X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=7483a0ad543bd74a091e7bee267c995aaec2ea47;hb=1340920fd1b15c9bc8cd2284def7ec176a4989d5;hp=2311a9f532f1a4220fec634e46fe41ae97973979;hpb=183b98840a8ee8d03a2c7f7f42044190d52f2595;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2311a9f..7483a0a 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -94,13 +94,13 @@ 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;
 
-      if(av.getSelection().size()>0)
-        seq = (Sequence)(av.getSelection().sequenceAt(0));
+      if(av.getSelectionGroup().getSize()>0)
+        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
       else
         seq = (Sequence)av.getAlignment().getSequenceAt(0);
 
@@ -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.getRubberbandGroup();
-    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.getSelection().size()>0 && !av.getSelection().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) );