X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=e8c16d234f398bce693cd176b1601c56abf6a501;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=6b8df4b33d1d298e08fc24e8ecc72cd5095c0ae1;hpb=7131594a75aff4691699b4499fb91ec29b8952df;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 6b8df4b..e8c16d2 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -153,7 +153,10 @@ public class Finder extends GFinder
     {
         createNewGroup.setEnabled(false);
 
-        String searchString = textfield.getText().toUpperCase().trim();
+        String searchString = textfield.getText().trim();
+        if(!caseSensitive.isSelected())
+          searchString = searchString.toUpperCase();
+
         if(searchString.length()<1)
           return;
 
@@ -170,7 +173,7 @@ public class Finder extends GFinder
         {
             int res = Integer.parseInt(searchString);
             found = true;
-            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
             {
               seq = (Sequence) av.getAlignment().getSequenceAt(0);
             }
@@ -193,7 +196,7 @@ public class Finder extends GFinder
 
         if (selection != null)
         {
-            if ((selection.getSize() < 1) ||
+            if ((selection.getSize(false) < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -204,7 +207,7 @@ public class Finder extends GFinder
         {
             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-            if ((selection != null) && !selection.sequences.contains(seq))
+            if ((selection != null) && !selection.getSequences(false).contains(seq))
             {
                 seqIndex++;
                 resIndex = 0;
@@ -212,7 +215,9 @@ public class Finder extends GFinder
                 continue;
             }
 
-            item = seq.getSequence().toUpperCase();
+            item = seq.getSequence();
+            if(!caseSensitive.isSelected())
+              item = item.toUpperCase();
 
             if ((selection != null) &&
                     (selection.getEndRes() < av.alignment.getWidth()-1))