X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=7483a0ad543bd74a091e7bee267c995aaec2ea47;hb=fdaf66178c7596335c3675ec3db0da8503dc61b2;hp=1ff31fe25eddb2c68b36d2c1b79968e8adf794c8;hpb=1f183a4e9d63b2af6cf7184274affc80e11ef344;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1ff31fe..7483a0a 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -6,7 +6,6 @@ import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-import java.util.regex.*;
 import java.awt.*;
 
 public class Finder extends GFinder
@@ -92,16 +91,16 @@ public class Finder extends GFinder
     int [] allResults = null;
 
     Sequence seq;
-    String item;
+    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);
 
@@ -109,9 +108,9 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
 
-
-      //av.getAlignment().getSequenceAt(seq).findPosition(res)
     }catch(NumberFormatException ex){}
+    ///////////////////////////////////////////////
+
 
     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
     Color [] newColors = new Color[24];
@@ -122,18 +121,29 @@ public class Finder extends GFinder
 
     searchGroup = new SuperGroup(searchString, ucs , true, true, false);
 
-    while( !found && seqIndex<av.getAlignment().getHeight())
+    int end = av.alignment.getHeight();
+
+    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);
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
+      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+
+
+      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(selection!=null && selection.getEndRes()<av.alignment.getWidth())
+          item = item.substring(0, selection.getEndRes()+1);
 
       ///Shall we ignore gaps????
       StringBuffer noGaps = new StringBuffer();
@@ -153,23 +163,24 @@ public class Finder extends GFinder
       }
 
 
-      Pattern pattern = Pattern.compile(searchString);
-      Matcher matcher = pattern.matcher(noGaps);
+      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
 
       for(int r = resIndex; r<noGaps.length(); r++)
       {
 
-       if( matcher.find( r ) )
+       if( regex.searchFrom( noGaps.toString(), r ) )
        {
-         resIndex = matcher.start();
+         resIndex = regex.matchedFrom();
+         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
+           continue;
 
          searchResults.add( Integer.toString( seqIndex) );
          searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
-         searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString()) ) );
+         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );
 
          SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
                                              resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
-                                      matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())
+                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())
             );
          sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
          searchGroup.addGroup( sg );
@@ -182,7 +193,7 @@ public class Finder extends GFinder
            break;
          }
 
-         r=resIndex+1;
+         r=resIndex;
        }
       }
       if(!found)
@@ -190,7 +201,7 @@ public class Finder extends GFinder
         seqIndex++;
         resIndex = 0;
       }
-          }
+    }
 
     if(searchResults.size()>0)
     {