X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=6d205b6e009c0fca5e9ae5fcebb5cb3a3b2e2b55;hb=060d6bde353cf30ac112572ec8b8d3bcc072f77b;hp=4f698d2f2ce973baecbe7f968a0d63a264ec0e19;hpb=42fe80f86baa12e456936ff789ea5f0f8f03c574;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 4f698d2..6d205b6 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 (Version 2.4)
+ * Copyright (C) 2008 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.*;
@@ -26,24 +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();
     }
@@ -61,6 +63,7 @@ public class Finder
         ap.highlightSearchResults(null);
       }
     });
+    textfield.requestFocus();
   }
 
   public void actionPerformed(ActionEvent evt)
@@ -89,43 +92,26 @@ public class Finder
 
   public void createNewGroup_actionPerformed()
   {
-
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
-    cap.accept.setLabel("Accept");
-    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
-    dialog.add(cap);
-
-    cap.setText(textfield.getText());
-
-    dialog.setBounds(frame.getLocation().x + frame.getSize().width + 5,
-                     frame.getLocation().y + 20, 300, 100);
-    dialog.show();
-
-    String featureName = cap.getText().trim();
-    if (featureName.length() < 1)
-    {
-      return;
-    }
+    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+    SequenceFeature[] features = new SequenceFeature[searchResults
+            .getSize()];
 
     for (int i = 0; i < searchResults.getSize(); i++)
     {
-      SequenceI seq = searchResults.getResultSequence(i);
-
-      SequenceFeature sf = new SequenceFeature(featureName,
-                                               null, null,
-                                               searchResults.getResultStart(i),
-                                               searchResults.getResultEnd(i),
-                                               "Search Results");
+      seqs[i] = searchResults.getResultSequence(i);
 
-      ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-          featureName, new Color(60, 160, 115));
-      seq.addSequenceFeature(sf);
+      features[i] = new SequenceFeature(textfield.getText().trim(),
+              "Search Results", null, searchResults.getResultStart(i),
+              searchResults.getResultEnd(i), "Search Results");
     }
 
-    ap.seqPanel.seqCanvas.getFeatureRenderer().featuresAdded();
-    ap.alignFrame.sequenceFeatures.setState(true);
-    av.showSequenceFeatures(true);
-    ap.highlightSearchResults(null);
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
+    {
+      ap.alignFrame.sequenceFeatures.setState(true);
+      av.showSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
   }
 
   void doSearch(boolean findAll)
@@ -136,8 +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);
 
@@ -166,30 +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");