From 9ba5c46b6fb472ffa1a9299e98d1825f61557c53 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 27 Feb 2011 18:37:45 +0000
Subject: [PATCH] patch for JAL-780

---
 src/jalview/analysis/Finder.java |   45 +++++++++++++++++++-------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 41d3185..1179435 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -82,31 +82,11 @@ public class Finder
     Sequence seq;
     String item = null;
     boolean found = false;
+    int end = alignment.getHeight();
 
-    // //// is the searchString a residue number?
-    try
-    {
-      int res = Integer.parseInt(searchString);
-      found = true;
-      if (selection == null || selection.getSize() < 1)
-      {
-        seq = (Sequence) alignment.getSequenceAt(0);
-      }
-      else
-      {
-        seq = (Sequence) (selection.getSequenceAt(0));
-      }
-
-      searchResults.addResult(seq, res, res);
-      hasResults = true;
-    } catch (NumberFormatException ex)
-    {
-    }
 
     // /////////////////////////////////////////////
 
-    int end = alignment.getHeight();
-
     if (selection != null)
     {
       if ((selection.getSize() < 1)
@@ -119,7 +99,7 @@ public class Finder
     while (!found && (seqIndex < end))
     {
       seq = (Sequence) alignment.getSequenceAt(seqIndex);
-
+      
       if ((selection != null && selection.getSize() > 0)
               && !selection.getSequences(null).contains(seq))
       {
@@ -131,6 +111,27 @@ public class Finder
       if (resIndex < 0)
       {
         resIndex = 0;
+        // test for one off matches - sequence position and sequence ID
+        // //// is the searchString a residue number?
+        try
+        {
+          int res = Integer.parseInt(searchString);
+          // possibly a residue number - check if valid for seq
+          if (seq.getEnd() >= res)
+          {
+            searchResults.addResult(seq, res, res);
+            hasResults = true;
+            //resIndex=seq.getLength();
+            // seqIndex++;
+            if (!findAll) {
+              found = true;
+              break;
+            }
+          }
+        } catch (NumberFormatException ex)
+        {
+        }
+
         if (regex.search(seq.getName()))
         {
           idMatch.addElement(seq);
-- 
1.7.10.2