Fix for orientation value: compare to Character, not to String

Yana Valasatava · Yana Valasatava · commit 1f3a6dc7a466 · 2017-03-23T16:07:39.000-07:00
Enhancement: return transcription as all upper case string
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -1145,7 +1145,7 @@ public String getTranscriptSequence(GeneChromosomePosition gcp) throws IOExcepti
 	public String getTranscriptSequence(List<Integer> exonStarts, List<Integer> exonEnds, int codingStart, int codingEnd, Character orientation) throws IOException, CompoundNotFoundException {
 
 		List<Range<Integer>> cdsRegion;
-		if (orientation.equals("-")) {
+		if (orientation.equals('-')) {
 			cdsRegion = getCDSRegionsReverse(exonStarts, exonEnds, codingStart, codingEnd);
 		}
 		else {
@@ -1157,12 +1157,12 @@ public String getTranscriptSequence(List<Integer> exonStarts, List<Integer> exon
 			int length = range.upperEndpoint() - range.lowerEndpoint();
 			transcription += parser.loadFragment(range.lowerEndpoint(), length);
 		}
-		if (orientation.equals("-")) {
+		if (orientation.equals('-')) {
 			transcription = new StringBuilder(transcription).reverse().toString();
 			DNASequence dna = new DNASequence(transcription);
 			SequenceView<NucleotideCompound> compliment = dna.getComplement();
 			transcription = compliment.getSequenceAsString();
 		}
-		return transcription;
+		return transcription.toUpperCase();
 	}
 }

Original file line number	Diff line number	Diff line change
`@@ -1145,7 +1145,7 @@ public String getTranscriptSequence(GeneChromosomePosition gcp) throws IOExcepti`
`1145`	`1145`	`public String getTranscriptSequence(List<Integer> exonStarts, List<Integer> exonEnds, int codingStart, int codingEnd, Character orientation) throws IOException, CompoundNotFoundException {`
`1146`	`1146`
`1147`	`1147`	`List<Range<Integer>> cdsRegion;`
`1148`		`- if (orientation.equals("-")) {`
	`1148`	`+ if (orientation.equals('-')) {`
`1149`	`1149`	`cdsRegion = getCDSRegionsReverse(exonStarts, exonEnds, codingStart, codingEnd);`
`1150`	`1150`	`}`
`1151`	`1151`	`else {`
`@@ -1157,12 +1157,12 @@ public String getTranscriptSequence(List<Integer> exonStarts, List<Integer> exon`
`1157`	`1157`	`int length = range.upperEndpoint() - range.lowerEndpoint();`
`1158`	`1158`	`transcription += parser.loadFragment(range.lowerEndpoint(), length);`
`1159`	`1159`	`}`
`1160`		`- if (orientation.equals("-")) {`
	`1160`	`+ if (orientation.equals('-')) {`
`1161`	`1161`	`transcription = new StringBuilder(transcription).reverse().toString();`
`1162`	`1162`	`DNASequence dna = new DNASequence(transcription);`
`1163`	`1163`	`SequenceView<NucleotideCompound> compliment = dna.getComplement();`
`1164`	`1164`	`transcription = compliment.getSequenceAsString();`
`1165`	`1165`	`}`
`1166`		`- return transcription;`
	`1166`	`+ return transcription.toUpperCase();`
`1167`	`1167`	`}`
`1168`	`1168`	`}`