cleanup continued; core and structure unit tests still pass, other modules untested

me · me · commit 031f84bddbf0 · 2020-03-07T16:39:03.000-05:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
@@ -417,7 +417,7 @@ private String readLine(boolean ignoreLF) throws IOException {
 	public String readLine() throws IOException {
 		String line = readLine(false);
 		if (line != null) {
-			bytesRead = bytesRead + line.length();
+			bytesRead += line.length();
 		}
 		return line;
 	}
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/FuzzyPoint.java
@@ -70,11 +70,14 @@ public FuzzyPoint(int minPoint, int maxPoint, Resolver<FuzzyPoint> resolver, boo
 	}
 
 	@Override
-	public Integer getPosition() {
-		if(super.getPosition() == -1) {
-			super.setPosition(getResolver().resolve(this));
-		}
-		return super.getPosition();
+	public int getPosition() {
+		int prevPos = super.getPosition();
+		if(prevPos == -1) {
+			int nextPos = getResolver().resolve(this);
+			super.setPosition(nextPos);
+			return nextPos;
+		} else
+			return prevPos;
 	}
 
 	protected Integer getMax() {
@@ -106,6 +109,7 @@ public Point offset(int distance) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			FuzzyPoint p = (FuzzyPoint) obj;
@@ -130,6 +134,7 @@ public int hashCode() {
 
 	@Override
 	public int compareTo(Point point) {
+		if (this == point) return 0;
 		//If we can assign this to a FuzzyPoint then work with a bit more info
 		if(FuzzyPoint.class.isAssignableFrom(point.getClass())) {
 			FuzzyPoint fuzzy = (FuzzyPoint)point;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java
@@ -56,7 +56,7 @@ public SimplePoint(int position, boolean unknown, boolean uncertain) {
 	}
 
 	@Override
-	public Integer getPosition() {
+	public int getPosition() {
 		return position;
 	}
 
@@ -100,6 +100,7 @@ protected int reverse(int position, int length) {
 
 	@Override
 	public boolean equals(Object obj) {
+		if (this == obj) return true;
 		boolean equals = false;
 		if (Equals.classEqual(this, obj)) {
 			SimplePoint p = (SimplePoint) obj;
@@ -125,8 +126,9 @@ public String toString() {
 	}
 
 	@Override
-	public int compareTo(Point o) {
-		return getPosition().compareTo(o.getPosition());
+	public int compareTo(Point point) {
+		if (this == point) return 0;
+		return Integer.compare(getPosition(), point.getPosition());
 	}
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Point.java
@@ -36,7 +36,7 @@ interface Resolver<T extends Point> {
 	/**
 	 * Returns the position held by this object
 	 */
-	Integer getPosition();
+	int getPosition();
 
 	/**
 	 * Returns true if the current position is unknown but is
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java
@@ -166,7 +166,7 @@ public boolean isValidSequence(Sequence<C> sequence) {
 
 
 	@Override
-public List<C> getAllCompounds() {
+	public List<C> getAllCompounds() {
 		return new ArrayList<>(charSeqToCompound.values());
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
@@ -45,7 +45,7 @@ protected void addNucleotideCompound(String base, String complement, String... e
 		C upper = newNucleotideCompound(base.toUpperCase(), complement.toUpperCase(), upperEquivalents);
 		C lower = newNucleotideCompound(base.toLowerCase(), complement.toLowerCase(), lowerEquivalents);
 
-		List<C> equivalentCompounds = new ArrayList<>();
+		List<C> equivalentCompounds = new ArrayList<>(equivalents.length*2);
 
 		for(int i=0; i<equivalents.length; i++) {
 			equivalentCompounds.add(getCompoundForString(upperEquivalents[i]));
@@ -68,9 +68,8 @@ protected void calculateIndirectAmbiguities() {
 
 		List<NucleotideCompound> ambiguousCompounds = new ArrayList<>();
 		for(NucleotideCompound compound: getAllCompounds()) {
-			if (!compound.isAmbiguous()) {
+			if (!compound.isAmbiguous())
 				continue;
-			}
 			ambiguousCompounds.add(compound);
 		}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -35,6 +35,7 @@
 import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
 import org.biojava.nbio.core.sequence.location.SequenceLocation;
 import org.biojava.nbio.core.sequence.location.SimpleLocation;
+import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
 import org.biojava.nbio.core.sequence.location.template.Location;
 import org.biojava.nbio.core.sequence.reference.AbstractReference;
 import org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader;
@@ -126,7 +127,7 @@ public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
 
 		if (proxyLoader instanceof FeatureRetriever) {
 			this.setFeatureRetriever((FeatureRetriever) sequenceStorage);
-			HashMap<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
+			Map<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
 			for (ArrayList<AbstractFeature> abstractFeatures : ff.values()){
 				for (AbstractFeature f: abstractFeatures){
 					this.addFeature(f);
@@ -153,11 +154,7 @@ public SequenceReader<C> getProxySequenceReader() {
 	 * @return the bioBegin
 	 */
 	public Integer getBioBegin() {
-		if (bioBegin == null) {
-			return 1;
-		} else {
-			return bioBegin;
-		}
+		return bioBegin == null ? 1 : bioBegin;
 	}
 
 	/**
@@ -171,11 +168,7 @@ public void setBioBegin(Integer bioBegin) {
 	 * @return the bioEnd
 	 */
 	public Integer getBioEnd() {
-		if (bioEnd == null) {
-			return this.getLength();
-		} else {
-			return bioEnd;
-		}
+		return bioEnd == null ? this.getLength() : bioEnd;
 	}
 
 	/**
@@ -265,13 +258,10 @@ public void setParentSequence(AbstractSequence<?> parentSequence) {
 	 * @return the source
 	 */
 	public String getSource() {
-		if (source != null) {
+		if (source != null)
 			return source;
-		}
-		if (parentSequence != null) {
-			return parentSequence.getSource();
-		}
-		return null;
+		else
+			return parentSequence != null ? parentSequence.getSource() : null;
 	}
 
 	/**
@@ -353,7 +343,8 @@ public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(String feature
 		List<FeatureInterface<AbstractSequence<C>, C>> features = getFeaturesByType(featureType);
 		if (features != null) {
 			for (FeatureInterface<AbstractSequence<C>, C> feature : features) {
-				if (bioSequencePosition >= feature.getLocations().getStart().getPosition() && bioSequencePosition <= feature.getLocations().getEnd().getPosition()) {
+				AbstractLocation locs = feature.getLocations();
+				if (bioSequencePosition >= locs.getStart().getPosition() && bioSequencePosition <= locs.getEnd().getPosition()) {
 					featureHits.add(feature);
 				}
 			}
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
@@ -117,9 +117,9 @@ public void testGetAlignmentIndexAtOutOfBounds4() {
 
 	@Test
 	public void testGetEnd() {
-		assertEquals(global.getEnd().getPosition(), Integer.valueOf(6));
-		assertEquals(local.getEnd().getPosition(), Integer.valueOf(8));
-		assertEquals(local2.getEnd().getPosition(), Integer.valueOf(3));
+		assertEquals(6, global.getEnd().getPosition());
+		assertEquals(8, local.getEnd().getPosition());
+		assertEquals(3, local2.getEnd().getPosition());
 	}
 
 	@Test
@@ -211,9 +211,9 @@ public void testGetSequenceIndexAtOutOfBounds4() {
 
 	@Test
 	public void testGetStart() {
-		assertEquals(global.getStart().getPosition(), Integer.valueOf(2));
-		assertEquals(local.getStart().getPosition(), Integer.valueOf(1));
-		assertEquals(local2.getStart().getPosition(), Integer.valueOf(1));
+		assertEquals(2, global.getStart().getPosition());
+		assertEquals(1, local.getStart().getPosition());
+		assertEquals(1, local2.getStart().getPosition());
 	}
 
 	@Test
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java
@@ -222,12 +222,11 @@ public void testCreateVirtualCBAtom(){
 
 		if ( g1.getPDBName().equals("GLY")){
 			if ( g1 instanceof AminoAcid){
-				try {
-					Atom cb = Calc.createVirtualCBAtom((AminoAcid)g1);
-					g1.addAtom(cb);
-				} catch (StructureException e){
-					fail ("createVirtualCBAtom failed with " + e.getMessage());
-				}
+//				try {
+				g1.addAtom(Calc.createVirtualCBAtom((AminoAcid)g1));
+//				} catch (StructureException e){
+//					fail ("createVirtualCBAtom failed with " + e.getMessage());
+//				}
 			}
 		} else {
 			fail("the group at position 11 is not a GLY!");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -76,7 +76,7 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
 
 	private MultipleAlignment multAln;
 	private List<Atom[]> transformedAtoms;
-	private final JCheckBox colorByBlocks;
+	private JCheckBox colorByBlocks;
 	private final List<JCheckBox> selectedStructures;
 
 	private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java
@@ -325,7 +325,7 @@ public void windowClosing(WindowEvent e) {
 
 	@Override
 	protected void initCoords() {
-		try {
+//		try {
 			if (ca1 == null || ca2 == null) {
 				if (structure != null)
 					setStructure(structure);
@@ -342,9 +342,9 @@ protected void initCoords() {
 			header.setTitle(title);
 			artificial.setPDBHeader(header);
 			setStructure(artificial);
-		} catch (StructureException e) {
-			e.printStackTrace();
-		}
+//		} catch (StructureException e) {
+//			e.printStackTrace();
+//		}
 	}
 
 	@Override
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
@@ -82,7 +82,7 @@ public void actionPerformed(ActionEvent ae) {
 
 					break;
 				}
-				case "Optimal Self Alignment":
+				case "Optimal Self Alignment": {
 					Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
 					AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
 							symm.getSelfAlignment(), symm.getAtoms(), cloned);
@@ -91,14 +91,12 @@ public void actionPerformed(ActionEvent ae) {
 					jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
 
 					break;
+				}
 				case "Show Symmetry Group":
-					String script = SymmetryDisplay.printSymmetryGroup(symm);
-					jmol.evalString(script);
-
+					jmol.evalString(SymmetryDisplay.printSymmetryGroup(symm));
 					break;
 				case "Show Symmetry Axes": {
-					String s = SymmetryDisplay.printSymmetryAxes(symm);
-					jmol.evalString(s);
+					jmol.evalString(SymmetryDisplay.printSymmetryAxes(symm));
 					break;
 				}
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -75,7 +75,7 @@ public class SubstructureIdentifier implements StructureIdentifier {
 	private static final Logger logger = LoggerFactory.getLogger(SubstructureIdentifier.class);
 
 
-	private final String pdbId;
+	public final String pdbId;
 	private final List<ResidueRange> ranges;
 
 	/**
@@ -290,10 +290,8 @@ public Structure reduce(Structure s) throws StructureException {
 	 */
 	@Override
 	public Structure loadStructure(AtomCache cache) throws IOException, StructureException {
-		String pdb = getPdbId();
-		if(pdb == null)
-			return null;
-		return cache.getStructureForPdbId(pdb);
+		String pdb = pdbId;
+		return pdb == null ? null : cache.getStructureForPdbId(pdb);
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -308,7 +308,7 @@ private boolean initFromPDB(String suffix) {
 		SubstructureIdentifier si = new SubstructureIdentifier(suffix);
 		base = si; // Safe to realize immediately
 
-		pdbId = si.getPdbId();
+        pdbId = si.pdbId;
 		// Set chainName if unique
 		Set<String> chains = getChainNames(si);
 		if(chains.size() == 1) {
@@ -361,7 +361,7 @@ private static Set<String> getChainNames(SubstructureIdentifier si) {
 	 */
 	public String getPdbId() throws StructureException {
 		if( pdbId == null) {
-			pdbId = toCanonical().getPdbId();
+            pdbId = toCanonical().pdbId;
 		}
 		return pdbId;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -173,7 +173,8 @@ public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 		calculationTime = afp.getCalculationTime();
 
 		MultipleAlignment msa = new MultipleAlignmentImpl(this);
-		setMultipleAlignments(Collections.singletonList(msa));
+		ArrayList<MultipleAlignment> ms1 = new ArrayList<>(1); ms1.add(msa);
+		setMultipleAlignments(ms1);
 
 		// Convert the rotation and translation to a Matrix4D and set it
 		Matrix4d ident = new Matrix4d();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -326,7 +326,7 @@ public static String to3DFormat(MultipleAlignment alignment,
 		StructureIdentifier tName = alignment.getEnsemble().getStructureIdentifiers()
 				.get(templateIndex);
 		SubstructureIdentifier canon = tName.toCanonical();
-		String tPdbId = canon.getPdbId();
+        String tPdbId = canon.pdbId;
 		String tChain = null;
 		for(ResidueRange range : canon.getResidueRanges()) {
 			tChain = range.getChainName();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDPDomain.java
@@ -56,8 +56,8 @@ public String getIdentifier() {
 	}
 
 	public String getPdbId() {
-		return canonical.getPdbId();
-	}
+        return canonical.pdbId;
+    }
 
 	@Override
 	public SubstructureIdentifier toCanonical() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/RemotePDPProvider.java
@@ -196,9 +196,9 @@ public PDPDomain getPDPDomain(String pdpDomainName) throws IOException{
 		List<ResidueRange> ranges = new ArrayList<>();
 		for(String domainRange : domainRanges) {
 			SubstructureIdentifier strucId = new SubstructureIdentifier(domainRange);
-			if(pdbId == null) {
-				pdbId = strucId.getPdbId();
-			} else if(!pdbId.equals(strucId.getPdbId())) {
+            if(pdbId == null) {
+                pdbId = strucId.pdbId;
+			} else if(!pdbId.equals(strucId.pdbId)) {
 				// should never happen with correct server implementation
 				throw new RuntimeException("Don't know how to take the union of domains from multiple PDB IDs.");
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java

Original file line number	Diff line number	Diff line change
`@@ -417,7 +417,7 @@ private String readLine(boolean ignoreLF) throws IOException {`
`417`	`417`	`public String readLine() throws IOException {`
`418`	`418`	`String line = readLine(false);`
`419`	`419`	`if (line != null) {`
`420`		`- bytesRead = bytesRead + line.length();`
	`420`	`+ bytesRead += line.length();`
`421`	`421`	`}`
`422`	`422`	`return line;`
`423`	`423`	`}`
Original file line number	Diff line number	Diff line change
`@@ -56,7 +56,7 @@ public SimplePoint(int position, boolean unknown, boolean uncertain) {`
`56`	`56`	`}`
`57`	`57`
`58`	`58`	`@Override`
`59`		`- public Integer getPosition() {`
	`59`	`+ public int getPosition() {`
`60`	`60`	`return position;`
`61`	`61`	`}`
`62`	`62`
`@@ -100,6 +100,7 @@ protected int reverse(int position, int length) {`
`100`	`100`
`101`	`101`	`@Override`
`102`	`102`	`public boolean equals(Object obj) {`
	`103`	`+ if (this == obj) return true;`
`103`	`104`	`boolean equals = false;`
`104`	`105`	`if (Equals.classEqual(this, obj)) {`
`105`	`106`	`SimplePoint p = (SimplePoint) obj;`
`@@ -125,8 +126,9 @@ public String toString() {`
`125`	`126`	`}`
`126`	`127`
`127`	`128`	`@Override`
`128`		`- public int compareTo(Point o) {`
`129`		`- return getPosition().compareTo(o.getPosition());`
	`129`	`+ public int compareTo(Point point) {`
	`130`	`+ if (this == point) return 0;`
	`131`	`+ return Integer.compare(getPosition(), point.getPosition());`
`130`	`132`	`}`
`131`	`133`
`132`	`134`	`@Override`
Original file line number	Diff line number	Diff line change
`@@ -166,7 +166,7 @@ public boolean isValidSequence(Sequence<C> sequence) {`
`166`	`166`
`167`	`167`
`168`	`168`	`@Override`
`169`		`-public List<C> getAllCompounds() {`
	`169`	`+ public List<C> getAllCompounds() {`
`170`	`170`	`return new ArrayList<>(charSeqToCompound.values());`
`171`	`171`	`}`
`172`	`172`