Simplified boolean expressions.

rthornton · rthornton · commit fb30b9ab5d45 · 2012-01-16T11:38:35.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9503 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java b/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java
@@ -66,7 +66,7 @@ public double getMolecularWeight(ProteinSequence sequence) {
 	@Override
 	public double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException {
 		File elementMassFile = new File("./src/main/resources/ElementMass.xml");
-		if(elementMassFile.exists() == false){
+		if(!elementMassFile.exists()){
 			throw new FileNotFoundException("Cannot locate ElementMass.xml. " +
 					"Please use getMolecularWeight(ProteinSequence, File, File) to specify ElementMass.xml location.");
 		}
@@ -99,7 +99,7 @@ public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCo
 	public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) 
 		throws JAXBException, FileNotFoundException{
 		File elementMassFile = new File("./src/main/resources/ElementMass.xml");
-		if(elementMassFile.exists() == false){
+		if(!elementMassFile.exists()){
 			throw new FileNotFoundException("Cannot locate ElementMass.xml. " +
 					"Please use getMolecularWeight(ProteinSequence, File, File) to specify ElementMass.xml location.");
 		}
@@ -140,7 +140,7 @@ public double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeC
 		Map<AminoAcidCompound, Integer> extinctAA2Count = this.getExtinctAACount(sequence);
 		
 		double eProt;
-		if(assumeCysReduced == false){
+		if(!assumeCysReduced){
 			eProt = extinctAA2Count.get(aaSet.getCompoundForString("Y")) * 
 				Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("Y")) + 
 				extinctAA2Count.get(aaSet.getCompoundForString("W")) * 
diff --git a/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Utils.java b/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/Utils.java
@@ -44,7 +44,7 @@ public final static double roundToDecimals(double d, int c) {
 	 */
 	public final static boolean doesSequenceContainInvalidChar(String sequence, Set<Character> cSet){
 		for(char c:sequence.toCharArray()){
-			if(cSet.contains(c) == false) return true;
+			if(!cSet.contains(c)) return true;
 		}
 		return false;
 	}
@@ -68,7 +68,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set<Character> c
 		else cArray = sequence.toCharArray();
 		if(cSet == null) cSet = PeptideProperties.standardAASet;
 		for(char c:cArray){
-			if(cSet.contains(c) == false) total++;
+			if(!cSet.contains(c)) total++;
 		}
 		return total;
 	}
@@ -89,7 +89,7 @@ public final static String cleanSequence(String sequence, Set<Character> cSet){
 		String cleanSeq = "";
 		if(cSet == null) cSet = PeptideProperties.standardAASet; 
 		for(char c:sequence.toCharArray()){
-			if(cSet.contains(c) == false){
+			if(!cSet.contains(c)){
 				cleanSeq += "-";
 				invalidCharSet.add(c);
 			}else{
diff --git a/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
@@ -128,7 +128,7 @@ public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet() {
 
     public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
         Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);
-        return (equivalents == null) ? false : equivalents.contains(compoundTwo);
+        return (equivalents != null) && equivalents.contains(compoundTwo);
     }
 
     public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AminoAcidCompoundSet.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/compound/AminoAcidCompoundSet.java
@@ -133,7 +133,7 @@ public static AminoAcidCompoundSet getAminoAcidCompoundSet() {
 
     public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
         Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);
-        return (equivalents == null) ? false : equivalents.contains(compoundTwo);
+        return (equivalents != null) && equivalents.contains(compoundTwo);
     }
 
     public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/io/FastaReaderHelper.java
@@ -49,7 +49,7 @@ public class FastaReaderHelper {
      * @throws Exception
      */
     public static LinkedHashMap<String, DNASequence> readFastaDNASequence(File file, boolean lazySequenceLoad) throws Exception {
-        if (lazySequenceLoad == false) {
+        if (!lazySequenceLoad) {
             return readFastaDNASequence(file);
         }
 
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/io/GenericFastaHeaderParser.java
@@ -76,7 +76,7 @@ private String[] getHeaderValues(String header) {
     //        System.out.println("accession=" + data[0]);
         //    return data;
         //} else
-         if (header.startsWith("PDB:") == false) {
+         if (!header.startsWith("PDB:")) {
             for (int i = 0; i < header.length(); i++) {
                 if (header.charAt(i) == '|') {
                     values.add(sb.toString());
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/SequenceFileProxyLoader.java
@@ -148,7 +148,7 @@ public int getLength() {
      * @return
      */
     public C getCompoundAt(int position) {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return this.parsedCompounds.get(position - 1);
@@ -160,7 +160,7 @@ public C getCompoundAt(int position) {
      * @return
      */
     public int getIndexOf(C compound) {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return this.parsedCompounds.indexOf(compound) + 1;
@@ -172,7 +172,7 @@ public int getIndexOf(C compound) {
      * @return
      */
     public int getLastIndexOf(C compound) {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return this.parsedCompounds.lastIndexOf(compound) + 1;
@@ -183,7 +183,7 @@ public int getLastIndexOf(C compound) {
      * @return
      */
     public String toString() {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return getSequenceAsString();
@@ -206,7 +206,7 @@ public String getSequenceAsString() {
      */
     public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand) {
 
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         SequenceAsStringHelper<C> sequenceAsStringHelper = new SequenceAsStringHelper<C>();
@@ -218,7 +218,7 @@ public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand stran
      * @return
      */
     public List<C> getAsList() {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return this.parsedCompounds;
@@ -232,7 +232,7 @@ public List<C> getAsList() {
      * @return
      */
     public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioEnd) {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return new SequenceProxyView<C>(SequenceFileProxyLoader.this, bioBegin, bioEnd);
@@ -243,7 +243,7 @@ public SequenceView<C> getSubSequence(final Integer bioBegin, final Integer bioE
      * @return
      */
     public Iterator<C> iterator() {
-        if (this.isInitialized() == false) {
+        if (!this.isInitialized()) {
             init();
         }
         return this.parsedCompounds.iterator();
diff --git a/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java b/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/UniprotProxySequenceReader.java
@@ -375,7 +375,7 @@ public static String getUniprotDirectoryCache() {
      */
     public static void setUniprotDirectoryCache(String aUniprotDirectoryCache) {
         File f = new File(aUniprotDirectoryCache);
-        if (f.exists() == false) {
+        if (!f.exists()) {
             f.mkdirs();
         }
         uniprotDirectoryCache = aUniprotDirectoryCache;
diff --git a/biojava3-core/src/main/java/org/biojava3/core/util/PrettyXMLWriter.java b/biojava3-core/src/main/java/org/biojava3/core/util/PrettyXMLWriter.java
@@ -59,7 +59,7 @@ public void declareNamespace(String nsURI, String prefixHint)
         throws IOException
     {
         if (!namespacePrefixes.containsKey(nsURI)) {
-            if (isOpeningTag == true) {
+            if (isOpeningTag) {
                 String prefix = allocPrefix(nsURI);
                 attribute("xmlns:" + prefix, nsURI);
             } else {
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/homology/GFF3FromUniprotBlastHits.java b/biojava3-genome/src/main/java/org/biojava3/genome/homology/GFF3FromUniprotBlastHits.java
@@ -83,7 +83,7 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap
                     for (ProteinSequence cdsProteinSequence : cdsProteinList) {
                         testSequence = testSequence + cdsProteinSequence.getSequenceAsString();
                     }
-                    if (testSequence.equals(predictedProteinSequence) == false && (predictedProteinSequence.equals(testSequence.substring(0, testSequence.length() - 1)) == false)) {
+                    if (!testSequence.equals(predictedProteinSequence) && (!predictedProteinSequence.equals(testSequence.substring(0, testSequence.length() - 1)))) {
                         DNASequence codingSequence = transcriptSequence.getDNACodingSequence();
                         System.out.println(codingSequence.getSequenceAsString());
                         System.out.println("Sequence agreement error");
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/query/OutputHitsGFF.java b/biojava3-genome/src/main/java/org/biojava3/genome/query/OutputHitsGFF.java
@@ -29,10 +29,10 @@ public void process(File blastXMLFile, File gffFile, File gffOutputFile, double
             FeatureList gene = listGenes.selectByAttribute("gene_id", gene_id);
             for (FeatureI geneFeature : gene) {
 
-                if (includeNegativeStrand == false && geneFeature.location().isNegative()) {
+                if (!includeNegativeStrand && geneFeature.location().isNegative()) {
                     continue;
                 }
-                if (includeFrameShift == false) {
+                if (!includeFrameShift) {
                     boolean frameShift = false;
                     FeatureList cdsList = gene.selectByType("CDS");
                     for(FeatureI cdsFeature : cdsList){
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/uniprot/UniprotToFasta.java b/biojava3-genome/src/main/java/org/biojava3/genome/uniprot/UniprotToFasta.java
@@ -58,7 +58,7 @@ public void process( String uniprotDatFileName,String fastaFileName ) throws Exc
                     id = data[3];
                 }else if(line.startsWith("SQ")){
                     line = br.readLine();
-                    while(line.startsWith("//") == false){
+                    while(!line.startsWith("//")){
 
                         for(int i = 0; i < line.length(); i++){
                             char aa = line.charAt(i);
diff --git a/biojava3-genome/src/main/java/org/biojava3/genome/util/SplitFasta.java b/biojava3-genome/src/main/java/org/biojava3/genome/util/SplitFasta.java
@@ -20,7 +20,7 @@
 public class SplitFasta {
 
     public void processNucleotides(File fastaFileName,String uniqueid, File outputDirectory ) throws Exception{
-        if(outputDirectory.exists() == false)
+        if(!outputDirectory.exists())
             outputDirectory.mkdirs();
 
         LinkedHashMap<String,DNASequence> dnaSequenceHashMap = FastaReaderHelper.readFastaDNASequence(fastaFileName);
diff --git a/biojava3-phylo/src/main/java/org/biojava3/phylo/CheckTreeAccuracy.java b/biojava3-phylo/src/main/java/org/biojava3/phylo/CheckTreeAccuracy.java
@@ -87,15 +87,15 @@ public double getNodeDistance(PhylogenyNode parentNode, PhylogenyNode childNode)
     }
 
     public PhylogenyNode findCommonParent(PhylogenyNode node) {
-        while (node.getPathToParent() == false) {
+        while (!node.getPathToParent()) {
             node = node.getParent();
         }
         return node;
     }
 
     public void markPathToRoot(PhylogenyNode node, boolean value) {
         node.setPathToParent(value);
-        while (node.isRoot() == false) {
+        while (!node.isRoot()) {
             node = node.getParent();
             node.setPathToParent(value);
         }
diff --git a/biojava3-phylo/src/main/java/org/biojava3/phylo/ProgessListenerStub.java b/biojava3-phylo/src/main/java/org/biojava3/phylo/ProgessListenerStub.java
@@ -13,7 +13,7 @@
 public class ProgessListenerStub implements NJTreeProgressListener {
 String priorState = "";
     public void progress(Object njtree,String state, int percentageComplete) {
-        if(priorState.equals(state) == false){
+        if(!priorState.equals(state)){
             priorState = state;
             System.out.println();
         }
@@ -24,7 +24,7 @@ public void progress(Object njtree,String state, int percentageComplete) {
 
 
     public void progress(Object njtree,String state, int currentCount, int totalCount) {
-               if(priorState.equals(state) == false){
+        if (!priorState.equals(state)){
             priorState = state;
             System.out.println();
         }
diff --git a/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/SystemInfo.java b/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/SystemInfo.java
@@ -194,7 +194,7 @@ public void addOneSystemProperty(
           * are loaded into the property list. We toss them
           * to avoid confusion.
           */
-         if (propValue != null && name.equals(propValue) == false) {
+         if (propValue != null && !name.equals(propValue)) {
             append("<b>"+name + "</b>:");
             boolean isReadable = true;
             for (int i = 0; i < propValue.length(); i++) {
@@ -204,7 +204,7 @@ public void addOneSystemProperty(
                   break;
                }
             }
-            if (isReadable == false) {
+            if (!isReadable) {
                for (int i = 0; i < propValue.length(); i++) {
                   char    c   = propValue.charAt(i);
                   if (Character.isLetterOrDigit(c)) {
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CECalculator.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CECalculator.java
@@ -1820,7 +1820,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 			align_se2[lcmp]=jMax; 
 			lcmp++;
 
-			if(brk_flg[i][j]==true) {
+			if(brk_flg[i][j]) {
 				//System.out.println("hit break flag at: " + i + "  " + j + " sum " + sum_ret + " lcmp " + lcmp);				
 				break;
 
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeCalculatorEnhanced.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1889,7 +1889,7 @@ private double dpAlign(int nSeq1, int nSeq2, double gapI, double gapE,
 				prevGapEnd = alignmentPositionOrLength;
 			alignmentPositionOrLength++;
 
-			if(brk_flg[i][j]==true) {
+			if(brk_flg[i][j]) {
 				//System.out.println("hit break flag at: " + i + "  " + j + " sum " + sum_ret + " lcmp " + alignmentPositionOrLength);				
 				break;
 

Original file line number	Diff line number	Diff line change
`@@ -128,7 +128,7 @@ public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet() {`
`128`	`128`
`129`	`129`	`public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {`
`130`	`130`	`Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);`
`131`		`- return (equivalents == null) ? false : equivalents.contains(compoundTwo);`
	`131`	`+ return (equivalents != null) && equivalents.contains(compoundTwo);`
`132`	`132`	`}`
`133`	`133`
`134`	`134`	`public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {`
Original file line number	Diff line number	Diff line change
`@@ -133,7 +133,7 @@ public static AminoAcidCompoundSet getAminoAcidCompoundSet() {`
`133`	`133`
`134`	`134`	`public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {`
`135`	`135`	`Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);`
`136`		`- return (equivalents == null) ? false : equivalents.contains(compoundTwo);`
	`136`	`+ return (equivalents != null) && equivalents.contains(compoundTwo);`
`137`	`137`	`}`
`138`	`138`
`139`	`139`	`public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {`
Original file line number	Diff line number	Diff line change
`@@ -49,7 +49,7 @@ public class FastaReaderHelper {`
`49`	`49`	`* @throws Exception`
`50`	`50`	`*/`
`51`	`51`	`public static LinkedHashMap<String, DNASequence> readFastaDNASequence(File file, boolean lazySequenceLoad) throws Exception {`
`52`		`- if (lazySequenceLoad == false) {`
	`52`	`+ if (!lazySequenceLoad) {`
`53`	`53`	`return readFastaDNASequence(file);`
`54`	`54`	`}`
`55`	`55`
Original file line number	Diff line number	Diff line change
`@@ -375,7 +375,7 @@ public static String getUniprotDirectoryCache() {`
`375`	`375`	`*/`
`376`	`376`	`public static void setUniprotDirectoryCache(String aUniprotDirectoryCache) {`
`377`	`377`	`File f = new File(aUniprotDirectoryCache);`
`378`		`- if (f.exists() == false) {`
	`378`	`+ if (!f.exists()) {`
`379`	`379`	`f.mkdirs();`
`380`	`380`	`}`
`381`	`381`	`uniprotDirectoryCache = aUniprotDirectoryCache;`
Original file line number	Diff line number	Diff line change
`@@ -59,7 +59,7 @@ public void declareNamespace(String nsURI, String prefixHint)`
`59`	`59`	`throws IOException`
`60`	`60`	`{`
`61`	`61`	`if (!namespacePrefixes.containsKey(nsURI)) {`
`62`		`- if (isOpeningTag == true) {`
	`62`	`+ if (isOpeningTag) {`
`63`	`63`	`String prefix = allocPrefix(nsURI);`
`64`	`64`	`attribute("xmlns:" + prefix, nsURI);`
`65`	`65`	`} else {`
Original file line number	Diff line number	Diff line change
`@@ -83,7 +83,7 @@ public void process(LinkedHashMap<String, ArrayList<String>> hits, LinkedHashMap`
`83`	`83`	`for (ProteinSequence cdsProteinSequence : cdsProteinList) {`
`84`	`84`	`testSequence = testSequence + cdsProteinSequence.getSequenceAsString();`
`85`	`85`	`}`
`86`		`- if (testSequence.equals(predictedProteinSequence) == false && (predictedProteinSequence.equals(testSequence.substring(0, testSequence.length() - 1)) == false)) {`
	`86`	`+ if (!testSequence.equals(predictedProteinSequence) && (!predictedProteinSequence.equals(testSequence.substring(0, testSequence.length() - 1)))) {`
`87`	`87`	`DNASequence codingSequence = transcriptSequence.getDNACodingSequence();`
`88`	`88`	`System.out.println(codingSequence.getSequenceAsString());`
`89`	`89`	`System.out.println("Sequence agreement error");`