Removed a bunch of unused local variables (PMD reports)

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Aug 30, 2014 · e6bf941 · e6bf941
1 parent fb8b0d2
commit e6bf941
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Showing 12 changed files with 2,880 additions and 2,914 deletions.
diff --git a/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java b/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
@@ -479,7 +479,6 @@ && getIfBondIsNotRotatable(
         }
 
         // Variables
-		double distance;
 		double sum;
 		double smooth = -20;
 		double partial;
@@ -501,7 +500,6 @@ && getIfBondIsNotRotatable(
 			IAtom cycloexBondAtom0;
 			IAtom cycloexBondAtom1;
 			IBond theInCycloexBond;
-			distance = 0;
 			limitInf = 0;
 			limitSup = Math.PI;
 			step = (limitSup - limitInf) / 13;
@@ -510,7 +508,6 @@ && getIfBondIsNotRotatable(
 			angle = 0;
 			int ya_counter = 0;
 			List<IAtom> connAtoms;
-			int counter = 0;
 			for (double g3r = 0; g3r < limitSup; g3r = g3r + step) {
 				sum = 0;
                 for (Integer aBondsInCycloex : bondsInCycloex) {
@@ -561,7 +558,6 @@ && getIfBondIsNotRotatable(
                 // g3r_function.add(new Double(sum));
 				rdfProtonCalculatedValues.add(sum);
 				logger.debug("RDF g3r prob.: "+sum+ " at distance "+g3r);
-				counter++;
 			}
 		}
 		else {

diff --git a/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java b/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
@@ -387,7 +387,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 
 ///////////////////////THE FIRST CALCULATED DESCRIPTOR IS g(H)r	 WITH PARTIAL CHARGES:		
 		if(atoms.size() > 0) {
-			int counter = 0;
 			for(double ghr = limitInf; ghr < limitSup; ghr = ghr + step) {
 				sum = 0;
                 for (Object atom1 : atoms) {
@@ -403,7 +402,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
                 rdfProtonCalculatedValues.add(sum);
 
 				logger.debug("RDF gr distance prob.: "+sum+ " at distance "+ghr);				
-				counter++;
 			}
 		}
 		else {
@@ -509,7 +507,6 @@ private int getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bon
         double[] values;
         double distance = 0;
         IAtom atom0 = bond.getAtom(0);
-        IAtom atom1 = bond.getAtom(1);
         List<IBond> bondsAtLeft = mol.getConnectedBondsList(atom0);
         int partial;
         for (int i = 0; i < bondsAtLeft.size(); i++) {

diff --git a/.../main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java b/.../main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
@@ -396,7 +396,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 
 	if(atoms.size() > 0) {
 		//ArrayList gHr_topol_function = new ArrayList(15);
-		int counter = 0;
         ShortestPaths shortestPaths = new ShortestPaths(mol, startVertex);
 		for(double ghrt = limitInf; ghrt < limitSup; ghrt = ghrt + step) {  
 			sum = 0;
@@ -416,7 +415,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 			//gHr_topol_function.add(new Double(sum));
 			rdfProtonCalculatedValues.add(sum);
 			logger.debug("RDF gr-topol distance prob.: "+sum+ " at distance "+ghrt);
-			counter++;
 		}
 	}
 	else {
@@ -525,7 +523,6 @@ private int getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bon
         double[] values;
         double distance = 0;
         IAtom atom0 = bond.getAtom(0);
-        IAtom atom1 = bond.getAtom(1);
         List<IBond> bondsAtLeft = mol.getConnectedBondsList(atom0);
         int partial;
         for (int i = 0; i < bondsAtLeft.size(); i++) {

diff --git a/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java b/...ic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
@@ -371,7 +371,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 
         //Variables
         double[] values; // for storage of results of other methods
-        double distance;
         double sum;
         double smooth = -20;
         double partial;
@@ -394,14 +393,12 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 		double dist1;
 		IAtom singleBondAtom0;
 		IAtom singleBondAtom1;
-		distance = 0;
 		position = 0;
 		IBond theSingleBond = null;
 		limitInf = 0;
 		limitSup = Math.PI / 2;
 		step = (limitSup - limitInf)/7;
 		smooth = -1.15;
-		int counter = 0;
 		for(double ghs = 0; ghs < limitSup; ghs = ghs + step) {
 			sum = 0;
 			for( int sing = 0; sing < singles.size(); sing++ ) {
@@ -433,7 +430,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRing
 			//gSr_function.add(new Double(sum));
 			rdfProtonCalculatedValues.add(sum);
 			logger.debug("RDF gSr prob.: " + sum +  " at distance " + ghs);
-			counter++;
 		}
 	}
 	else {