regular expression added

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