squid:S1197 - Array designators should be on the type, not the variable

Mohamed Ezzat · Mohamed Ezzat · commit 713171bb1c9f · 2016-06-04T17:29:38.000+02:00
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
@@ -322,7 +322,7 @@ private double getIsoelectricPointInnovagen(ProteinSequence sequence){
 	//
 	// Ct Nt Sm Sc Sn
 	//
-	private final double cPk[][] = {
+	private final double[][] cPk = {
 			{3.55, 7.59, 0.0},  // A
 			{3.55, 7.50, 0.0},  // B
 			{3.55, 7.50, 9.00}, // C
@@ -365,7 +365,7 @@ private double getIsoelectricPointExpasy(String sequence){
 		//
 		// Compute the amino-acid composition.
 		//
-		int comp[] = new int[26];
+		int[] comp = new int[26];
 		for(int i = 0; i < sequence.length(); i++){
 			int index = sequence.charAt(i) - 'A';
 			if(index < 0 || index >= 26) continue;
@@ -430,7 +430,7 @@ private double getNetChargeExpasy(String sequence, double pHPoint){
 		//
 		// Compute the amino-acid composition.
 		//
-		int comp[] = new int[26];
+		int[] comp = new int[26];
 		for(int i = 0; i < sequence.length(); i++){
 			int index = sequence.charAt(i) - 'A';
 			if(index < 0 || index >= 26) continue;
@@ -444,7 +444,7 @@ private double getNetChargeExpasy(String sequence, double pHPoint){
 		return getNetChargeExpasy(comp, nTermResidue, cTermResidue, pHPoint);
 	}
 
-	private double getNetChargeExpasy(int comp[], int nTermResidue, int cTermResidue, double ph){
+	private double getNetChargeExpasy(int[] comp, int nTermResidue, int cTermResidue, double ph){
 		double cter = 0.0;
 		if(cTermResidue >= 0 && cTermResidue < 26) cter = exp10(-cPk[cTermResidue][0]) / (exp10(-cPk[cTermResidue][0]) + exp10(-ph));
 		double nter = 0.0;
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
@@ -65,7 +65,7 @@
 public class BufferedReaderBytesRead extends Reader {
 
 	private Reader in;
-	private char cb[];
+	private char[] cb;
 	private int nChars, nextChar;
 	private static final int INVALIDATED = -2;
 	private static final int UNMARKED = -1;
@@ -150,7 +150,7 @@ private void fill() throws IOException {
 					dst = delta;
 				} else {
 					/* Reallocate buffer to accommodate read-ahead limit */
-					char ncb[] = new char[readAheadLimit];
+					char[] ncb = new char[readAheadLimit];
 					System.arraycopy(cb, markedChar, ncb, 0, delta);
 					cb = ncb;
 					markedChar = 0;
@@ -286,7 +286,7 @@ private int read1(char[] cbuf, int off, int len) throws IOException {
 	 * @exception  IOException  If an I/O error occurs
 	 */
 	@Override
-	public int read(char cbuf[], int off, int len) throws IOException {
+	public int read(char[] cbuf, int off, int len) throws IOException {
 		synchronized (lock) {
 			ensureOpen();
 			if ((off < 0) || (off > cbuf.length) || (len < 0)
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -130,7 +130,7 @@ public static LinkedHashMap<String, DNASequence> readFastaDNASequence(
 		return dnaSequences;
 	}
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		LinkedHashMap<String, DNASequence> dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("fasta.fna"));
 		for (DNASequence sequence : dnaSequences.values()) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -161,7 +161,7 @@ public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
 		return dnaSequences;
 	}
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(new File("src/test/resources/NM_000266.gb"), true);
 		for (DNASequence sequence : dnaSequences.values()) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -296,7 +296,7 @@ private Strand getGroupLocationStrand(List<Location> ll){
 		return returnStrand;
 	}
 
-	public static void main(String args[]){
+	public static void main(String[] args){
 		String[] testStrings = {
 			"J00194.1:100..202",
 			"A00001.5:34..45",
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
@@ -481,7 +481,7 @@ static public void uncompress( String fileInName, FileOutputStream out) throws I
 
 	private static final boolean debugTiming = false;
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 		if (args.length != 1) {
 			logger.info("Usage: UncompressInputStream <file>");
 			System.exit(1);
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -875,7 +875,7 @@ static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<Ch
 		return geneSequenceHashMap;
 	}
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 /*        if (false) {
 			LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneMarkGTF(new File("Scaffolds.fna"), new File("genemark_hmm.gtf"));
 			LinkedHashMap<String, ProteinSequence> proteinSequenceList = GeneFeatureHelper.getProteinSequences(chromosomeSequenceList.values());
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Feature.java
@@ -317,7 +317,7 @@ public String toString() {
 	 * @deprecated
 	 */
 	@Deprecated
-	public static void main(String args[])
+	public static void main(String[] args)
 			throws Exception {
 		//Feature f= new Feature();
 		//intentionally perverse
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java
@@ -488,7 +488,7 @@ public int compare(FeatureI a, FeatureI b) {
 	 * whose seqnames differ.
 	 */
 	public FeatureList sortByStart() {
-		FeatureI array[] = toArray(new FeatureI[1]);
+		FeatureI[] array = toArray(new FeatureI[1]);
 
 		Arrays.sort(array, new FeatureComparator());
 
@@ -501,7 +501,7 @@ public FeatureList sortByStart() {
 	 */
 	// FIXME features may have a null location() !!
 	@Deprecated
-	static public void main(String args[]) {
+	static public void main(String[] args) {
 	}
 
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java
@@ -170,7 +170,7 @@ private static Feature parseLine(String s) {
 
 
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 		long start = System.currentTimeMillis();
 		@SuppressWarnings("unused")
 		FeatureList listGenes = GFF3Reader.read("/home/melo/workspace/release/stdout.combined.checked2.gtf");
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -138,7 +138,7 @@ private String getGFF3Note(ArrayList<String> notesList) {
 		return notes;
 	}
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		if (true) {
 			FileOutputStream fo = new FileOutputStream("/Users/Scooter/scripps/dyadic/geneid/geneid/c1-geneid.gff3");//-16
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.java
@@ -202,7 +202,7 @@ private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
 	}
 
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		FeatureList listGenes = GeneIDGFF2Reader.read("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gtf");
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java
@@ -194,7 +194,7 @@ private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
 	}
  */
 
-	public static void main(String args[]) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		FeatureList listGenes = GeneMarkGTFReader.read("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/genemark_hmm.gtf");
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java
@@ -252,7 +252,7 @@ public void remove()
 	 * @deprecated
 	 */
 	@Deprecated
-	public static void main( String args[] )
+	public static void main(String[] args )
 	{
 
 		Location r= new Location( 10, 21 );
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -906,7 +906,7 @@ static private Location R( int s, int e )
 	 */
 	@Deprecated
 	@SuppressWarnings("unused")
-	public static void main( String args[] )
+	public static void main(String[] args )
 	throws Exception
 	{
 		Location p3_7= new Location( 3, 7 );
diff --git a/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java b/biojava-structure-gui/src/main/java/demo/DemoShowCATHDomain.java
@@ -40,7 +40,7 @@ public class DemoShowCATHDomain {
 	private static final String DEFAULT_SCRIPT ="select * ; cartoon on; spacefill off; wireframe off; select ligands; wireframe on; spacefill on;";
 	private static final String[] colors = new String[]{"red","green","blue","yellow"};
 
-	public static void main(String args[]){
+	public static void main(String[] args){
 
 		UserConfiguration config = new UserConfiguration();
 		config.setPdbFilePath("/tmp/");
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.java
@@ -121,8 +121,7 @@ public static void showDialog(){
 		vBox.add(instance);
 
 
-
-		UIManager.LookAndFeelInfo lookAndFeels[] = UIManager.getInstalledLookAndFeels();
+		UIManager.LookAndFeelInfo[] lookAndFeels = UIManager.getInstalledLookAndFeels();
 		JPanel panel = new JPanel();
 
 		for(int i = 0; i < lookAndFeels.length; i++){
@@ -219,7 +218,7 @@ public MyAction(JDialog dialog) {
 	public void actionPerformed(ActionEvent ae){
 		Object EventSource = ae.getSource();
 		String lookAndFeelClassName = null;
-		UIManager.LookAndFeelInfo looks[] = UIManager.getInstalledLookAndFeels();
+		UIManager.LookAndFeelInfo[] looks = UIManager.getInstalledLookAndFeels();
 		for(int i = 0; i < looks.length; i++){
 			if(ae.getActionCommand().equals(looks[i].getName())){
 				lookAndFeelClassName = looks[i].getClassName();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
@@ -115,7 +115,7 @@ public class Surface extends JPanel implements Runnable {
 		private Font font = new Font("Times New Roman", Font.PLAIN, 11);
 		private Runtime r = Runtime.getRuntime();
 		private int columnInc;
-		private int pts[];
+		private int[] pts;
 		private int ptNum;
 		private int ascent, descent;
 		//private float freeMemory, totalMemory;
@@ -234,7 +234,7 @@ public void paint(Graphics g) {
 				pts = new int[graphW];
 				ptNum = 0;
 			} else if (pts.length != graphW) {
-				int tmp[] = null;
+				int[] tmp = null;
 				if (ptNum < graphW) {
 					tmp = new int[ptNum];
 					System.arraycopy(pts, 0, tmp, 0, tmp.length);
@@ -321,7 +321,7 @@ public void run() {
 	}
 
 
-	public static void main(String s[]) {
+	public static void main(String[] s) {
 		final MemoryMonitor demo = new MemoryMonitor();
 		WindowListener l = new WindowAdapter() {
 			@Override
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java
@@ -48,7 +48,7 @@ public static void main(String[] args){
 		int i = -1;
 		for ( Color color : colorWheel){
 			i++;
-			float af[] = Color.RGBtoHSB(color.getRed(),color.getGreen(),color.getBlue(), null);
+			float[] af = Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), null);
 			System.out.println("position "  + i + "  " + af[0] + " " + af[1] + " " + af[2]);
 			//System.out.println(rotateHue(color, 0.1f));
 		}
@@ -66,7 +66,7 @@ public static String toHexColor(Color col){
 	 */
 	public static Color rotateHue (Color color, float fraction) {
 
-		float af[] = Color.RGBtoHSB(color.getRed(),color.getGreen(),color.getBlue(), null);
+		float[] af = Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), null);
 
 		float hue = af[0];
 		float saturation = af[1];
@@ -80,9 +80,9 @@ public static Color rotateHue (Color color, float fraction) {
 
 	public static Color getIntermediate(Color start, Color end, int stepSize, int position ){
 
-		float af1[] = Color.RGBtoHSB(start.getRed(),start.getGreen(),start.getBlue(), null);
+		float[] af1 = Color.RGBtoHSB(start.getRed(), start.getGreen(), start.getBlue(), null);
 
-		float af2[] = Color.RGBtoHSB(end.getRed(),end.getGreen(),end.getBlue(), null);
+		float[] af2 = Color.RGBtoHSB(end.getRed(), end.getGreen(), end.getBlue(), null);
 
 		float hue1 = af1[0];
 		float hue2 = af2[0];
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
@@ -32,7 +32,7 @@ public class HSVColorSpace extends ColorSpace {
 
 	private static final long serialVersionUID = 8324413992279510075L;
 
-	public static void main(String args[]) {
+	public static void main(String[] args) {
 		HSVColorSpace csHSV = new HSVColorSpace();
 		ColorSpace csRGB = ColorSpace.getInstance(CS_sRGB);
 		Color c;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.java
@@ -29,7 +29,7 @@ public static Color4f convertColor4f(Color color) {
 		return new Color4f(color);
 	}
 
-	public static Color4f[] convertColor4f(Color colors[]) {
+	public static Color4f[] convertColor4f(Color[] colors) {
 		Color4f[] colors4 = new Color4f[colors.length];
 		for (int i = 0; i < colors.length; i++) {
 			colors4[i] = convertColor4f(colors[i]);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -71,7 +71,7 @@ public class CECalculator {
 	protected int[][] bestTraces2;
 	protected int nBestTrace;
 	protected int nBestTraces;
-	double d_[] = new double[20];
+	double[] d_ = new double[20];
 	protected int[] bestTracesN;
 	protected double bestTraceScore;
 	protected int nTrace;
@@ -2070,29 +2070,29 @@ protected double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
 		return(0.0);
 	}
 
-	private static final double scoreAv8[]={2.54, 2.51, 2.72, 3.01, 3.31, 3.61, 3.90, 4.19, 4.47, 4.74,
+	private static final double[] scoreAv8 ={2.54, 2.51, 2.72, 3.01, 3.31, 3.61, 3.90, 4.19, 4.47, 4.74,
 		4.99, 5.22, 5.46, 5.70, 5.94, 6.13, 6.36, 6.52, 6.68, 6.91};
-	private static final double scoreSd8[]={1.33, 0.88, 0.73, 0.71, 0.74, 0.80, 0.86, 0.92, 0.98, 1.04,
+	private static final double[] scoreSd8 ={1.33, 0.88, 0.73, 0.71, 0.74, 0.80, 0.86, 0.92, 0.98, 1.04,
 		1.08, 1.10, 1.15, 1.19, 1.23, 1.25, 1.32, 1.34, 1.36, 1.45};
-	private static final double gapsAv8[]={0.00, 11.50, 23.32, 35.95, 49.02, 62.44, 76.28, 90.26,
+	private static final double[] gapsAv8 ={0.00, 11.50, 23.32, 35.95, 49.02, 62.44, 76.28, 90.26,
 		104.86, 119.97, 134.86, 150.54, 164.86, 179.57, 194.39,
 		209.38, 224.74, 238.96, 253.72, 270.79};
-	private static final double gapsSd8[]={0.00, 9.88, 14.34, 17.99, 21.10, 23.89, 26.55, 29.00, 31.11,
+	private static final double[] gapsSd8 ={0.00, 9.88, 14.34, 17.99, 21.10, 23.89, 26.55, 29.00, 31.11,
 		33.10, 35.02, 36.03, 37.19, 38.82, 41.04, 43.35, 45.45,
 		48.41, 50.87, 52.27};
-	private static final double scoreAv6[]={1.98, 1.97, 2.22, 2.54, 2.87, 3.18, 3.48, 3.77, 4.05, 4.31,
+	private static final double[] scoreAv6 ={1.98, 1.97, 2.22, 2.54, 2.87, 3.18, 3.48, 3.77, 4.05, 4.31,
 		4.57, 4.82, 5.03, 5.24, 5.43, 5.64, 5.82, 6.02, 6.21, 6.42};
-	private static final double scoreSd6[]={1.15, 0.73, 0.63, 0.64, 0.71, 0.80, 0.87, 0.95, 1.01, 1.07,
+	private static final double[] scoreSd6 ={1.15, 0.73, 0.63, 0.64, 0.71, 0.80, 0.87, 0.95, 1.01, 1.07,
 		1.13, 1.19, 1.22, 1.25, 1.28, 1.32, 1.35, 1.39, 1.45, 1.50};
-	private static final double gapsAv6[]={0.00, 10.12, 20.25, 31.29, 42.95, 55.20, 67.53, 80.15,
+	private static final double[] gapsAv6 ={0.00, 10.12, 20.25, 31.29, 42.95, 55.20, 67.53, 80.15,
 		93.30, 106.47, 120.52, 134.38, 148.59, 162.58, 176.64,
 		191.23, 204.12, 218.64, 231.82, 243.43};
-	private static final double gapsSd6[]={0.00, 9.80, 14.44, 18.14, 21.35, 24.37, 27.00, 29.68, 32.22,
+	private static final double[] gapsSd6 ={0.00, 9.80, 14.44, 18.14, 21.35, 24.37, 27.00, 29.68, 32.22,
 		34.37, 36.65, 38.63, 40.31, 42.16, 43.78, 44.98, 47.08,
 		49.09, 50.78, 52.15};
 
 
-	private static final double tableZtoP[]={
+	private static final double[] tableZtoP={
 		1.0, 9.20e-01,8.41e-01,7.64e-01,6.89e-01,6.17e-01,5.49e-01,4.84e-01,4.24e-01,3.68e-01,
 		3.17e-01,2.71e-01,2.30e-01,1.94e-01,1.62e-01,1.34e-01,1.10e-01,8.91e-02,7.19e-02,5.74e-02,
 		4.55e-02,3.57e-02,2.78e-02,2.14e-02,1.64e-02,1.24e-02,9.32e-03,6.93e-03,5.11e-03,3.73e-03,
@@ -2108,7 +2108,7 @@ protected double zStrAlign(int winSize, int nTrace, double score, int nGaps) {
 		3.55e-33,1.06e-33,3.11e-34,9.06e-35,2.61e-35,7.47e-36,2.11e-36,5.91e-37,1.64e-37,4.50e-38,
 		1.22e-38,3.29e-39,8.77e-40,2.31e-40,6.05e-41,1.56e-41,4.00e-42,1.02e-42,2.55e-43,6.33e-44,
 		1.56e-44,3.80e-45,9.16e-46,2.19e-46,5.17e-47,1.21e-47,2.81e-48,6.45e-49,1.46e-49,3.30e-50};
-	private static final double tablePtoZ[]={
+	private static final double[] tablePtoZ ={
 		0.00,0.73,1.24,1.64,1.99,2.30,2.58,2.83,3.07,3.29,
 		3.50,3.70,3.89,4.07,4.25,4.42,4.58,4.74,4.89,5.04,
 		5.19,5.33,5.46,5.60,5.73,5.86,5.99,6.11,6.23,6.35,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/SynchronizedOutFile.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java

Original file line number	Diff line number	Diff line change
`@@ -130,7 +130,7 @@ public static LinkedHashMap<String, DNASequence> readFastaDNASequence(`
`130`	`130`	`return dnaSequences;`
`131`	`131`	`}`
`132`	`132`
`133`		`- public static void main(String args[]) throws Exception {`
	`133`	`+ public static void main(String[] args) throws Exception {`
`134`	`134`
`135`	`135`	`LinkedHashMap<String, DNASequence> dnaSequences = FastaReaderHelper.readFastaDNASequence(new File("fasta.fna"));`
`136`	`136`	`for (DNASequence sequence : dnaSequences.values()) {`
Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@ public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(`
`161`	`161`	`return dnaSequences;`
`162`	`162`	`}`
`163`	`163`
`164`		`- public static void main(String args[]) throws Exception {`
	`164`	`+ public static void main(String[] args) throws Exception {`
`165`	`165`
`166`	`166`	`LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(new File("src/test/resources/NM_000266.gb"), true);`
`167`	`167`	`for (DNASequence sequence : dnaSequences.values()) {`
Original file line number	Diff line number	Diff line change
`@@ -296,7 +296,7 @@ private Strand getGroupLocationStrand(List<Location> ll){`
`296`	`296`	`return returnStrand;`
`297`	`297`	`}`
`298`	`298`
`299`		`- public static void main(String args[]){`
	`299`	`+ public static void main(String[] args){`
`300`	`300`	`String[] testStrings = {`
`301`	`301`	`"J00194.1:100..202",`
`302`	`302`	`"A00001.5:34..45",`
Original file line number	Diff line number	Diff line change
`@@ -875,7 +875,7 @@ static public LinkedHashMap<String, GeneSequence> getGeneSequences(Collection<Ch`
`875`	`875`	`return geneSequenceHashMap;`
`876`	`876`	`}`
`877`	`877`
`878`		`- public static void main(String args[]) throws Exception {`
	`878`	`+ public static void main(String[] args) throws Exception {`
`879`	`879`	`/* if (false) {`
`880`	`880`	`LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneMarkGTF(new File("Scaffolds.fna"), new File("genemark_hmm.gtf"));`
`881`	`881`	`LinkedHashMap<String, ProteinSequence> proteinSequenceList = GeneFeatureHelper.getProteinSequences(chromosomeSequenceList.values());`