From df3d63b97cc55ee0e7d078d050775f7f58ab3c42 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 12 Aug 2005 14:26:15 +0000
Subject: [PATCH] fixed leafMapping bug for Id's like SequenceX (where X=14
 matches all X=1,10,11,12,13). Fixes Mantis 0009227

---
 src/jalview/analysis/SequenceIdMatcher.java |   44 ++++++++++++++++-----------
 1 file changed, 27 insertions(+), 17 deletions(-)

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 1efe498..b88a03f 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -26,7 +26,8 @@ import jalview.datamodel.*;
  * <p>Title: </p>
  * SequenceIdMatcher
  * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
+ * Routine which does approximate Sequence Id resolution by name using
+ * string containment (on word boundaries) rather than equivalence
  * <p>Copyright: Copyright (c) 2004</p>
  *
  * <p>Company: Dundee University</p>
@@ -41,7 +42,6 @@ public class SequenceIdMatcher
   public SequenceIdMatcher(SequenceI[] seqs)
   {
     names = new Hashtable();
-
     for (int i = 0; i < seqs.length; i++)
     {
       names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
@@ -83,13 +83,13 @@ public class SequenceIdMatcher
    */
   SequenceI[] findIdMatch(SequenceI[] seqs)
   {
-    SequenceI[] namedseqs = new SequenceI[seqs.length];
-
+    SequenceI[] namedseqs = null;
     int i = 0;
     SeqIdName nam;
 
     if (seqs.length > 0)
     {
+      namedseqs = new SequenceI[seqs.length];
       do
       {
         nam = new SeqIdName(seqs[i].getName());
@@ -103,7 +103,7 @@ public class SequenceIdMatcher
           namedseqs[i] = null;
         }
       }
-      while (i++ < seqs.length);
+      while (++i < seqs.length);
     }
 
     return namedseqs;
@@ -140,24 +140,34 @@ public class SequenceIdMatcher
       return false;
     }
 
+    /**
+     * matches if one ID properly contains another at a whitespace boundary.
+     * TODO: (JBPNote) These are not efficient. should use char[] for speed
+     * @param s SeqIdName
+     * @return boolean
+     */
     public boolean equals(SeqIdName s)
     {
-      if (id.startsWith(s.id) || s.id.startsWith(id))
-      {
-        return true;
-      }
-
-      return false;
+      if (id.length()>s.id.length()) {
+        return id.startsWith(s.id) ?
+            (id.equals(s.id) ? true : id.startsWith(s.id+" "))
+            : false;
+      } else
+        return s.id.startsWith(id) ?
+            (s.id.equals(id) ? true : s.id.startsWith(id+" "))
+            : false;
     }
 
     public boolean equals(String s)
     {
-      if (id.startsWith(s) || s.startsWith(id))
-      {
-        return true;
-      }
-
-      return false;
+      if (id.length()>s.length()) {
+        return id.startsWith(s) ?
+            (id.equals(s) ? true : id.startsWith(s+" "))
+            : false;
+      } else
+        return s.startsWith(id) ?
+            (s.equals(id) ? true : s.startsWith(id+" "))
+            : false;
     }
   }
 }
-- 
1.7.10.2