From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jan 2005 18:28:00 +0000 (+0000)
Subject: SuperGroup added
X-Git-Tag: Release_2_0~745
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1f183a4e9d63b2af6cf7184274affc80e11ef344;p=jalview.git

SuperGroup added
---

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index c2cf25b..1ff31fe 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -7,6 +7,7 @@ import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
 import java.util.regex.*;
+import java.awt.*;
 
 public class Finder extends GFinder
 {
@@ -14,6 +15,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;
   JInternalFrame frame;
   String searchString;
+  SuperGroup searchGroup;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -32,11 +34,14 @@ public class Finder extends GFinder
         SwingUtilities.invokeLater(new Runnable()
         {
           public void run()
-          {
-            textfield.requestFocus();
-          }
+          {   textfield.requestFocus();      }
        });
-   }
+     }
+
+     public void internalFrameClosing(InternalFrameEvent evt)
+     {
+       cancel_actionPerformed(null);
+     }
 });
 
   }
@@ -63,13 +68,24 @@ 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();
@@ -97,6 +113,14 @@ public class Finder extends GFinder
       //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);
 
     while( !found && seqIndex<av.getAlignment().getHeight())
     {
@@ -142,6 +166,14 @@ public class Finder extends GFinder
          searchResults.add( Integer.toString( seqIndex) );
          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()) ) );
+
+         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
+                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
+                                      matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())
+            );
+         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
+         searchGroup.addGroup( sg );
+
          if(!findAll)
          {
            // thats enough, break and display the result
@@ -158,7 +190,7 @@ public class Finder extends GFinder
         seqIndex++;
         resIndex = 0;
       }
-    }
+          }
 
     if(searchResults.size()>0)
     {
@@ -166,6 +198,7 @@ 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
     {