From 8503d69aa0d56c0eec95d3c89bc90ada7272997b Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 12 Nov 2015 17:58:42 +0000
Subject: [PATCH] JAL-1965 case insensitive & word matching SequenceIdMatcher
 .. nearly passes tests

Signed-off-by: Jim Procter <jprocter@issues.jalview.org>
---
 src/jalview/analysis/SequenceIdMatcher.java |   52 ++++++++++++++++++++++-----
 1 file changed, 43 insertions(+), 9 deletions(-)

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 454bc09..8dda255 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -280,7 +280,7 @@ public class SequenceIdMatcher
     {
       if (s != null)
       {
-        id = new String(s);
+        id = new String(s).toLowerCase();
       }
       else
       {
@@ -341,27 +341,61 @@ public class SequenceIdMatcher
       // 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;
+        return check_wordmatch(id, s.id);
       }
       else
       {
-        return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
-                .indexOf(s.id.charAt(id.length())) > -1)) : false;
+        return check_wordmatch(s.id, id);
+      }
+    }
+
+    private boolean check_wordmatch(String longer, String shorter)
+    {
+      boolean elen = longer.length() == shorter.length();
+      int sp = longer.indexOf(shorter);
+      if (sp == -1)
+      {
+        return false;
+      }
+
+      if (sp == 0)
+      {
+        // end of match is word boundary
+        return elen ? true : (WORD_SEP.indexOf(longer.charAt(shorter
+                .length() + sp)) > -1);
+      }
+      if (WORD_SEP.indexOf(longer.charAt(sp - 1)) > -1)
+      {
+        if (sp + shorter.length() == longer.length())
+        {
+          return true;
+        }
+        else
+        {
+          // end of match is word boundary
+          return elen ? false
+                  : sp + shorter.length() == longer.length() ? true
+                          : (WORD_SEP.indexOf(longer.charAt(shorter
+                                  .length() + sp)) > -1);
+        }
+      }
+      else
+      {
+        // prefix of match is not a word boundary
+        return false;
       }
     }
 
     public boolean equals(String s)
     {
+      s = s.toLowerCase(); // TODO: employ faster to lower case operation
       if (id.length() > s.length())
       {
-        return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
-                : false;
+        return check_wordmatch(id, s);
       }
       else
       {
-        return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
-                .indexOf(s.charAt(id.length())) > -1)) : false;
+        return check_wordmatch(s, id);
       }
     }
   }
-- 
1.7.10.2