Updated molecular formula to use the new equals method from Isotope. …

…This methods checks for equality of two instances using symbol, mass num, exact mass and natural abundance
cdk · Oct 17, 2010 · e280bc2 · e280bc2
1 parent 4945c3f
commit e280bc2
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Showing 2 changed files with 14 additions and 81 deletions.
diff --git a/src/main/org/openscience/cdk/formula/MolecularFormula.java b/src/main/org/openscience/cdk/formula/MolecularFormula.java
@@ -23,20 +23,18 @@
  */
 package org.openscience.cdk.formula;
 
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.List;
-import java.util.ArrayList;
-
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecularFormula;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
+
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
 /**
  * Class defining a molecular formula object. It maintains
  * a list of list {@link IIsotope}.
@@ -120,20 +118,11 @@ public IMolecularFormula addIsotope(IIsotope isotope) {
 	 */
     @TestMethod("testAddIsotope_IIsotope_int")
 	public IMolecularFormula addIsotope(IIsotope isotope, int count) {
-		boolean flag = false;
-		for (IIsotope thisIsotope : isotopes.keySet()) {
-            System.out.println("thisIsotope = " + thisIsotope);
-			if(isTheSame(isotope, thisIsotope)){
-				isotopes.put(thisIsotope, isotopes.get(thisIsotope) + count);
-				flag = true;
-				break;
-			}
-		}
-		if(!flag){
-            System.out.println("Saw "+isotope.getSymbol()+" for first time with count = "+count);
-			isotopes.put(isotope, count);
-		}
-
+        if (isotopes.containsKey(isotope)) {
+            isotopes.put(isotope, isotopes.get(isotope) + count);
+        } else {
+            isotopes.put(isotope, count);
+        }
 		return this;
 	}
 
@@ -147,12 +136,7 @@ public IMolecularFormula addIsotope(IIsotope isotope, int count) {
 	 */
     @TestMethod("testContains_IIsotope")
 	public boolean contains(IIsotope isotope) {
-		for (IIsotope thisIsotope : isotopes()) {
-			if(isTheSame(thisIsotope, isotope)){
-				return true;
-			}
-		}
-		return false;
+        return isotopes.containsKey(isotope);
 	}
 
 	/**
@@ -204,7 +188,7 @@ public int getIsotopeCount() {
 	 */
 	private IIsotope getIsotope(IIsotope isotope){
 		for (IIsotope thisIsotope : isotopes()) {
-			if(isTheSame(isotope,thisIsotope))
+			if(isotope.equals(thisIsotope))
 				return thisIsotope;
 		}
 		return null;
@@ -371,34 +355,6 @@ public void setProperties(Map<Object, Object> properties){
 			lazyProperties().put(key, properties.get(key));
 		}
 	}
-	/**
-	 * Compare to IIsotope. The method doesn't compare instance but if they
-	 * have the same symbol, natural abundance and exact mass.
-	 * 
-	 * @param isotopeOne   The first Isotope to compare
-	 * @param isotopeTwo   The second Isotope to compare
-	 * @return             True, if both isotope are the same
-	 */
-    @TestMethod("testIsTheSame")
-	protected boolean isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) {
-
-        Double natAbund1 = isotopeOne.getNaturalAbundance();
-        Double natAbund2 = isotopeTwo.getNaturalAbundance();
-
-        Double exactMass1 = isotopeOne.getExactMass();
-        Double exactMass2 = isotopeTwo.getExactMass();
-
-        if (natAbund1 == null) natAbund1 = -1.0;
-        if (natAbund2 == null) natAbund2 = -1.0;
-        if (exactMass1 == null) exactMass1 = -1.0;
-        if (exactMass2 == null) exactMass2 = -1.0;
-
-		if(!isotopeOne.getSymbol().equals(isotopeTwo.getSymbol() ))
-			return false;
-		if(natAbund1.doubleValue() != natAbund2.doubleValue())
-			return false;
-		return exactMass1.doubleValue() == exactMass2.doubleValue();
-	}
 
     public IChemObjectBuilder getBuilder() {
         return DefaultChemObjectBuilder.getInstance();

diff --git a/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java b/src/test/org/openscience/cdk/formula/MolecularFormulaTest.java
@@ -24,14 +24,11 @@
  */
 package org.openscience.cdk.formula;
 
-import java.io.IOException;
-
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.interfaces.AbstractMolecularFormulaTest;
-import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 
 /**
@@ -57,25 +54,5 @@ public void testMolecularFormula() {
 
         IMolecularFormula mf = getBuilder().newInstance(IMolecularFormula.class);
     	Assert.assertNotNull(mf);
-    }
-
-    @Test
-    public void testIsTheSame_IIsotope_IIsotope() throws IOException {
-        MolecularFormula mf = new MolecularFormula();
-        IIsotope carb = getBuilder().newInstance(IIsotope.class,"C");
-        IIsotope anotherCarb = getBuilder().newInstance(IIsotope.class,"C");
-        IIsotope h = getBuilder().newInstance(IIsotope.class,"H");
-
-        carb.setExactMass(12.0);
-        anotherCarb.setExactMass(12.0);
-        h.setExactMass(1.0);
-
-        carb.setNaturalAbundance(34.0);
-        anotherCarb.setNaturalAbundance(34.0);
-        h.setNaturalAbundance(99.0);
-
-        Assert.assertTrue(mf.isTheSame(carb, carb));
-        Assert.assertTrue(mf.isTheSame(carb, anotherCarb));
-        Assert.assertFalse(mf.isTheSame(carb, h));
-    }
+    }  
 }