X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=d41cdd4122d6535b0ef4335aa56a9b17a6c0f668;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=ee9389c04dc6697b89a8f2857e3948d4c3eb6ac1;hpb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index ee9389c..d41cdd4 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import java.util.Locale; + import jalview.analysis.Rna; import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.analysis.WUSSParseException; @@ -991,7 +993,7 @@ public class AlignmentAnnotation seqPos = i + startRes; } - sequenceMapping.put(new Integer(seqPos), annotations[i]); + sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]); } } @@ -1030,7 +1032,7 @@ public class AlignmentAnnotation { for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) { - index = new Integer(a); + index = Integer.valueOf(a); Annotation annot = sequenceMapping.get(index); if (annot != null) { @@ -1225,7 +1227,7 @@ public class AlignmentAnnotation { if (seqname && this.sequenceRef != null) { - int i = description.toLowerCase().indexOf(""); + int i = description.toLowerCase(Locale.ROOT).indexOf(""); if (i > -1) { // move the html tag to before the sequence reference.