X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=f9962a6e3d9fb345171946358ab6b7b77ad7cc82;hb=f2287ae5b61b6bf36ee90bd6bbf38d44331bf273;hp=2b742b21ba8418995add99fb07f998821a313d7d;hpb=0eca27bca577e774acd5aefb165e7c6396a1995e;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 2b742b2..f9962a6 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -26,25 +25,27 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class Finder
-    extends Panel implements ActionListener
+public class Finder extends Panel implements ActionListener
 {
   AlignViewport av;
+
   AlignmentPanel ap;
+
   Frame frame;
 
   SearchResults searchResults;
 
   int seqIndex = 0;
+
   int resIndex = 0;
+
   public Finder(final AlignmentPanel ap)
   {
     try
     {
       jbInit();
 
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -92,21 +93,20 @@ public class Finder
   public void createNewGroup_actionPerformed()
   {
     SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+    SequenceFeature[] features = new SequenceFeature[searchResults
+            .getSize()];
 
     for (int i = 0; i < searchResults.getSize(); i++)
     {
       seqs[i] = searchResults.getResultSequence(i);
 
       features[i] = new SequenceFeature(textfield.getText().trim(),
-                                        "Search Results", null,
-                                        searchResults.getResultStart(i),
-                                        searchResults.getResultEnd(i),
-                                        "Search Results");
+              "Search Results", null, searchResults.getResultStart(i),
+              searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-        .createNewFeatures(seqs, features, ap))
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
     {
       ap.alignFrame.sequenceFeatures.setState(true);
       av.showSequenceFeatures(true);
@@ -122,8 +122,8 @@ public class Finder
       av = ap.av;
     }
     createNewGroup.setEnabled(false);
-    jalview.analysis.Finder finder = new jalview.analysis.Finder(av.
-        getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+    jalview.analysis.Finder finder = new jalview.analysis.Finder(av
+            .getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.getState());
     finder.setFindAll(findAll);
 
@@ -152,30 +152,37 @@ public class Finder
       seqIndex = 0;
     }
 
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    // if allResults is null, this effectively switches displaySearch flag in
+    // seqCanvas
     ap.highlightSearchResults(searchResults);
 
     if (findAll)
     {
-      String message = (searchResults == null ? 0 : searchResults.getSize()) +
-          " matches found.";
-      ap.alignFrame.statusBar.setText("Search results: " + searchString + " : " +
-                                      message);
+      String message = (searchResults == null ? 0 : searchResults.getSize())
+              + " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: " + searchString
+              + " : " + message);
     }
 
   }
 
   Label jLabel1 = new Label();
+
   protected TextField textfield = new TextField();
+
   protected Button findAll = new Button();
+
   protected Button findNext = new Button();
+
   Panel jPanel1 = new Panel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   protected Button createNewGroup = new Button();
+
   Checkbox caseSensitive = new Checkbox();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
     jLabel1.setText("Find");