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[Jsbml-svn] SF.net SVN: jsbml:[2357] trunk
|
From: <and...@us...> - 2015-08-31 09:09:45
|
Revision: 2357
http://sourceforge.net/p/jsbml/code/2357
Author: andreas-draeger
Date: 2015-08-31 09:09:43 +0000 (Mon, 31 Aug 2015)
Log Message:
-----------
* Implemented new regex-based check for chemical formulas in the FBC package.
* Corrected quotation marks in Messages.xml
* Small changes for the Users' Guide code listing
* Corrected indentation etc. in some other files.
Modified Paths:
--------------
trunk/core/doc/user_guide/src/org/sbml/jsbml/gui/JSBMLvisualizer.java
trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
trunk/core/src/org/sbml/jsbml/validator/SBMLValidator.java
trunk/core/src/org/sbml/jsbml/validator/SyntaxChecker.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
Modified: trunk/core/doc/user_guide/src/org/sbml/jsbml/gui/JSBMLvisualizer.java
===================================================================
--- trunk/core/doc/user_guide/src/org/sbml/jsbml/gui/JSBMLvisualizer.java 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/core/doc/user_guide/src/org/sbml/jsbml/gui/JSBMLvisualizer.java 2015-08-31 09:09:43 UTC (rev 2357)
@@ -41,7 +41,7 @@
/**
* @param tree
- * The sbml root node of an SBML file
+ * The SBML root node of an SBML file
*/
public JSBMLvisualizer(SBase tree) {
super("SBML Structure Visualization");
@@ -57,7 +57,7 @@
* Main. Note: this doesn't perform error checking, but should. It is an
* illustration only.
*
- * @param args
+ * @param args path to an SBML file.
* @throws Exception
*/
public static void main(String[] args) throws Exception {
Modified: trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml
===================================================================
--- trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml 2015-08-31 09:09:43 UTC (rev 2357)
@@ -35,7 +35,7 @@
<entry key="SBMLCoreParser.instanciationError">The element ''{0}'' could not be instanciated as a Java object!</entry>
<entry key="SBMLCoreParser.namespaceIgnored">Namespace ignored on ''{0}''! {1} = {2}</entry>
<entry key="SBMLCoreParser.reactionWithoutParticipantsError">The reaction ''{0}'' does not contain any reactants or products.</entry>
- <entry key="SBMLCoreParser.unknownAttributeOnElement">Could not recognize the attribute \"{0}\" on the element {1}. Please check the specification for SBML.</entry>
+ <entry key="SBMLCoreParser.unknownAttributeOnElement">Could not recognize the attribute ''{0}'' on the element {1}. Please check the specification for SBML.</entry>
<entry key="SBMLCoreParser.unknownElement">The element ''{0}'' is not recognized.</entry>
<entry key="SBMLCoreParser.unknownReferenceError1">No {0} matches the {1} ''{2}'' of {3} ''{4}''.</entry>
<entry key="SBMLCoreParser.unknownReferenceError2">No {0} matches the {1} ''{2}'' of an {2}.</entry>
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-08-31 09:09:43 UTC (rev 2357)
@@ -11,7 +11,7 @@
* 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
+ * 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
@@ -37,14 +37,14 @@
* "(8639_AT1) || (26_AT1) || (314_AT2) || (314_AT1)".
* <p>
* Support almost the same syntax as defined in <a href="http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/libsbml.html#parseL3Formula(java.lang.String)">
- * the LibSBML L3 parser</a>.
+ * the LibSBML L3 parser</a>.
* <p>One of the main differences is that ID are allowed to start by a number so that ID like that '8639_AT1' are recognised as ID.
- *
+ *
* <p>The things not supported for now are the units associated with numbers.
*
* <p>
* Parsing of the various MathML functions and constants are all
- * case-sensitive by default: names such as
+ * case-sensitive by default: names such as
* <code>Cos</code> and <code>COS</code> are not parsed as the MathML cosine
* operator, <code><cos></code>.
*
@@ -81,8 +81,8 @@
<p>
- * In the table above, <em>operand</em> implies the construct is an operand,
- * <em>prefix</em> implies the operation is applied to the following arguments,
+ * In the table above, <em>operand</em> implies the construct is an operand,
+ * <em>prefix</em> implies the operation is applied to the following arguments,
* <em>unary</em> implies there is one argument, and <em>binary</em> implies there are
* two arguments. The values in the <b>Precedence</b> column show how the
* order of different types of operation are determined. For example, the
@@ -106,7 +106,7 @@
* functions added in SBML Level 2 and Level 3:
<p>
- * <table border="0" width="95%"
+ * <table border="0" width="95%"
class="centered text-table normal-font alt-row-colors">
<tr>
<th align="left" width="60">Name</th>
@@ -115,8 +115,8 @@
<th align="left" width="90">Argument Constraints</th>
<th align="left" width="90">Result constraints</th>
</tr>
-<tr><td><code>abs</code></td>
- <td><em>x</em></td>
+<tr><td><code>abs</code></td>
+ <td><em>x</em></td>
<td>Absolute value of <em>x</em>.</td>
<td></td>
<td></td>
@@ -470,16 +470,16 @@
*
* <p>The default behavior is to be case sensitive, meaning
* '{@code cos}' would be recognized as the mathematical <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a> but
- * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
+ * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
* as a name and read as a 'ci' element. If you pass {@code false} to this method
* all the different versions of {@code cos} would be recognized as the mathematical
- * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
+ * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
*
- * @param caseSensitive boolean to define if the parser should be case sensitive or not.
+ * @param caseSensitive boolean to define if the parser should be case sensitive or not.
*/
public void setCaseSensitive(boolean caseSensitive)
{
- this.ignoreCase = !caseSensitive;
+ ignoreCase = !caseSensitive;
}
private void checkSize(ArrayList < ASTNode > arguments, int i) throws ParseException
@@ -516,44 +516,44 @@
}
}
-/**
- * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- *
- * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
- *
- * @param leftChild
- * @param rightChild
- * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- * @see http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F
- */
+ /**
+ * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ *
+ * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
+ *
+ * @param leftChild
+ * @param rightChild
+ * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ * @see "http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F"
+ */
private ASTNode createModulo(ASTNode leftChild, ASTNode rightChild)
{
- ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
+ ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
- ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
- ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
- aDividedByB.addChild(leftChild);
- aDividedByB.addChild(rightChild);
+ ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
+ ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
+ aDividedByB.addChild(leftChild);
+ aDividedByB.addChild(rightChild);
- floorNode.addChild(aDividedByB);
- node.addChild(floorNode);
+ floorNode.addChild(aDividedByB);
+ node.addChild(floorNode);
- ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
- greaterThan.addChild(aDividedByB.clone());
- greaterThan.addChild(new ASTNode(0));
+ ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
+ greaterThan.addChild(aDividedByB.clone());
+ greaterThan.addChild(new ASTNode(0));
- node.addChild(greaterThan);
+ node.addChild(greaterThan);
- ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
- ceilNode.addChild(aDividedByB.clone());
+ ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
+ ceilNode.addChild(aDividedByB.clone());
- node.addChild(ceilNode);
+ node.addChild(ceilNode);
- return node;
+ return node;
}
final public Token string() throws ParseException {
- Token t;
+ Token t;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case LOG:
t = jj_consume_token(LOG);
@@ -566,19 +566,24 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) return t;}
+ {if (true) {
+ return t;
+ }}
throw new Error("Missing return statement in function");
}
+ @Override
final public ASTNode parse() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
node = expression();
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode expression() throws ParseException {
- ASTNode value = null;
+ ASTNode value = null;
value = termLevel2();
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case 0:
@@ -592,229 +597,243 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) return value;}
+ {if (true) {
+ return value;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel2() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel3();
label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = termLevel3();
- // TODO - do we want to ignore the case for those cases ?
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case BOOLEAN_LOGIC:
+ ;
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ break label_1;
+ }
+ t = jj_consume_token(BOOLEAN_LOGIC);
+ rightChild = termLevel3();
+ // TODO - do we want to ignore the case for those cases ?
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
- {
- type = ASTNode.Type.LOGICAL_OR;
+ if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
+ {
+ type = ASTNode.Type.LOGICAL_OR;
+ }
+ else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
+ {
+ type = ASTNode.Type.LOGICAL_AND;
+ }
+ else if (s.equalsIgnoreCase("xor"))
+ {
+ type = ASTNode.Type.LOGICAL_XOR;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
- {
- type = ASTNode.Type.LOGICAL_AND;
- }
- else if (s.equalsIgnoreCase("xor"))
- {
- type = ASTNode.Type.LOGICAL_XOR;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel3() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel4();
label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[3] = jj_gen;
- break label_2;
- }
- t = jj_consume_token(COMPARISON);
- rightChild = termLevel4();
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case COMPARISON:
+ ;
+ break;
+ default:
+ jj_la1[3] = jj_gen;
+ break label_2;
+ }
+ t = jj_consume_token(COMPARISON);
+ rightChild = termLevel4();
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("<"))
- {
- type = ASTNode.Type.RELATIONAL_LT;
+ if (s.equalsIgnoreCase("<"))
+ {
+ type = ASTNode.Type.RELATIONAL_LT;
+ }
+ else if (s.equalsIgnoreCase(">"))
+ {
+ type = ASTNode.Type.RELATIONAL_GT;
+ }
+ else if (s.equalsIgnoreCase("=="))
+ {
+ type = ASTNode.Type.RELATIONAL_EQ;
+ }
+ else if (s.equalsIgnoreCase("!="))
+ {
+ type = ASTNode.Type.RELATIONAL_NEQ;
+ }
+ else if (s.equalsIgnoreCase(">="))
+ {
+ type = ASTNode.Type.RELATIONAL_GEQ;
+ }
+ else if (s.equalsIgnoreCase("<="))
+ {
+ type = ASTNode.Type.RELATIONAL_LEQ;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- else if (s.equalsIgnoreCase(">"))
- {
- type = ASTNode.Type.RELATIONAL_GT;
- }
- else if (s.equalsIgnoreCase("=="))
- {
- type = ASTNode.Type.RELATIONAL_EQ;
- }
- else if (s.equalsIgnoreCase("!="))
- {
- type = ASTNode.Type.RELATIONAL_NEQ;
- }
- else if (s.equalsIgnoreCase(">="))
- {
- type = ASTNode.Type.RELATIONAL_GEQ;
- }
- else if (s.equalsIgnoreCase("<="))
- {
- type = ASTNode.Type.RELATIONAL_LEQ;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel4() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel5();
label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_3;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ case MINUS:
+ ;
+ break;
+ default:
+ jj_la1[4] = jj_gen;
+ break label_3;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ jj_consume_token(PLUS);
+ rightChild = termLevel5();
+ node = new ASTNode('+');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case MINUS:
+ jj_consume_token(MINUS);
+ rightChild = termLevel5();
+ node = new ASTNode('-');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[5] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = termLevel5();
- node = new ASTNode('+');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = termLevel5();
- node = new ASTNode('-');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel5() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel6();
label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_4;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ case DIVIDE:
+ case MODULO:
+ ;
+ break;
+ default:
+ jj_la1[6] = jj_gen;
+ break label_4;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ jj_consume_token(TIMES);
+ rightChild = termLevel6();
+ node = new ASTNode('*');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case DIVIDE:
+ jj_consume_token(DIVIDE);
+ rightChild = termLevel6();
+ Integer left, right;
+ left = getInteger(leftChild);
+ right = getInteger(rightChild);
+ // TODO - check if libsbml behave the same way
+ if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
+ {
+ node = new ASTNode();
+ node.setValue(left, right);
+ leftChild = node;
+ }
+ else
+ {
+ node = new ASTNode('/');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ break;
+ case MODULO:
+ jj_consume_token(MODULO);
+ rightChild = termLevel6();
+ node = createModulo(leftChild, rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[7] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = termLevel6();
- node = new ASTNode('*');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = termLevel6();
- Integer left, right;
- left = getInteger(leftChild);
- right = getInteger(rightChild);
- // TODO - check if libsbml behave the same way
- if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
- {
- node = new ASTNode();
- node.setValue(left, right);
- leftChild = node;
- }
- else
- {
- node = new ASTNode('/');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = termLevel6();
- node = createModulo(leftChild, rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel6() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case MINUS:
jj_consume_token(MINUS);
node = termLevel7();
- ASTNode uiMinus = new ASTNode('-');
- uiMinus.addChild(node);
- {if (true) return uiMinus;}
+ ASTNode uiMinus = new ASTNode('-');
+ uiMinus.addChild(node);
+ {if (true) {
+ return uiMinus;
+ }}
break;
case NOT:
jj_consume_token(NOT);
node = termLevel7();
- ASTNode not = new ASTNode(Type.LOGICAL_NOT);
- not.addChild(node);
- {if (true) return not;}
+ ASTNode not = new ASTNode(Type.LOGICAL_NOT);
+ not.addChild(node);
+ {if (true) {
+ return not;
+ }}
break;
case INTEGER:
case NUMBER:
@@ -824,7 +843,9 @@
case LOG:
case STRING:
node = termLevel7();
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[8] = jj_gen;
@@ -835,68 +856,76 @@
}
final private ASTNode termLevel7() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel8();
label_5:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case POWER:
+ ;
+ break;
+ default:
+ jj_la1[9] = jj_gen;
+ break label_5;
+ }
+ jj_consume_token(POWER);
+ rightChild = termLevel8();
+ node = new ASTNode(Type.POWER);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- jj_consume_token(POWER);
- rightChild = termLevel8();
- node = new ASTNode(Type.POWER);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel8() throws ParseException, NumberFormatException {
- Token t;
- double d;
- int i;
- ASTNode node = new ASTNode();
- ASTNode vector = null;
- ASTNode child, furtherChild;
- String s;
- String vals [ ];
- ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
+ Token t;
+ double d;
+ int i;
+ ASTNode node = new ASTNode();
+ ASTNode vector = null;
+ ASTNode child, furtherChild;
+ String s;
+ String vals [ ];
+ ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case INTEGER:
t = jj_consume_token(INTEGER);
- i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
- node.setValue(i);
- {if (true) return node;}
+ i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
+ node.setValue(i);
+ {if (true) {
+ return node;
+ }}
break;
case NUMBER:
t = jj_consume_token(NUMBER);
- d = Double.parseDouble(t.image);
- node.setValue(d);
- {if (true) return node;}
+ d = Double.parseDouble(t.image);
+ node.setValue(d);
+ {if (true) {
+ return node;
+ }}
break;
case EXPNUMBER:
t = jj_consume_token(EXPNUMBER);
- s = t.image;
- vals = s.toLowerCase().split("e");
- if (vals [ 1 ].startsWith("+"))
- {
- i = Integer.parseInt(vals [ 1 ].substring(1));
- }
- else
- {
- i = Integer.parseInt(vals [ 1 ]);
- }
- node.setValue(Double.parseDouble(vals [ 0 ]), i);
- {if (true) return node;}
+ s = t.image;
+ vals = s.toLowerCase().split("e");
+ if (vals [ 1 ].startsWith("+"))
+ {
+ i = Integer.parseInt(vals [ 1 ].substring(1));
+ }
+ else
+ {
+ i = Integer.parseInt(vals [ 1 ]);
+ }
+ node.setValue(Double.parseDouble(vals [ 0 ]), i);
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[14] = jj_gen;
@@ -905,226 +934,240 @@
jj_consume_token(OPEN_PAR);
child = termLevel2();
label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[10] = jj_gen;
+ break label_6;
+ }
+ jj_consume_token(SPLITTER);
+ furtherChild = termLevel2();
+ arguments.add(furtherChild);
}
- jj_consume_token(SPLITTER);
- furtherChild = termLevel2();
- arguments.add(furtherChild);
+ jj_consume_token(CLOSE_PAR);
+ s = t.image;
+ Type type = null;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
}
- jj_consume_token(CLOSE_PAR);
- s = t.image;
- Type type = null;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- if (stringToType.containsKey(s))
- {
- type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
- }
- if (s.equals("pow") || s.equals("power"))
- {
- checkSize(arguments, 1);
- node.addChild(child);
- }
- else if (s.equals("sqr"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- node.addChild(new ASTNode(2));
- }
- else if (s.equals("sqrt"))
- {
- checkSize(arguments, 0);
- node.addChild(new ASTNode(2));
- node.addChild(child);
- }
- else if (s.equals("not"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.LOGICAL_NOT;
- }
- else if (s.equals("ln"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.FUNCTION_LN;
- }
- else if (s.equals("lambda"))
- {
- node.addChild(child);
- type = Type.LAMBDA;
- }
- else if (s.equals("piecewise"))
- {
- node.addChild(child);
- type = Type.FUNCTION_PIECEWISE;
- }
- else if (s.equals("modulo") || s.equals("mod"))
- {
- checkSize(arguments, 1);
- ASTNode rightChild = arguments.get(0);
- arguments.clear();
- node = createModulo(child, rightChild);
- {if (true) return node;}
- }
- else
- {
- node.addChild(child);
- }
- if (type != null)
- {
- node.setType(type);
- // TODO - should we set the name of the ASTNode for FUNCTION, ...
- }
- else
- {
- node.setName(s);
- }
- for (ASTNode argument : arguments)
- {
- node.addChild(argument);
- }
- {if (true) return node;}
+ if (stringToType.containsKey(s))
+ {
+ type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
+ }
+ if (s.equals("pow") || s.equals("power"))
+ {
+ checkSize(arguments, 1);
+ node.addChild(child);
+ }
+ else if (s.equals("sqr"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ node.addChild(new ASTNode(2));
+ }
+ else if (s.equals("sqrt"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(new ASTNode(2));
+ node.addChild(child);
+ }
+ else if (s.equals("not"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.LOGICAL_NOT;
+ }
+ else if (s.equals("ln"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.FUNCTION_LN;
+ }
+ else if (s.equals("lambda"))
+ {
+ node.addChild(child);
+ type = Type.LAMBDA;
+ }
+ else if (s.equals("piecewise"))
+ {
+ node.addChild(child);
+ type = Type.FUNCTION_PIECEWISE;
+ }
+ else if (s.equals("modulo") || s.equals("mod"))
+ {
+ checkSize(arguments, 1);
+ ASTNode rightChild = arguments.get(0);
+ arguments.clear();
+ node = createModulo(child, rightChild);
+ {if (true) {
+ return node;
+ }}
+ }
+ else
+ {
+ node.addChild(child);
+ }
+ if (type != null)
+ {
+ node.setType(type);
+ // TODO - should we set the name of the ASTNode for FUNCTION, ...
+ }
+ else
+ {
+ node.setName(s);
+ }
+ for (ASTNode argument : arguments)
+ {
+ node.addChild(argument);
+ }
+ {if (true) {
+ return node;
+ }}
} else {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case OPEN_PAR:
jj_consume_token(OPEN_PAR);
node = termLevel2();
jj_consume_token(CLOSE_PAR);
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[15] = jj_gen;
if (jj_2_2(4)) {
t = jj_consume_token(STRING);
- ASTNode selector = new ASTNode();
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- selector.addChild(new ASTNode(t.image));
+ ASTNode selector = new ASTNode();
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ selector.addChild(new ASTNode(t.image));
label_7:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
+ while (true) {
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[11] = jj_gen;
+ break label_7;
+ }
}
- }
- {if (true) return selector;}
+ {if (true) {
+ return selector;
+ }}
} else if (jj_2_3(2)) {
jj_consume_token(LEFT_BRACES);
node = termLevel2();
- ASTNode selector = new ASTNode();
- vector = new ASTNode();
- boolean isSelector = false;
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- vector.setType(ASTNode.Type.VECTOR);
- vector.addChild(node);
+ ASTNode selector = new ASTNode();
+ vector = new ASTNode();
+ boolean isSelector = false;
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ vector.setType(ASTNode.Type.VECTOR);
+ vector.addChild(node);
label_8:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[12] = jj_gen;
- break label_8;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[12] = jj_gen;
+ break label_8;
+ }
+ jj_consume_token(SPLITTER);
+ node = termLevel2();
+ vector.addChild(node);
}
- jj_consume_token(SPLITTER);
- node = termLevel2();
- vector.addChild(node);
- }
jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
+ selector.addChild(vector);
label_9:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[13] = jj_gen;
- break label_9;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[13] = jj_gen;
+ break label_9;
+ }
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ isSelector = true;
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
}
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- isSelector = true;
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
- {if (true) return isSelector ? selector : vector;}
+ {if (true) {
+ return isSelector ? selector : vector;
+ }}
} else {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case LEFT_BRACES:
jj_consume_token(LEFT_BRACES);
- vector = new ASTNode();
- vector.setType(ASTNode.Type.VECTOR);
+ vector = new ASTNode();
+ vector.setType(ASTNode.Type.VECTOR);
jj_consume_token(RIGHT_BRACES);
- {if (true) return vector;}
+ {if (true) {
+ return vector;
+ }}
break;
case STRING:
t = jj_consume_token(STRING);
- s = t.image;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- // TODO - should we set the name of the ASTNode
- if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_TRUE);
- }
- else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_FALSE);
- }
- else if (s.equals("pi"))
- {
- node = new ASTNode(Type.CONSTANT_PI);
- }
- else if (s.equals("avogadro"))
- {
- node = new ASTNode(Type.NAME_AVOGADRO);
- }
- else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.NAME_TIME);
- }
- else if (s.equals("exponentiale"))
- {
- node = new ASTNode(Type.CONSTANT_E);
- }
- else if (s.equals("-infinity") || s.equals("-INF"))
- {
- node = new ASTNode(Double.NEGATIVE_INFINITY);
- }
- else if (s.equals("infinity") || s.equals("INF"))
- {
- node = new ASTNode(Double.POSITIVE_INFINITY);
- }
- else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Double.NaN);
- }
- else
- {
- node = new ASTNode(s);
- }
- {if (true) return node;}
+ s = t.image;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
+ }
+ // TODO - should we set the name of the ASTNode
+ if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_TRUE);
+ }
+ else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_FALSE);
+ }
+ else if (s.equals("pi"))
+ {
+ node = new ASTNode(Type.CONSTANT_PI);
+ }
+ else if (s.equals("avogadro"))
+ {
+ node = new ASTNode(Type.NAME_AVOGADRO);
+ }
+ else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.NAME_TIME);
+ }
+ else if (s.equals("exponentiale"))
+ {
+ node = new ASTNode(Type.CONSTANT_E);
+ }
+ else if (s.equals("-infinity") || s.equals("-INF"))
+ {
+ node = new ASTNode(Double.NEGATIVE_INFINITY);
+ }
+ else if (s.equals("infinity") || s.equals("INF"))
+ {
+ node = new ASTNode(Double.POSITIVE_INFINITY);
+ }
+ else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Double.NaN);
+ }
+ else
+ {
+ node = new ASTNode(s);
+ }
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[16] = jj_gen;
@@ -1163,49 +1206,75 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_23()) {
- jj_scanpos = xsp;
- if (jj_3R_24()) {
- jj_scanpos = xsp;
- if (jj_3R_25()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_24()) {
+ jj_scanpos = xsp;
+ if (jj_3R_25()) {
+ return true;
+ }
+ }
}
- }
return false;
}
private boolean jj_3R_23() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_29()) return true;
+ if (jj_scan_token(MINUS)) {
+ return true;
+ }
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
private boolean jj_3R_11() {
- if (jj_scan_token(LEFT_BRACKET)) return true;
- if (jj_3R_12()) return true;
- if (jj_scan_token(RIGHT_BRACKET)) return true;
+ if (jj_scan_token(LEFT_BRACKET)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
+ if (jj_scan_token(RIGHT_BRACKET)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_36() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_scan_token(RIGHT_BRACES)) return true;
+ if (jj_scan_token(LEFT_BRACES)) {
+ return true;
+ }
+ if (jj_scan_token(RIGHT_BRACES)) {
+ return true;
+ }
return false;
}
private boolean jj_3_1() {
- if (jj_3R_10()) return true;
- if (jj_scan_token(OPEN_PAR)) return true;
+ if (jj_3R_10()) {
+ return true;
+ }
+ if (jj_scan_token(OPEN_PAR)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_28() {
- if (jj_scan_token(MODULO)) return true;
+ if (jj_scan_token(MODULO)) {
+ return true;
+ }
return false;
}
private boolean jj_3_2() {
- if (jj_scan_token(STRING)) return true;
+ if (jj_scan_token(STRING)) {
+ return true;
+ }
Token xsp;
- if (jj_3R_11()) return true;
+ if (jj_3R_11()) {
+ return true;
+ }
while (true) {
xsp = jj_scanpos;
if (jj_3R_11()) { jj_scanpos = xsp; break; }
@@ -1214,28 +1283,40 @@
}
private boolean jj_3R_22() {
- if (jj_scan_token(MINUS)) return true;
+ if (jj_scan_token(MINUS)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_31() {
- if (jj_scan_token(POWER)) return true;
+ if (jj_scan_token(POWER)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_35() {
- if (jj_scan_token(OPEN_PAR)) return true;
- if (jj_3R_12()) return true;
+ if (jj_scan_token(OPEN_PAR)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
return false;
}
private boolean jj_3R_14() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
+ if (jj_scan_token(BOOLEAN_LOGIC)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_29() {
- if (jj_3R_30()) return true;
+ if (jj_3R_30()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1245,7 +1326,9 @@
}
private boolean jj_3R_12() {
- if (jj_3R_13()) return true;
+ if (jj_3R_13()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1258,24 +1341,32 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_22()) {
+ return true;
+ }
}
return false;
}
private boolean jj_3R_21() {
- if (jj_scan_token(PLUS)) return true;
+ if (jj_scan_token(PLUS)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_16() {
- if (jj_scan_token(COMPARISON)) return true;
+ if (jj_scan_token(COMPARISON)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_15() {
- if (jj_3R_17()) return true;
+ if (jj_3R_17()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1285,12 +1376,16 @@
}
private boolean jj_3R_34() {
- if (jj_scan_token(EXPNUMBER)) return true;
+ if (jj_scan_token(EXPNUMBER)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_13() {
- if (jj_3R_15()) return true;
+ if (jj_3R_15()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1300,17 +1395,23 @@
}
private boolean jj_3R_33() {
- if (jj_scan_token(NUMBER)) return true;
+ if (jj_scan_token(NUMBER)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_27() {
- if (jj_scan_token(DIVIDE)) return true;
+ if (jj_scan_token(DIVIDE)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_25() {
- if (jj_3R_29()) return true;
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
@@ -1318,14 +1419,18 @@
Token xsp;
xsp = jj_scanpos;
if (jj_scan_token(26)) {
- jj_scanpos = xsp;
- if (jj_scan_token(27)) return true;
+ jj_scanpos = xsp;
+ if (jj_scan_token(27)) {
+ return true;
+ }
}
return false;
}
private boolean jj_3R_32() {
- if (jj_scan_token(INTEGER)) return true;
+ if (jj_scan_token(INTEGER)) {
+ return true;
+ }
return false;
}
@@ -1333,47 +1438,59 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_32()) {
- jj_scanpos = xsp;
- if (jj_3R_33()) {
- jj_scanpos = xsp;
- if (jj_3R_34()) {
- jj_scanpos = xsp;
- if (jj_3_1()) {
- jj_scanpos = xsp;
- if (jj_3R_35()) {
- jj_scanpos = xsp;
- if (jj_3_2()) {
- jj_scanpos = xsp;
- if (jj_3_3()) {
- jj_scanpos = xsp;
- if (jj_3R_36()) {
- jj_scanpos = xsp;
- if (jj_3R_37()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_33()) {
+ jj_scanpos = xsp;
+ if (jj_3R_34()) {
+ jj_scanpos = xsp;
+ if (jj_3_1()) {
+ jj_scanpos = xsp;
+ if (jj_3R_35()) {
+ jj_scanpos = xsp;
+ if (jj_3_2()) {
+ jj_scanpos = xsp;
+ if (jj_3_3()) {
+ jj_scanpos = xsp;
+ if (jj_3R_36()) {
+ jj_scanpos = xsp;
+ if (jj_3R_37()) {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
- }
- }
- }
- }
- }
- }
- }
return false;
}
private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_12()) return true;
+ if (jj_scan_token(LEFT_BRACES)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
return false;
}
private boolean jj_3R_26() {
- if (jj_scan_token(TIMES)) return true;
+ if (jj_scan_token(TIMES)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_24() {
- if (jj_scan_token(NOT)) return true;
- if (jj_3R_29()) return true;
+ if (jj_scan_token(NOT)) {
+ return true;
+ }
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
@@ -1381,22 +1498,28 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_26()) {
- jj_scanpos = xsp;
- if (jj_3R_27()) {
- jj_scanpos = xsp;
- if (jj_3R_28()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_27()) {
+ jj_scanpos = xsp;
+ if (jj_3R_28()) {
+ return true;
+ }
+ }
}
- }
return false;
}
private boolean jj_3R_37() {
- if (jj_scan_token(STRING)) return true;
+ if (jj_scan_token(STRING)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_17() {
- if (jj_3R_19()) return true;
+ if (jj_3R_19()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1419,18 +1542,18 @@
final private int[] jj_la1 = new int[17];
static private int[] jj_la1_0;
static {
- jj_la1_init_0();
- }
- private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0xc000000,0x40000001,0x200000,0x100000,0x500,0x500,0x3800,0x3800,0xe014468,0x200,0x80,0x40000,0x80,0x40000,0x68,0x4000,0x8010000,};
- }
+ jj_la1_init_0();
+ }
+ private static void jj_la1_init_0() {
+ jj_la1_0 = new int[] {0xc000000,0x40000001,0x200000,0x100000,0x500,0x500,0x3800,0x3800,0xe014468,0x200,0x80,0x40000,0x80,0x40000,0x68,0x4000,0x8010000,};
+ }
final private JJCalls[] jj_2_rtns = new JJCalls[3];
private boolean jj_rescan = false;
private int jj_gc = 0;
/** Constructor with InputStream. */
public CobraFormulaParser(java.io.InputStream stream) {
- this(stream, null);
+ this(stream, null);
}
/** Constructor with InputStream and supplied encoding */
public CobraFormulaParser(java.io.InputStream stream, String encoding) {
@@ -1439,23 +1562,33 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.InputStream stream) {
- ReInit(stream, null);
+ ReInit(stream, null);
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.InputStream stream, String encoding) {
try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Constructor. */
@@ -1465,19 +1598,28 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.Reader stream) {
jj_input_stream.ReInit(stream, 1, 1);
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Constructor with generated Token Manager. */
@@ -1486,8 +1628,12 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
@@ -1496,14 +1642,21 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 17; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
private Token jj_consume_token(int kind) throws ParseException {
Token oldToken;
- if ((oldToken = token).next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
+ if ((oldToken = token).next != null) {
+ token = token.next;
+ } else {
+ token = token.next = token_source.getNextToken();
+ }
jj_ntk = -1;
if (token.kind == kind) {
jj_gen++;
@@ -1512,7 +1665,9 @@
for (int i = 0; i < jj_2_rtns.length; i++) {
JJCalls c = jj_2_rtns[i];
while (c != null) {
- if (c.gen < jj_gen) c.first = null;
+ if (c.gen < jj_gen) {
+ c.first = null;
+ }
c = c.next;
}
}
@@ -1540,38 +1695,51 @@
if (jj_rescan) {
int i = 0; Token tok = token;
while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
- if (tok != null) jj_add_error_token(kind, i);
+ if (tok != null) {
+ jj_add_error_token(kind, i);
+ }
}
- if (jj_scanpos.kind != kind) return true;
- if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
+ if (jj_scanpos.kind != kind) {
+ return true;
+ }
+ if (jj_la == 0 && jj_scanpos == jj_lastpos) {
+ throw jj_ls;
+ }
return false;
}
-/** Get the next Token. */
+ /** Get the next Token. */
final public Token getNextToken() {
- if (token.next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
+ if (token.next != null) {
+ token = token.next;
+ } else {
+ token = token.next = token_source.getNextToken();
+ }
jj_ntk = -1;
jj_gen++;
return token;
}
-/** Get the specific Token. */
+ /** Get the specific Token. */
final public Token getToken(int index) {
Token t = token;
for (int i = 0; i < index; i++) {
- if (t.next != null) t = t.next;
- else t = t.next = token_source.getNextToken();
+ if (t.next != null) {
+ t = t.next;
+ } else {
+ t = t.next = token_source.getNextToken();
+ }
}
return t;
}
private int jj_ntk() {
- if ((jj_nt=token.next) == null)
+ if ((jj_nt=token.next) == null) {
return (jj_ntk = (token.next=token_source.getNextToken()).kind);
- else
+ } else {
return (jj_ntk = jj_nt.kind);
+ }
}
private java.util.List<int[]> jj_expentries = new java.util.ArrayList<int[]>();
@@ -1581,7 +1749,9 @@
private int jj_endpos;
private void jj_add_error_token(int kind, int pos) {
- if (pos >= 100) return;
+ if (pos >= 100) {
+ return;
+ }
if (pos == jj_endpos + 1) {
jj_lasttokens[jj_endpos++] = kind;
} else if (jj_endpos != 0) {
@@ -1601,7 +1771,9 @@
break jj_entries_loop;
}
}
- if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
+ if (pos != 0) {
+ jj_lasttokens[(jj_endpos = pos) - 1] = kind;
+ }
}
}
@@ -1650,19 +1822,19 @@
private void jj_rescan_token() {
jj_rescan = true;
for (int i = 0; i < 3; i++) {
- try {
- JJCalls p = jj_2_rtns[i];
- do {
- if (p.gen > jj_gen) {
- jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
- switch (i) {
+ try {
+ JJCalls p = jj_2_rtns[i];
+ do {
+ if (p.gen > jj_gen) {
+ jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
+ switch (i) {
case 0: jj_3_1(); break;
case 1: jj_3_2(); break;
case 2: jj_3_3(); break;
+ }
}
- }
- p = p.next;
- } while (p != null);
+ p = p.next;
+ } while (p != null);
} catch(LookaheadSuccess ls) { }
}
jj_rescan = false;
Modified: trunk/core/src/org/sbml/jsbml/validator/SBMLValidator.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/validator/SBMLValidator.java 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/core/src/org/sbml/jsbml/validator/SBMLValidator.java 2015-08-31 09:09:43 UTC (rev 2357)
@@ -545,7 +545,7 @@
try {
SBMLErrorLog sbmlErrorLog = (SBMLErrorLog) xstream.fromXML(reader);
- logger.debug("Call and Parsing of the results done !!!");
+ logger.debug("Call and Parsing of the results done!");
// logger.debug("File = " + resultsObj.getFile().getName());
Modified: trunk/core/src/org/sbml/jsbml/validator/SyntaxChecker.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/validator/SyntaxChecker.java 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/core/src/org/sbml/jsbml/validator/SyntaxChecker.java 2015-08-31 09:09:43 UTC (rev 2357)
@@ -44,11 +44,60 @@
public class SyntaxChecker {
/**
+ *
+ */
+ private static Pattern chemicalFormulaPattern;
+
+ /**
* The only instance of this class.
*/
private static final SyntaxChecker syntaxChecker = new SyntaxChecker();
/**
+ *
+ * @return
+ */
+ private static Pattern initChemicalFormulaPattern() {
+ String period[] = new String[7];
+ String lanthanide = "La|Ce|Pr|Nd|Pm|Sm|Eu|Gd|Tb|Dy|Ho|Er|Tm|Yb|Lu";
+ String actinide = "Ac|Th|Pa|U|Np|Pu|Am|Cm|Bk|Cf|Es|Fm|Md|No|Lr";
+ period[0] = "H|He";
+ period[1] = "Li|Be|B|C|N|O|F|Ne";
+ period[2] = "Na|Mg|Al|Si|P|S|Cl|Ar";
+ period[3] = "K|Ca|Sc|Ti|V|Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr";
+ period[4] = "Rb|Sr|Y|Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I|Xe";
+ period[5] = "Cs|Ba|" + lanthanide + "|Hf|Ta|W|Re|Os|Ir|Pt|Au|Hg|Tl|Pb|Bi|Po|At|Rn";
+ period[6] = "Fr|Ra|" + actinide + "Rf|Db|Sg|Bh|Hs|Mt|Ds|Rg|Cn|Uut|Fl|Uup|Lv|Uus|Uuo";
+
+ StringBuilder atoms = new StringBuilder();
+ atoms.append(period[0]);
+ for (int i = 1; i < period.length; i++) {
+ atoms.append('|');
+ atoms.append(period[i]);
+ }
+
+ String compoundName = "[A-Z][a-z]*";
+
+ String residues = "[A-Z][a-z]*";
+
+ String regex = "((" + atoms.toString() + "|" + residues + ")+\\d*)*|(" + compoundName + ")?";
+
+ return Pattern.compile(regex);
+ }
+
+ /**
+ *
+ * @param chemicalFormula
+ * @return
+ */
+ public static boolean isValidChemicalFormula(String chemicalFormula) {
+ if (chemicalFormulaPattern == null) {
+ SyntaxChecker.chemicalFormulaPattern = initChemicalFormulaPattern();
+ }
+ return SyntaxChecker.chemicalFormulaPattern.matcher(chemicalFormula).matches();
+ }
+
+ /**
* Definition of valid e-mail address {@link String}s.
* <table>
* <tr>
@@ -96,6 +145,7 @@
return syntaxChecker.emailPattern.matcher(email).matches();
}
+
/**
* Checks whether the given idCandidate is a valid identifier according to
* the SBML specifications.
@@ -149,7 +199,6 @@
return syntaxChecker.SIdL2Pattern.matcher(idCandidate).matches();
}
-
/**
* Checks if the given identifier candidate satisfies the requirements for a
* valid meta identifier (see SBML L2V4 p. 12 for details).
@@ -179,17 +228,11 @@
* Definition of valid e-mail addresses. Initialized upon first use.
*/
private Pattern emailPattern;
-
/**
* {@link Pattern} to recognize valid meta-identifier strings for SBML
* elements.
*/
private Pattern metaIdPattern;
- /**
- * Simplified {@link Pattern} to recognize valid meta-identifier strings for
- * SBML elements.
- */
- private Pattern simpleMetaIdPattern;
/**
* Collection of reserved names that must not be used as identifiers (names)
@@ -209,6 +252,12 @@
private Pattern SIdL2Pattern;
/**
+ * Simplified {@link Pattern} to recognize valid meta-identifier strings for
+ * SBML elements.
+ */
+ private Pattern simpleMetaIdPattern;
+
+ /**
* Name {@link Pattern} for SBML Level 1 version 1.
*/
private Pattern SNameL1V1;
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java 2015-08-28 00:19:09 UTC (rev 2356)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java 2015-08-31 09:09:43 UTC (rev 2357)
@@ -27,10 +27,12 @@
import javax.swing.tree.TreeNode;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.validator.SyntaxChecker;
/**
* {@link FBCSpeciesPlugin} is the extended {@link Species} class with the additional
@@ -44,6 +46,11 @@
*/
public class FBCSpeciesPlugin extends AbstractFBCSBasePlugin {
+ /**
+ * A {@link Logger} for this class.
+ */
+ private static final transient Logger logger = Logger.getLogger(FBCSpeciesPlugin.class);
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#getParent()
*/
@@ -213,7 +220,11 @@
setCharge(StringTools.parseSBMLInt(value));
return true;
} else if (attributeName.equals(FBCConstants.chemicalFormula)) {
- setChemicalFormula(value);
+ try {
+ setChemicalFormula(value);
+ } catch (IllegalArgumentException exc) {
+ logger.error("Skipped invalid chemical formula: " + chemicalFormula);
+ }
return true;
}
@@ -236,14 +247,19 @@
/**
* Sets the value of chemicalFormula.
*
- * The format of chemical formula must consist only of atomic names (as in the Periodic Table)
- * or user defined compounds either of which take the form of a single capital letter followed
- * by zero or more lower-case letters. Where there is more than a single atom present,
- * this is indicated with an integer. With regards to o...
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