From 7b53427e0e375aeb5146867c3022c712f637959b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 16 Mar 2005 14:51:41 +0000
Subject: [PATCH] selection area search bugs fixed

---
 src/jalview/gui/Finder.java |   31 ++++++++++++++-----------------
 1 file changed, 14 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 8567451..7483a0a 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -94,7 +94,7 @@ public class Finder extends GFinder
     String item=null;
     boolean found = false;
 
-    /// is the searchString a residue number?
+    ////// is the searchString a residue number?
     try{
       int res = Integer.parseInt(searchString);
       found = true;
@@ -109,6 +109,8 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
 
     }catch(NumberFormatException ex){}
+    ///////////////////////////////////////////////
+
 
     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
     Color [] newColors = new Color[24];
@@ -121,30 +123,27 @@ public class Finder extends GFinder
 
     int end = av.alignment.getHeight();
 
-
-    SequenceGroup rubberband = av.getSelectionGroup();
-    if(rubberband!=null)
-      end = rubberband.getEndRes();
-
-
+    SequenceGroup selection = av.getSelectionGroup();
+    if(selection!=null)
+     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
+      selection = null;
 
     while( !found && seqIndex<end)
     {
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
+      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
 
-      if(   av.getSelectionGroup().getSize()>0 && !av.getSelectionGroup().sequences.contains(seq)
-            || (rubberband!=null && !rubberband.sequences.contains(seq))  )
+
+      if(selection!=null && !selection.sequences.contains(seq))
       {
-        // if a selection has been made, only search within that selection
         seqIndex++;
         resIndex=0;
         continue;
       }
 
-      item = seq.getSequence();
+      item = seq.getSequence().toUpperCase();
 
-      if(rubberband!=null)
-        item = item.substring(0, rubberband.getEndRes()+1);
+      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
+          item = item.substring(0, selection.getEndRes()+1);
 
       ///Shall we ignore gaps????
       StringBuffer noGaps = new StringBuffer();
@@ -172,9 +171,7 @@ public class Finder extends GFinder
        if( regex.searchFrom( noGaps.toString(), r ) )
        {
          resIndex = regex.matchedFrom();
-
-
-         if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())
+         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
            continue;
 
          searchResults.add( Integer.toString( seqIndex) );
-- 
1.7.10.2