From b321b54427b86297419763808dda86e9b10e7a00 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Feb 2006 15:18:41 +0000
Subject: [PATCH] Feature replaces new superGroup

---
 src/jalview/appletgui/Finder.java |   36 +++++++++++-------------------------
 1 file changed, 11 insertions(+), 25 deletions(-)

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index ac7bc2c..fb8c280 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -31,7 +31,6 @@ public class Finder extends Panel implements ActionListener
   AlignViewport av;
   AlignmentPanel ap;
   Frame frame;
-  SuperGroup searchGroup;
 
   SearchResults searchResults;
 
@@ -84,36 +83,23 @@ public class Finder extends Panel implements ActionListener
 
   public void createNewGroup_actionPerformed()
   {
-    Color[] newColors = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      newColors[i] = new Color(60, 160, 115);
-    }
-
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-        newColors);
-    String searchString = textfield.getText();
-
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
     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;
+        SequenceI seq = searchResults.getResultSequence(i);
 
-      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(textfield.getText(),
+            "Search Results", null,
+            searchResults.getResultStart(i),
+           searchResults.getResultEnd(i));
 
+        ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+            textfield.getText(), new Color(60,160,115));
+        seq.addSequenceFeature(sf);
     }
 
-    ap.av.alignment.addSuperGroup(searchGroup);
+    ap.alignFrame.sequenceFeatures.setState(true);
+    av.showSequenceFeatures(true);
     ap.highlightSearchResults(null);
   }
 
@@ -321,7 +307,7 @@ public class Finder extends Panel implements ActionListener
       gridLayout1.setVgap(2);
       createNewGroup.setEnabled(false);
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      createNewGroup.setLabel("Create new group");
+      createNewGroup.setLabel("New Feature");
       createNewGroup.addActionListener(this);
       jPanel1.add(findNext, null);
       jPanel1.add(findAll, null);
-- 
1.7.10.2