From 183b98840a8ee8d03a2c7f7f42044190d52f2595 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 24 Jan 2005 17:25:31 +0000
Subject: [PATCH] now uses 1.1 friendly regex

---
 src/jalview/gui/Finder.java |   42 ++++++++++++++++++++++++++++--------------
 1 file changed, 28 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1ff31fe..2311a9f 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
@@ -92,7 +91,7 @@ public class Finder extends GFinder
     int [] allResults = null;
 
     Sequence seq;
-    String item;
+    String item=null;
     boolean found = false;
 
     /// is the searchString a residue number?
@@ -109,8 +108,6 @@ 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();
@@ -122,10 +119,21 @@ 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 rubberband = av.getRubberbandGroup();
+    if(rubberband!=null)
+      end = rubberband.getEndRes();
+
+
+
+    while( !found && seqIndex<end)
     {
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
+
+      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)
+            || (rubberband!=null && !rubberband.sequences.contains(seq))  )
       {
         // if a selection has been made, only search within that selection
         seqIndex++;
@@ -135,6 +143,9 @@ public class Finder extends GFinder
 
       item = seq.getSequence();
 
+      if(rubberband!=null)
+        item = item.substring(0, rubberband.getEndRes()+1);
+
       ///Shall we ignore gaps????
       StringBuffer noGaps = new StringBuffer();
       int insertCount=0;
@@ -153,23 +164,26 @@ 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(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.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 +196,7 @@ public class Finder extends GFinder
            break;
          }
 
-         r=resIndex+1;
+         r=resIndex;
        }
       }
       if(!found)
@@ -190,7 +204,7 @@ public class Finder extends GFinder
         seqIndex++;
         resIndex = 0;
       }
-          }
+    }
 
     if(searchResults.size()>0)
     {
-- 
1.7.10.2