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[Cdk-commits] SF.net SVN: cdk:[13121] cdk/branches/cdk-1.2.x/src
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From: <mig...@us...> - 2008-11-16 10:20:17
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Revision: 13121
http://cdk.svn.sourceforge.net/cdk/?rev=13121&view=rev
Author: miguelrojasch
Date: 2008-11-16 10:20:07 +0000 (Sun, 16 Nov 2008)
Log Message:
-----------
Added in MolecularFormulaManipulator the option to choose for set the integer value 1 or not in the character formula when a chemical formula contains an element with one atom.
Modified Paths:
--------------
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java
cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java 2008-11-16 10:15:56 UTC (rev 13120)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java 2008-11-16 10:20:07 UTC (rev 13121)
@@ -162,8 +162,10 @@
/**
* Returns the string representation of the molecule formula.
*
- * @param formula The IMolecularFormula Object
+ * @param formula The IMolecularFormula Object
* @param orderElements The order of Elements
+ * @param setOne True, when must be set the value 1 for elements with
+ * one atom
* @return A String containing the molecular formula
*
* @see #getHTML(IMolecularFormula)
@@ -172,13 +174,13 @@
* @see #generateOrderEle_Hill_WithCarbons()
*
*/
- @TestMethod("testGetString_IMolecularFormula_String")
- public static String getString(IMolecularFormula formula, String[] orderElements) {
+ @TestMethod("testGetString_IMolecularFormula_arrayString_boolean")
+ public static String getString(IMolecularFormula formula, String[] orderElements, boolean setOne) {
String stringMF = "";
List<IIsotope> isotopesList = putInOrder(orderElements, formula);
for (IIsotope isotope : isotopesList) {
int elemCount = getElementCount(formula, isotope);
- if (elemCount == 1)
+ if (elemCount == 1 && !setOne)
stringMF = stringMF + isotope.getSymbol();
else
stringMF = stringMF + isotope.getSymbol() + getElementCount(formula, isotope);
@@ -203,10 +205,32 @@
@TestMethod("testGetString_IMolecularFormula")
public static String getString(IMolecularFormula formula) {
+ return getString(formula, false);
+ }
+
+ /**
+ * Returns the string representation of the molecule formula.
+ * Based on Hill System. The Hill system is a system of writing
+ * chemical formulas such that the number of carbon atoms in a
+ * molecule is indicated first, the number of hydrogen atoms next,
+ * and then the number of all other chemical elements subsequently,
+ * in alphabetical order. When the formula contains no carbon, all
+ * the elements, including hydrogen, are listed alphabetically.
+ *
+ * @param formula The IMolecularFormula Object
+ * @param setOne True, when must be set the value 1 for elements with
+ * one atom
+ * @return A String containing the molecular formula
+ *
+ * @see #getHTML(IMolecularFormula)
+ */
+ @TestMethod("testGetString_IMolecularFormula_boolean")
+ public static String getString(IMolecularFormula formula, boolean setOne) {
+
if(containsElement(formula, formula.getBuilder().newElement("C")))
- return getString(formula, generateOrderEle_Hill_WithCarbons());
+ return getString(formula, generateOrderEle_Hill_WithCarbons(), setOne);
else
- return getString(formula, generateOrderEle_Hill_NoCarbons());
+ return getString(formula, generateOrderEle_Hill_NoCarbons(), setOne);
}
public static List<IIsotope> putInOrder(String[] orderElements, IMolecularFormula formula) {
Modified: cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java 2008-11-16 10:15:56 UTC (rev 13120)
+++ cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/formula/MassToFormulaToolTest.java 2008-11-16 10:20:07 UTC (rev 13121)
@@ -579,12 +579,12 @@
boolean found = false;
for(IMolecularFormula formula : mfSet.molecularFormulas()) {
String mf = MolecularFormulaManipulator.getString(formula);
- if(mf.equals("C4H11N1O4")){
+ if(mf.equals("C4H11NO4")){
found = true;
break;
}
}
- Assert.assertTrue("The molecular formula C4H11N1O4 should be found",found);
+ Assert.assertTrue("The molecular formula C4H11NO4 should be found",found);
}
/**
@@ -624,12 +624,12 @@
boolean found = false;
for(IMolecularFormula formula : mfSet.molecularFormulas()) {
String mf = MolecularFormulaManipulator.getString(formula);
- if(mf.equals("C11H10N1O2")){
+ if(mf.equals("C11H10NO2")){
found = true;
break;
}
}
- Assert.assertTrue("The molecular formula C4H11N1O4 should be found",found);
+ Assert.assertTrue("The molecular formula C4H11NO4 should be found",found);
}
/**
* A unit test suite for JUnit. C5H11N2O
Modified: cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java 2008-11-16 10:15:56 UTC (rev 13120)
+++ cdk/branches/cdk-1.2.x/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java 2008-11-16 10:20:07 UTC (rev 13121)
@@ -166,7 +166,7 @@
* @return The test suite
*/
@Test
- public void testGetString_IMolecularFormula_arrayString() {
+ public void testGetString_IMolecularFormula_arrayString_boolean() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"), 2);
formula.addIsotope(builder.newIsotope("H"), 2);
@@ -176,7 +176,7 @@
newOrder[0] = "H";
newOrder[1] = "C";
- Assert.assertEquals("H2C2",MolecularFormulaManipulator.getString(formula,newOrder));
+ Assert.assertEquals("H2C2",MolecularFormulaManipulator.getString(formula,newOrder,true));
}
/**
@@ -253,7 +253,19 @@
Assert.assertEquals("CH4", MolecularFormulaManipulator.getString(mf1));
}
+ /**
+ *
+ */
@Test
+ public void testGetString_IMolecularFormula_boolean() {
+ IMolecularFormula mf1 = new MolecularFormula();
+ mf1.addIsotope(builder.newIsotope("C"), 1);
+ mf1.addIsotope(builder.newIsotope("H"), 4);
+
+ Assert.assertEquals("C1H4", MolecularFormulaManipulator.getString(mf1,true));
+ }
+
+ @Test
public void testGetString_Isotopes() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C",12),9);
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