X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=7483a0ad543bd74a091e7bee267c995aaec2ea47;hb=1340920fd1b15c9bc8cd2284def7ec176a4989d5;hp=e1a3082e23d142d8ac37748115cac1f2bcf131ed;hpb=5b6d555458f48c4631883a8769fcc1dd5f578e34;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e1a3082..7483a0a 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.*;
+import java.awt.*;
 
 public class Finder extends GFinder
 {
@@ -14,6 +14,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;
   JInternalFrame frame;
   String searchString;
+  SuperGroup searchGroup;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -32,11 +33,14 @@ public class Finder extends GFinder
         SwingUtilities.invokeLater(new Runnable()
         {
           public void run()
-          {
-            textfield.requestFocus();
-          }
+          {   textfield.requestFocus();      }
        });
-   }
+     }
+
+     public void internalFrameClosing(InternalFrameEvent evt)
+     {
+       cancel_actionPerformed(null);
+     }
 });
 
   }
@@ -63,29 +67,40 @@ public class Finder extends GFinder
     try{
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
       ap.highlightSearchResults( null );
-      frame.setClosed(true);
+     // frame.setClosed(true);
     }catch(Exception ex){ }
+  }
+
 
+  public void createNewGroup_actionPerformed(ActionEvent e)
+  {
+    for(int i=0; i<searchGroup.getSize(); i++)
+      av.alignment.addGroup( searchGroup.getGroupeAt(i));
+
+    ap.av.alignment.addSuperGroup(searchGroup);
+    ap.highlightSearchResults( null );
   }
 
+
   void doSearch(boolean findAll)
   {
+    createNewGroup.setEnabled(false);
     searchString = textfield.getText().toUpperCase();
 
     ArrayList searchResults = new ArrayList();
     int [] allResults = null;
 
     Sequence seq;
-    String item;
+    String item=null;
     boolean found = false;
 
-    /// is the searchString a residue number?
+    ////// is the searchString a residue number?
     try{
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelection().size()>0)
-        seq = (Sequence)(av.getSelection().sequenceAt(0));
+      if(av.getSelectionGroup().getSize()>0)
+        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
       else
         seq = (Sequence)av.getAlignment().getSequenceAt(0);
 
@@ -93,38 +108,83 @@ 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();
+    Color [] newColors = new Color[24];
+    for(int i=0; i<24; i++)
+      newColors[i] = new Color(60,160,115);
+
+    ucs.setColourScheme(newColors);
+
+    searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+
+    int end = av.alignment.getHeight();
 
+    SequenceGroup selection = av.getSelectionGroup();
+    if(selection!=null)
+     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
+      selection = null;
 
-    while( !found && seqIndex<av.getAlignment().getHeight())
+    while( !found && seqIndex<end)
     {
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
+      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
 
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
+
+      if(selection!=null && !selection.sequences.contains(seq))
       {
-        // if a selection has been made, only search within that selection
         seqIndex++;
         resIndex=0;
         continue;
       }
 
-      item = seq.getSequence();
+      item = seq.getSequence().toUpperCase();
+
+      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
+          item = item.substring(0, selection.getEndRes()+1);
+
+      ///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);
+      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
 
-      for(int r = resIndex; r<item.length(); r++)
+      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(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
+           continue;
 
          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( 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()) ,
+                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())
+            );
+         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
+         searchGroup.addGroup( sg );
+
          if(!findAll)
          {
            // thats enough, break and display the result
@@ -133,7 +193,7 @@ public class Finder extends GFinder
            break;
          }
 
-         r=resIndex+1;
+         r=resIndex;
        }
       }
       if(!found)
@@ -149,6 +209,7 @@ public class Finder extends GFinder
       for(int i=0; i<searchResults.size(); i++)
         allResults[i] = Integer.parseInt(searchResults.get(i).toString());
 
+      createNewGroup.setEnabled(true);
     }
     else
     {