();
+ }
+
+ /**
+ * @param plugin
+ */
+ public AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin plugin) {
+ super(plugin);
+ }
+
+ /**
+ * @param extendedSBase
+ */
+ public AbstractSpatialSBasePlugin(SBase extendedSBase) {
+ super(extendedSBase);
+ initDefaults();
+ }
+
+ @Override
+ public abstract AbstractSpatialSBasePlugin clone();
+
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#getParent()
+ */
+ @Override
+ public SBase getParent() {
+ if (isSetExtendedSBase()) {
+ return (SBase) getExtendedSBase().getParent();
+ }
+
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
+ */
+ @Override
+ public SBase getParentSBMLObject() {
+ return getParent();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
+ */
+ @Override
+ public String getPackageName() {
+ return SpatialConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
+ */
+ @Override
+ public String getPrefix() {
+ return SpatialConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
+ */
+ @Override
+ public String getURI() {
+ return getElementNamespace();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
+ */
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#writeXMLAttributes()
+ */
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ return super.writeXMLAttributes();
+ }
+
+ /**
+ * @return
+ */
+ public Model getModel() {
+ SBMLDocument doc = getSBMLDocument();
+ return doc != null ? doc.getModel() : null;
+ }
+
+ @Override
+ public String toString() {
+ return super.toString();
+ }
+
+}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -39,14 +39,13 @@
/**
* Generated serial version identifier.
*/
- private static final long serialVersionUID = 8982184068116596444L;
-
+ private static final long serialVersionUID = 8982184068116596444L;
+
/**
*
*/
private CoordinateKind coordinate;
-
/**
*
*/
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -33,7 +33,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -283,5 +284,16 @@
}
return equal;
}
+
+ @Override
+ public int hashCode() {
+ final int prime = 1039;//Change this prime number
+ int hashCode = super.hashCode();
+ if (isSetListOfAnalyticVolumes()) {
+ hashCode += prime * getListOfAnalyticVolumes().hashCode();
+ }
+ return hashCode;
+ }
+
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -35,7 +35,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -102,14 +103,17 @@
public AnalyticVolume(AnalyticVolume node) {
super(node);
if (node.isSetSpatialId()) {
- spatialId = new String(node.getSpatialId());
+ setSpatialId(node.getSpatialId());
}
if (node.isSetOrdinal()) {
- ordinal = new Integer(node.getOrdinal());
+ setOrdinal(node.getOrdinal());
}
if (node.isSetFunctionType()) {
- functionType = node.getFunctionType();
+ setFunctionType(node.getFunctionType());
}
+ if (node.isSetDomainType()) {
+ setDomainType(node.getDomainType());
+ }
}
/**
@@ -302,7 +306,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -315,7 +319,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
@@ -372,7 +376,7 @@
*/
@Override
public int hashCode() {
- final int prime = 431;//Change this prime number
+ final int prime = 1093;//Changed. It was 431
int hashCode = super.hashCode();
if (isSetSpatialId()) {
hashCode += prime * getSpatialId().hashCode();
@@ -411,14 +415,7 @@
attributes.remove("functionType");
attributes.put(SpatialConstants.shortLabel + ":functionType", getFunctionType().toString());
}
- if (isSetSBOTerm()) {
- attributes.remove(TreeNodeChangeEvent.sboTerm);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.sboTerm, getSBOTermID());
- }
- if (isSetMetaId()) {
- attributes.remove(TreeNodeChangeEvent.metaId);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.metaId, getMetaId());
- }
+
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -126,7 +126,7 @@
* @param value
*/
public void setValue(double value) {
- double oldValue = this.value;
+ Double oldValue = this.value;
this.value = value;
firePropertyChange(SpatialConstants.value, oldValue, this.value);
}
@@ -140,7 +140,7 @@
*/
public boolean unsetValue() {
if (isSetValue()) {
- double oldValue = value;
+ Double oldValue = value;
value = null;
firePropertyChange(SpatialConstants.value, oldValue, value);
return true;
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -99,8 +100,20 @@
return new CSGHomogeneousTransformation(this);
}
-
@Override
+ public int hashCode() {
+ final int prime = 1697;
+ int hashCode = super.hashCode();
+ if (isSetForwardTransformation()) {
+ hashCode += prime * getForwardTransformation().hashCode();
+ }
+ if (isSetReverseTransformation()) {
+ hashCode += prime * getReverseTransformation().hashCode();
+ }
+ return hashCode;
+ }
+
+ @Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -79,19 +79,15 @@
*/
public CSGObject(CSGObject csgo) {
super(csgo);
-
if (csgo.isSetDomainType()) {
- domainType = new String(csgo.getDomainType());
+ setDomainType(csgo.getDomainType());
}
-
if (csgo.isSetOrdinal()) {
- ordinal = new Integer(csgo.getOrdinal());
+ setOrdinal(csgo.getOrdinal());
}
-
if (csgo.isSetCSGNode()) {
setCSGNode((CSGNode) csgo.getCSGNode().clone());
}
-
}
@@ -228,7 +224,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -242,7 +238,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
@@ -303,7 +299,7 @@
@Override
public int hashCode() {
- final int prime = 1999;//Change this prime number
+ final int prime = 1669;
int hashCode = super.hashCode();
if (isSetOrdinal()) {
hashCode += prime * getOrdinal();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -103,12 +103,9 @@
*/
public CSGPrimitive(CSGPrimitive csgp) {
super(csgp);
-
-
if (csgp.isSetPrimitiveType()) {
- primitiveType = csgp.getPrimitiveType();
+ setPrimitiveType(csgp.getPrimitiveType());
}
-
}
@@ -213,7 +210,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1081;
int hashCode = super.hashCode();
if (isSetPrimitiveType()) {
hashCode += prime * getPrimitiveType().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -64,11 +64,9 @@
*/
public CSGPseudoPrimitive(CSGPseudoPrimitive csgp) {
super(csgp);
-
if (csgp.isSetCsgObjectRef()) {
- csgObjectRef = new String(csgp.getCsgObjectRef());
+ setCsgObjectRef(csgp.getCsgObjectRef());
}
-
}
@@ -166,7 +164,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1741;
int hashCode = super.hashCode();
if (isSetCsgObjectRef()) {
hashCode += prime * getCsgObjectRef().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -70,17 +71,19 @@
public CSGRotation(CSGRotation csgt) {
super(csgt);
if (csgt.isSetRotateAxisX()) {
- rotateAxisX = new Double(csgt.getRotateAxisX());
+ setRotateAxisX(csgt.getRotateAxisX());
}
if (csgt.isSetRotateAxisY()) {
- rotateAxisY = new Double(csgt.getRotateAxisY());
+ setRotateAxisY(csgt.getRotateAxisY());
}
if (csgt.isSetRotateAxisZ()) {
- rotateAxisZ = new Double(csgt.getRotateAxisZ());
+ setRotateAxisZ(csgt.getRotateAxisZ());
}
+ if (csgt.isSetRotateAngleInRadians()) {
+ setRotateAngleInRadians(csgt.getRotateAngleInRadians());
+ }
}
-
/**
* @param level
* @param version
@@ -165,7 +168,7 @@
* @param rotateAxisX
*/
public void setRotateAxisX(double rotateAxisX) {
- double oldRotateAxisX = this.rotateAxisX;
+ Double oldRotateAxisX = this.rotateAxisX;
this.rotateAxisX = rotateAxisX;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, this.rotateAxisX);
}
@@ -179,7 +182,7 @@
*/
public boolean unsetRotateAxisX() {
if (isSetRotateAxisX()) {
- double oldRotateAxisX = rotateAxisX;
+ Double oldRotateAxisX = rotateAxisX;
rotateAxisX = null;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, rotateAxisX);
return true;
@@ -217,7 +220,7 @@
* @param rotateAxisY
*/
public void setRotateAxisY(double rotateAxisY) {
- double oldRotateAxisY = this.rotateAxisY;
+ Double oldRotateAxisY = this.rotateAxisY;
this.rotateAxisY = rotateAxisY;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, this.rotateAxisY);
}
@@ -231,7 +234,7 @@
*/
public boolean unsetRotateAxisY() {
if (isSetRotateAxisY()) {
- double oldRotateAxisY = rotateAxisY;
+ Double oldRotateAxisY = rotateAxisY;
rotateAxisY = null;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, rotateAxisY);
return true;
@@ -269,7 +272,7 @@
* @param rotateAxisZ
*/
public void setRotateAxisZ(double rotateAxisZ) {
- double oldRotateAxisZ = this.rotateAxisZ;
+ Double oldRotateAxisZ = this.rotateAxisZ;
this.rotateAxisZ = rotateAxisZ;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, this.rotateAxisZ);
}
@@ -283,7 +286,7 @@
*/
public boolean unsetRotateAxisZ() {
if (isSetRotateAxisZ()) {
- double oldRotateAxisZ = rotateAxisZ;
+ Double oldRotateAxisZ = rotateAxisZ;
rotateAxisZ = null;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, rotateAxisZ);
return true;
@@ -321,7 +324,7 @@
* @param rotateAngleInRadians
*/
public void setRotateAngleInRadians(double rotateAngleInRadians) {
- double oldRotateAngleInRadians = this.rotateAngleInRadians;
+ Double oldRotateAngleInRadians = this.rotateAngleInRadians;
this.rotateAngleInRadians = rotateAngleInRadians;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, this.rotateAngleInRadians);
}
@@ -335,7 +338,7 @@
*/
public boolean unsetRotateAngleInRadians() {
if (isSetRotateAngleInRadians()) {
- double oldRotateAngleInRadians = rotateAngleInRadians;
+ Double oldRotateAngleInRadians = rotateAngleInRadians;
rotateAngleInRadians = null;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, rotateAngleInRadians);
return true;
@@ -345,7 +348,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1787;
int hashCode = super.hashCode();
if (isSetRotateAxisX()) {
hashCode += prime * getRotateAxisX();
@@ -367,20 +370,16 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetRotateAxisX()) {
- attributes.remove("rotateAxisX");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", String.valueOf(getRotateAxisX()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", rotateAxisX.toString());
}
if (isSetRotateAxisY()) {
- attributes.remove("rotateAxisY");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", String.valueOf(getRotateAxisY()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", rotateAxisY.toString());
}
if (isSetRotateAxisZ()) {
- attributes.remove("rotateAxisZ");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", String.valueOf(getRotateAxisZ()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", rotateAxisZ.toString());
}
if (isSetRotateAngleInRadians()) {
- attributes.remove("rotateAngleInRadians");
- attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", String.valueOf(getRotateAngleInRadians()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", rotateAngleInRadians.toString());
}
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -30,6 +30,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -68,13 +69,13 @@
public CSGScale(CSGScale csgt) {
super(csgt);
if (csgt.isSetScaleX()) {
- scaleX = new Double(csgt.getScaleX());
+ setScaleX(csgt.getScaleX());
}
if (csgt.isSetScaleY()) {
- scaleY = new Double(csgt.getScaleY());
+ setScaleY(csgt.getScaleY());
}
if (csgt.isSetScaleZ()) {
- scaleZ = new Double(csgt.getScaleZ());
+ setScaleZ(csgt.getScaleZ());
}
}
@@ -159,7 +160,7 @@
* @param scaleX
*/
public void setScaleX(double scaleX) {
- double oldScaleX = this.scaleX;
+ Double oldScaleX = this.scaleX;
this.scaleX = scaleX;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, this.scaleX);
}
@@ -173,7 +174,7 @@
*/
public boolean unsetScaleX() {
if (isSetScaleX()) {
- double oldScaleX = scaleX;
+ Double oldScaleX = scaleX;
scaleX = null;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, scaleX);
return true;
@@ -211,7 +212,7 @@
* @param scaleY
*/
public void setScaleY(double scaleY) {
- double oldScaleY = this.scaleY;
+ Double oldScaleY = this.scaleY;
this.scaleY = scaleY;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, this.scaleY);
}
@@ -225,7 +226,7 @@
*/
public boolean unsetScaleY() {
if (isSetScaleY()) {
- double oldScaleY = scaleY;
+ Double oldScaleY = scaleY;
scaleY = null;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, scaleY);
return true;
@@ -263,7 +264,7 @@
* @param scaleZ
*/
public void setScaleZ(double scaleZ) {
- double oldScaleZ = this.scaleZ;
+ Double oldScaleZ = this.scaleZ;
this.scaleZ = scaleZ;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, this.scaleZ);
}
@@ -277,7 +278,7 @@
*/
public boolean unsetScaleZ() {
if (isSetScaleZ()) {
- double oldScaleZ = scaleZ;
+ Double oldScaleZ = scaleZ;
scaleZ = null;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, scaleZ);
return true;
@@ -288,7 +289,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1777;
int hashCode = super.hashCode();
if (isSetScaleX()) {
hashCode += prime * getScaleX();
@@ -307,16 +308,13 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetScaleX()) {
- attributes.remove("scaleX");
- attributes.put(SpatialConstants.shortLabel + ":scaleX", String.valueOf(getScaleX()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleX", scaleX.toString());
}
if (isSetScaleY()) {
- attributes.remove("scaleY");
- attributes.put(SpatialConstants.shortLabel + ":scaleY", String.valueOf(getScaleY()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleY", scaleY.toString());
}
if (isSetScaleZ()) {
- attributes.remove("scaleZ");
- attributes.put(SpatialConstants.shortLabel + ":scaleZ", String.valueOf(getScaleZ()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleZ", scaleZ.toString());
}
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -36,6 +36,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -105,15 +106,15 @@
}
if (csgso.isSetOperationType()) {
- operationType = csgso.getOperationType();
+ setOperationType(csgso.getOperationType());
}
if (csgso.isSetComplementA()) {
- complementA = new String(csgso.getComplementA());
+ setComplementA(csgso.getComplementA());
}
if (csgso.isSetComplementB()) {
- complementB = new String(csgso.getComplementB());
+ setComplementB(csgso.getComplementB());
}
}
@@ -638,7 +639,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1861;
int hashCode = super.hashCode();
if (isSetOperationType()) {
hashCode += prime * getOperationType().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
Modified: branches/astnode2-merging-...
[truncated message content] |
|
From: <nik...@us...> - 2015-04-30 15:40:39
|
Revision: 2266
http://sourceforge.net/p/jsbml/code/2266
Author: niko-rodrigue
Date: 2015-04-30 15:40:25 +0000 (Thu, 30 Apr 2015)
Log Message:
-----------
added the svn:keywords property to everything
Modified Paths:
--------------
branches/astnode2-merging-alternate/NEWS.txt
branches/astnode2-merging-alternate/README.txt
branches/astnode2-merging-alternate/build.xml
branches/astnode2-merging-alternate/core/README
branches/astnode2-merging-alternate/core/build.xml
branches/astnode2-merging-alternate/core/doc/publications/Bioinformatics2011ApplicationNote/crop.sty
branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/celldesigner/SimpleCellDesignerPlugin.java
branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/celldesigner/SimpleCellDesignerPluginAction.java
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[truncated message content] |
|
From: <nik...@us...> - 2015-04-30 15:16:50
|
Revision: 2265
http://sourceforge.net/p/jsbml/code/2265
Author: niko-rodrigue
Date: 2015-04-30 15:16:48 +0000 (Thu, 30 Apr 2015)
Log Message:
-----------
changed svn:ignore properties
Removed Paths:
-------------
branches/astnode2-merging-alternate/extensions/arrays/dist/
Property Changed:
----------------
branches/astnode2-merging-alternate/extensions/arrays/
branches/astnode2-merging-alternate/extensions/comp/
branches/astnode2-merging-alternate/extensions/distrib/
branches/astnode2-merging-alternate/extensions/dyn/
branches/astnode2-merging-alternate/extensions/fbc/
branches/astnode2-merging-alternate/extensions/groups/
branches/astnode2-merging-alternate/extensions/layout/
branches/astnode2-merging-alternate/extensions/multi/
branches/astnode2-merging-alternate/extensions/qual/
branches/astnode2-merging-alternate/extensions/render/
branches/astnode2-merging-alternate/extensions/req/
branches/astnode2-merging-alternate/extensions/spatial/
Index: branches/astnode2-merging-alternate/extensions/arrays
===================================================================
--- branches/astnode2-merging-alternate/extensions/arrays 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/arrays 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/arrays
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
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+dist
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+.factorypath
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Index: branches/astnode2-merging-alternate/extensions/comp
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/comp 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/comp
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
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+.apt_generated
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Index: branches/astnode2-merging-alternate/extensions/distrib
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/distrib 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/distrib
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
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+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/dyn
===================================================================
--- branches/astnode2-merging-alternate/extensions/dyn 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/dyn 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/dyn
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
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+dist
+build
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+jsbml.log
+.apt_generated
+.factorypath
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Index: branches/astnode2-merging-alternate/extensions/fbc
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/fbc 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/fbc
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/groups
===================================================================
--- branches/astnode2-merging-alternate/extensions/groups 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/groups 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/groups
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/layout
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/layout 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/layout
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/multi
===================================================================
--- branches/astnode2-merging-alternate/extensions/multi 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/multi 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/multi
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/qual
===================================================================
--- branches/astnode2-merging-alternate/extensions/qual 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/qual 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/qual
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/render
===================================================================
--- branches/astnode2-merging-alternate/extensions/render 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/render 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/render
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/req
===================================================================
--- branches/astnode2-merging-alternate/extensions/req 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/req 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/req
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
Index: branches/astnode2-merging-alternate/extensions/spatial
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial 2015-04-30 14:16:49 UTC (rev 2264)
+++ branches/astnode2-merging-alternate/extensions/spatial 2015-04-30 15:16:48 UTC (rev 2265)
Property changes on: branches/astnode2-merging-alternate/extensions/spatial
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,9 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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From: <nik...@us...> - 2015-04-30 14:16:52
|
Revision: 2264
http://sourceforge.net/p/jsbml/code/2264
Author: niko-rodrigue
Date: 2015-04-30 14:16:49 +0000 (Thu, 30 Apr 2015)
Log Message:
-----------
added the new ASTNode.Types added while designing the ASTNode2 classes. This is in order to be able to use the old ASTNode class within the new branch, instead of using ASTNode2. So that we can produce two jars, one using the old unchanged ASTNode class, one using the ASTNode facade to ASTNode2
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-04-30 14:01:37 UTC (rev 2263)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-04-30 14:16:49 UTC (rev 2264)
@@ -84,6 +84,14 @@
*/
CONSTANT_PI,
/**
+ *
+ */
+ CONSTRUCTOR_PIECE,
+ /**
+ *
+ */
+ CONSTRUCTOR_OTHERWISE,
+ /**
*
*/
CONSTANT_TRUE,
@@ -298,6 +306,22 @@
*/
POWER,
/**
+ *
+ */
+ PRODUCT,
+ /**
+ *
+ */
+ QUALIFIER_BVAR,
+ /**
+ *
+ */
+ QUALIFIER_DEGREE,
+ /**
+ *
+ */
+ QUALIFIER_LOGBASE,
+ /**
* An {@link ASTNode} of this {@link Type} contains two integer values:
* a numerator and a denominator.
*/
@@ -339,6 +363,10 @@
*/
RELATIONAL_NEQ,
/**
+ *
+ */
+ SUM,
+ /**
*
*/
TIMES,
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|
