Cleanup - squid:S1858 - "toString()" should never be called on a String object

Mohamed Ezzat · Mohamed Ezzat · commit 082d8607ed01 · 2016-07-01T18:39:14.000+02:00
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
@@ -301,7 +301,7 @@ public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolea
 	private String[] splitSeqName(String sequenceName) {
 		String[] result = new String[3];
 
-		String[] barSplit = sequenceName.toString().split("/");
+		String[] barSplit = sequenceName.split("/");
 		if (barSplit.length == 2) {
 			result[0] = barSplit[0];
 			String[] positions = barSplit[1].split("-");
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
@@ -181,7 +181,7 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
 
 			DNASequence dnaCodingSequence = null;
 			try {
-				dnaCodingSequence = new DNASequence(codingSequence.toString().toUpperCase());
+				dnaCodingSequence = new DNASequence(codingSequence.toUpperCase());
 			} catch (CompoundNotFoundException e) {
 				// if I understand this should not happen, please correct if I'm wrong - JD 2014-10-24
 				logger.error("Could not create DNA coding sequence, {}. This is most likely a bug.", e.getMessage());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompound.java
@@ -126,6 +126,6 @@ public boolean equalsIgnoreCase(Compound compound) {
 			return false;
 		}
 		AbstractCompound them = (AbstractCompound) compound;
-		return this.base.toString().equalsIgnoreCase(them.base.toString());
+		return this.base.equalsIgnoreCase(them.base);
 	}
 }
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
@@ -165,10 +165,10 @@ public LocalPDBDirectory(String path) {
 		if( path == null) {
 			UserConfiguration config = new UserConfiguration();
 			path = config.getPdbFilePath();
-			logger.debug("Initialising from system property/environment variable to path: {}", path.toString());
+			logger.debug("Initialising from system property/environment variable to path: {}", path);
 		} else {
 			path = FileDownloadUtils.expandUserHome(path);
-			logger.debug("Initialising with path {}", path.toString());
+			logger.debug("Initialising with path {}", path);
 		}
 		this.path = new File(path);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -224,7 +224,7 @@ private void writeID(String contents, String currentID) throws IOException{
 
 		try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {
 
-			pw.print(contents.toString());
+			pw.print(contents);
 			pw.flush();
 		}
 	}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
@@ -153,7 +153,7 @@ private static double[][] rowsum(double[][] rr, ArrayList<String> sets) throws E
 	   //     Collections.sort(index);
 
 			for (int m = 0; m < index.size(); m++) {
-				String key = index.get(m).toString();
+				String key = index.get(m);
 				sum[m][j] = sumMap.get(key);
 			}
 

Original file line number	Diff line number	Diff line change
`@@ -126,6 +126,6 @@ public boolean equalsIgnoreCase(Compound compound) {`
`126`	`126`	`return false;`
`127`	`127`	`}`
`128`	`128`	`AbstractCompound them = (AbstractCompound) compound;`
`129`		`- return this.base.toString().equalsIgnoreCase(them.base.toString());`
	`129`	`+ return this.base.equalsIgnoreCase(them.base);`
`130`	`130`	`}`
`131`	`131`	`}`
Original file line number	Diff line number	Diff line change
`@@ -224,7 +224,7 @@ private void writeID(String contents, String currentID) throws IOException{`
`224`	`224`
`225`	`225`	`try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {`
`226`	`226`
`227`		`- pw.print(contents.toString());`
	`227`	`+ pw.print(contents);`
`228`	`228`	`pw.flush();`
`229`	`229`	`}`
`230`	`230`	`}`
Original file line number	Diff line number	Diff line change
`@@ -153,7 +153,7 @@ private static double[][] rowsum(double[][] rr, ArrayList<String> sets) throws E`
`153`	`153`	`// Collections.sort(index);`
`154`	`154`
`155`	`155`	`for (int m = 0; m < index.size(); m++) {`
`156`		`- String key = index.get(m).toString();`
	`156`	`+ String key = index.get(m);`
`157`	`157`	`sum[m][j] = sumMap.get(key);`
`158`	`158`	`}`
`159`	`159`