X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=b89287c3ed133d3bc77b2eb5ced3425dfe2b7416;hb=f3da4113cd7d574966523982ed5145a918c63556;hp=5b812dd28c5c8fe55d23272be4c49aee0976c585;hpb=204617b73ee07ba28dcec3ffdf6b8e8eb2062011;p=jalview.git

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 5b812dd..b89287c 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -58,14 +58,14 @@ public class SequenceIdMatcher
       // associated with this key.
       names.put(new SeqIdName(seq.getDisplayId(true)), seq);
       SequenceI dbseq = seq;
-      while (dbseq.getDatasetSequence()!=null)
+      while (dbseq.getDatasetSequence() != null)
       {
         dbseq = dbseq.getDatasetSequence();
       }
       // add in any interesting identifiers
-      if (dbseq.getDBRef() != null)
+      if (dbseq.getDBRefs() != null)
       {
-        DBRefEntry dbr[] = dbseq.getDBRef();
+        DBRefEntry dbr[] = dbseq.getDBRefs();
         SeqIdName sid = null;
         for (int r = 0; r < dbr.length; r++)
         {
@@ -191,7 +191,7 @@ public class SequenceIdMatcher
 
     SeqIdName nam = new SeqIdName(seqnam);
     List<SequenceI> m = findAllIdMatches(nam);
-    if (m!=null)
+    if (m != null)
     {
       return m.toArray(new SequenceI[m.size()]);
     }
@@ -272,7 +272,7 @@ public class SequenceIdMatcher
     return r;
   }
 
-  private class SeqIdName
+  class SeqIdName
   {
     String id;
 
@@ -304,7 +304,7 @@ public class SequenceIdMatcher
       }
       if (s instanceof SeqIdName)
       {
-        return this.equals((SeqIdName) s);
+        return this.equals(((SeqIdName) s).id);
       }
       else
       {
@@ -332,25 +332,8 @@ public class SequenceIdMatcher
      * todo: (JBPNote) Set separator characters appropriately
      * 
      * @param s
-     *          SeqIdName
      * @return boolean
      */
-    public boolean equals(SeqIdName s)
-    {
-      // TODO: JAL-732 patch for cases when name includes a list of IDs, and the
-      // match contains one ID flanked
-      if (id.length() > s.id.length())
-      {
-        return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
-                .length())) > -1) : false;
-      }
-      else
-      {
-        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
-                .indexOf(s.id.charAt(id.length())) > -1)) : false;
-      }
-    }
-
     public boolean equals(String s)
     {
       if (id.length() > s.length())