develop merge

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 454bc09..b89287c 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -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())