From 8302463adc038c6385cde595bcb3a7ef5b2fd07c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Feb 2006 15:24:50 +0000
Subject: [PATCH] Set as feature, not new group

---
 src/jalview/gui/Finder.java |   45 ++++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5f215ed..5d800ce 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -42,7 +42,6 @@ public class Finder extends GFinder
     AlignViewport av;
     AlignmentPanel ap;
     JInternalFrame frame;
-    SuperGroup searchGroup;
     int seqIndex = 0;
     int resIndex = 0;
 
@@ -109,34 +108,36 @@ public class Finder extends GFinder
      */
     public void createNewGroup_actionPerformed(ActionEvent e)
     {
-        Color[] newColors = new Color[24];
-
-        for (int i = 0; i < 24; i++)
-        {
-            newColors[i] = new Color(60, 160, 115);
-        }
+        JLabel label = new JLabel("Enter name of new sequence feature");
+        JTextField textinput = new JTextField(textfield.getText());
+        JPanel panel = new JPanel(new BorderLayout());
+        panel.add(label, BorderLayout.NORTH);
+        panel.add(textinput, BorderLayout.SOUTH);
 
-        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-        String searchString = textfield.getText();
+         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            panel, "New Sequence Feature Name",
+          JOptionPane.OK_CANCEL_OPTION );
 
-        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+         if(reply != JOptionPane.OK_OPTION)
+           return;
 
         for (int i = 0; i < searchResults.getSize(); i ++ )
         {
-            // its possible edits may have occurred since search was performed
-            // account for this here
             SequenceI seq = searchResults.getResultSequence(i);
-            int startRes = seq.findIndex(searchResults.getResultStart(i)) - 1;
-            int endRes = seq.findIndex(searchResults.getResultEnd(i)) - 1;
-
-            SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
-                    false, startRes, endRes);
-            sg.addSequence(seq, false);
-            av.alignment.addGroup(sg);
-            searchGroup.addGroup(sg);
+
+            SequenceFeature sf = new SequenceFeature(textinput.getText(),
+                "Search Results", null,
+                searchResults.getResultStart(i),
+               searchResults.getResultEnd(i));
+
+            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+                textinput.getText(), new Color(60,160,115));
+
+            seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.av.alignment.addSuperGroup(searchGroup);
+        ap.alignFrame.sequenceFeatures.setSelected(true);
+        ap.alignFrame.sequenceFeatures_actionPerformed(null);
         ap.highlightSearchResults(null);
     }
 
@@ -191,7 +192,7 @@ public class Finder extends GFinder
 
         jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
 
-        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+      //SG  searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
         int end = av.alignment.getHeight();
 
-- 
1.7.10.2