now uses 1.1 friendly regex

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 1ff31fe..2311a9f 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -6,7 +6,6 @@ import java.awt.event.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 import java.util.*;\r
-import java.util.regex.*;\r
 import java.awt.*;\r
 \r
 public class Finder extends GFinder\r
@@ -92,7 +91,7 @@ public class Finder extends GFinder
     int [] allResults = null;\r
 \r
     Sequence seq;\r
-    String item;\r
+    String item=null;\r
     boolean found = false;\r
 \r
     /// is the searchString a residue number?\r
@@ -109,8 +108,6 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
 \r
-\r
-      //av.getAlignment().getSequenceAt(seq).findPosition(res)\r
     }catch(NumberFormatException ex){}\r
 \r
     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
@@ -122,10 +119,21 @@ public class Finder extends GFinder
 \r
     searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
 \r
-    while( !found && seqIndex<av.getAlignment().getHeight())\r
+    int end = av.alignment.getHeight();\r
+\r
+\r
+    SequenceGroup rubberband = av.getRubberbandGroup();\r
+    if(rubberband!=null)\r
+      end = rubberband.getEndRes();\r
+\r
+\r
+\r
+    while( !found && seqIndex<end)\r
     {\r
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))\r
+\r
+      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)\r
+            || (rubberband!=null && !rubberband.sequences.contains(seq))  )\r
       {\r
         // if a selection has been made, only search within that selection\r
         seqIndex++;\r
@@ -135,6 +143,9 @@ public class Finder extends GFinder
 \r
       item = seq.getSequence();\r
 \r
+      if(rubberband!=null)\r
+        item = item.substring(0, rubberband.getEndRes()+1);\r
+\r
       ///Shall we ignore gaps????\r
       StringBuffer noGaps = new StringBuffer();\r
       int insertCount=0;\r
@@ -153,23 +164,26 @@ public class Finder extends GFinder
       }\r
 \r
 \r
-      Pattern pattern = Pattern.compile(searchString);\r
-      Matcher matcher = pattern.matcher(noGaps);\r
+      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
 \r
       for(int r = resIndex; r<noGaps.length(); r++)\r
       {\r
 \r
-       if( matcher.find( r ) )\r
+       if( regex.searchFrom( noGaps.toString(), r ) )\r
        {\r
-         resIndex = matcher.start();\r
+         resIndex = regex.matchedFrom();\r
+\r
+\r
+         if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())\r
+           continue;\r
 \r
          searchResults.add( Integer.toString( seqIndex) );\r
          searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
-         searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString()) ) );\r
+         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );\r
 \r
          SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
                                              resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
-                                      matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())\r
+                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())\r
             );\r
          sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
          searchGroup.addGroup( sg );\r
@@ -182,7 +196,7 @@ public class Finder extends GFinder
            break;\r
          }\r
 \r
-         r=resIndex+1;\r
+         r=resIndex;\r
        }\r
       }\r
       if(!found)\r
@@ -190,7 +204,7 @@ public class Finder extends GFinder
         seqIndex++;\r
         resIndex = 0;\r
       }\r
-          }\r
+    }\r
 \r
     if(searchResults.size()>0)\r
     {\r