X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=3ec162d440b8c426ff052b9bc21f9ca7d5c6ad10;hb=8f08ed712138cea8987594a62b6053a0bfdba327;hp=c12de4e948fba91535e3b38174eb8dca74754f89;hpb=9c39e96af6b84257604da448101505361dced686;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index c12de4e..3ec162d 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
@@ -74,13 +76,13 @@ public class SequenceIdMatcher
       dbseq = dbseq.getDatasetSequence();
     }
     // add in any interesting identifiers
-    if (dbseq.getDBRefs() != null)
+    List<DBRefEntry> dbr = dbseq.getDBRefs(); 
+    if (dbr != null)
     {
-      DBRefEntry dbr[] = dbseq.getDBRefs();
       SeqIdName sid = null;
-      for (int r = 0; r < dbr.length; r++)
+      for (int r = 0, nr = dbr.size(); r < nr; r++)
       {
-        sid = new SeqIdName(dbr[r].getAccessionId());
+        sid = new SeqIdName(dbr.get(r).getAccessionId());
         if (!names.containsKey(sid))
         {
           names.put(sid, seq);
@@ -147,9 +149,8 @@ public class SequenceIdMatcher
       names.put(new SeqIdName(cand.getName()), cand);
       int q, w, candlen = cand.getName().length();
       // keep the one with an id 'closer' to the given seqnam string
-      if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
-              - namlen))
-              && candlen > matchlen)
+      if ((q = Math.abs(matchlen - namlen)) > (w = Math
+              .abs(candlen - namlen)) && candlen > matchlen)
       {
         best.clear();
         match = cand;
@@ -290,7 +291,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = s.toLowerCase();
+        id = s.toLowerCase(Locale.ROOT);
       }
       else
       {
@@ -301,8 +302,8 @@ public class SequenceIdMatcher
     @Override
     public int hashCode()
     {
-      return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
-              .hashCode());
+      return ((id.length() >= 4) ? id.substring(0, 4).hashCode()
+              : id.hashCode());
     }
 
     @Override
@@ -320,7 +321,7 @@ public class SequenceIdMatcher
       {
         if (s instanceof String)
         {
-          return this.stringequals(((String) s).toLowerCase());
+          return this.stringequals(((String) s).toLowerCase(Locale.ROOT));
         }
       }
 
@@ -348,13 +349,16 @@ public class SequenceIdMatcher
     {
       if (id.length() > s.length())
       {
-        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+        return id.startsWith(s)
+                ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
                 : false;
       }
       else
       {
-        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
-                .indexOf(s.charAt(id.length())) > -1)) : false;
+        return s.startsWith(id)
+                ? (s.equals(id) ? true
+                        : (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
+                : false;
       }
     }