squid:S1157 - Case insensitive string comparisons should be made without intermediate upper or lower casing

Mohamed Ezzat · Mohamed Ezzat · commit 320fa7b98e34 · 2016-06-14T09:26:56.000+02:00
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/InputParameters.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/InputParameters.java
@@ -105,10 +105,10 @@ ResultLayout parseFormat(String format) {
 		return ResultLayout.VERTICAL;
 	}
 	format = format.trim().substring(InputParameters.formatKey.length());
-	if (format.toUpperCase().equals("V")) {
+	if ("V".equalsIgnoreCase(format)) {
 		return ResultLayout.VERTICAL;
 	}
-	if (format.toUpperCase().equals("H")) {
+	if ("H".equalsIgnoreCase(format)) {
 		return ResultLayout.HORIZONTAL;
 	}
 	throw new IllegalArgumentException("Unrecognised format: '" + format
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -395,11 +395,11 @@ public void setXtalInfo(String spaceGroupString, float[] unitCell, double[][] nc
 	 */
 	private int getGroupTypIndicator(String currentGroupType) {
 		// At the moment - peptide like is a HETATM group (consistent with biojava)
-		if(currentGroupType.toUpperCase().equals("PEPTIDE-LIKE")){
+		if("PEPTIDE-LIKE".equalsIgnoreCase(currentGroupType)){
 			return 0;
 		}
 		// Again to correspond with Biojava - but I suspect we really want this to be 1
-		if(currentGroupType.toUpperCase().equals("D-PEPTIDE LINKING")){
+		if("D-PEPTIDE LINKING".equalsIgnoreCase(currentGroupType)){
 			return 0;
 		}
 		if(currentGroupType.toUpperCase().contains("PEPTIDE")){

Original file line number	Diff line number	Diff line change
`@@ -105,10 +105,10 @@ ResultLayout parseFormat(String format) {`
`105`	`105`	`return ResultLayout.VERTICAL;`
`106`	`106`	`}`
`107`	`107`	`format = format.trim().substring(InputParameters.formatKey.length());`
`108`		`- if (format.toUpperCase().equals("V")) {`
	`108`	`+ if ("V".equalsIgnoreCase(format)) {`
`109`	`109`	`return ResultLayout.VERTICAL;`
`110`	`110`	`}`
`111`		`- if (format.toUpperCase().equals("H")) {`
	`111`	`+ if ("H".equalsIgnoreCase(format)) {`
`112`	`112`	`return ResultLayout.HORIZONTAL;`
`113`	`113`	`}`
`114`	`114`	`throw new IllegalArgumentException("Unrecognised format: '" + format`
Original file line number	Diff line number	Diff line change
`@@ -395,11 +395,11 @@ public void setXtalInfo(String spaceGroupString, float[] unitCell, double[][] nc`
`395`	`395`	`*/`
`396`	`396`	`private int getGroupTypIndicator(String currentGroupType) {`
`397`	`397`	`// At the moment - peptide like is a HETATM group (consistent with biojava)`
`398`		`- if(currentGroupType.toUpperCase().equals("PEPTIDE-LIKE")){`
	`398`	`+ if("PEPTIDE-LIKE".equalsIgnoreCase(currentGroupType)){`
`399`	`399`	`return 0;`
`400`	`400`	`}`
`401`	`401`	`// Again to correspond with Biojava - but I suspect we really want this to be 1`
`402`		`- if(currentGroupType.toUpperCase().equals("D-PEPTIDE LINKING")){`
	`402`	`+ if("D-PEPTIDE LINKING".equalsIgnoreCase(currentGroupType)){`
`403`	`403`	`return 0;`
`404`	`404`	`}`
`405`	`405`	`if(currentGroupType.toUpperCase().contains("PEPTIDE")){`