From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 12 Jan 2005 18:14:44 +0000 (+0000)
Subject: regular expression added
X-Git-Tag: Release_2_0~783
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=5b6d555458f48c4631883a8769fcc1dd5f578e34;p=jalview.git

regular expression added
---

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 909ba1f..e1a3082 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -6,7 +6,7 @@ import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-
+import java.util.regex.*;
 
 public class Finder extends GFinder
 {
@@ -112,15 +112,19 @@ public class Finder extends GFinder
 
       item = seq.getSequence();
 
+      Pattern pattern = Pattern.compile(searchString);
+      Matcher matcher = pattern.matcher(item);
+
       for(int r = resIndex; r<item.length(); r++)
       {
-       if(item.indexOf(searchString,r)>-1)
+
+       if( matcher.find( r ) )
        {
-         resIndex = item.indexOf(searchString,r);
+         resIndex = matcher.start();
 
-         searchResults.add( Integer.toString(seqIndex) );
+         searchResults.add( Integer.toString( seqIndex) );
          searchResults.add( Integer.toString( resIndex) );
-         searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );
+         searchResults.add( Integer.toString( matcher.end()-1 ) );
          if(!findAll)
          {
            // thats enough, break and display the result
@@ -141,19 +145,10 @@ public class Finder extends GFinder
 
     if(searchResults.size()>0)
     {
-
       allResults = new int[searchResults.size()];
       for(int i=0; i<searchResults.size(); i++)
         allResults[i] = Integer.parseInt(searchResults.get(i).toString());
 
-      if (findAll)
-      {
-        String message =  (searchResults.size()/3) + " matches found.";
-        JOptionPane.showInternalMessageDialog(this, message, null,
-                                              JOptionPane.INFORMATION_MESSAGE);
-      }
-
-
     }
     else
     {
@@ -165,6 +160,12 @@ public class Finder extends GFinder
     // if allResults is null, this effectively switches displaySearch flag in seqCanvas
     ap.highlightSearchResults( allResults );
 
+    if (findAll)
+    {
+      String message =  (searchResults.size()/3) + " matches found.";
+      JOptionPane.showInternalMessageDialog(this, message, null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+    }
 
   }