From e79b8060ca9b0806e621774859a6cf2c77867fc8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 13 Jan 2005 12:02:50 +0000
Subject: [PATCH] Ignores gaps when searching

---
 src/jalview/gui/Finder.java |   27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e1a3082..c2cf25b 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -101,7 +101,6 @@ public class Finder extends GFinder
     while( !found && seqIndex<av.getAlignment().getHeight())
     {
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
-
       if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
       {
         // if a selection has been made, only search within that selection
@@ -112,10 +111,28 @@ public class Finder extends GFinder
 
       item = seq.getSequence();
 
+      ///Shall we ignore gaps????
+      StringBuffer noGaps = new StringBuffer();
+      int insertCount=0;
+      ArrayList spaces = new ArrayList();
+
+      for (int j=0; j < item.length(); j++)
+      {
+
+        if(!jalview.util.Comparison.isGap(item.charAt(j)))
+         {
+           noGaps.append(item.charAt(j));
+           spaces.add(new Integer(insertCount));
+         }
+        else
+           insertCount++;
+      }
+
+
       Pattern pattern = Pattern.compile(searchString);
-      Matcher matcher = pattern.matcher(item);
+      Matcher matcher = pattern.matcher(noGaps);
 
-      for(int r = resIndex; r<item.length(); r++)
+      for(int r = resIndex; r<noGaps.length(); r++)
       {
 
        if( matcher.find( r ) )
@@ -123,8 +140,8 @@ public class Finder extends GFinder
          resIndex = matcher.start();
 
          searchResults.add( Integer.toString( seqIndex) );
-         searchResults.add( Integer.toString( resIndex) );
-         searchResults.add( Integer.toString( matcher.end()-1 ) );
+         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()) ) );
          if(!findAll)
          {
            // thats enough, break and display the result
-- 
1.7.10.2