JAL-1965 hang onto original string so best match (including case) can be picked

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index ad36ebe..17ff216 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -270,9 +270,12 @@ public class SequenceIdMatcher
       addSeq(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)
+      boolean is_closer = ((q = Math.abs(matchlen - namlen)) > (w = Math
+              .abs(candlen - namlen)) && candlen > matchlen);
+      // if not closer, then check if current best is actually identical in case
+      // as
+      // well
+      if (is_closer || (!candName.equalsCase(best.get(0).getName())))
       {
         best.clear();
         match = cand;
@@ -281,6 +284,7 @@ public class SequenceIdMatcher
       }
       if (q == w && candlen == matchlen)
       {
+        // equivalently good, and matches with case as well. so
         // record any ties
         best.add(cand);
       }
@@ -407,13 +411,14 @@ public class SequenceIdMatcher
 
   private class SeqIdName
   {
-    String id;
+    String id, origid;
 
     SeqIdName(String s)
     {
       if (s != null)
       {
         id = new String(s).toLowerCase();
+        origid = new String(s);
       }
       else
       {
@@ -528,5 +533,22 @@ public class SequenceIdMatcher
     {
       return id;
     }
+
+    public boolean equalsCase(String s)
+    {
+      if (origid.length() > s.length())
+      {
+        return check_wordmatch(origid, s);
+      }
+      else
+      {
+        return check_wordmatch(s, origid);
+      }
+    }
+
+    public boolean equalsCase(SeqIdName sid)
+    {
+      return equalsCase(sid.origid);
+    }
   }
 }