X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=e0ceeef67f4039a5644cf334096025ac37f00343;hb=6343ef96ba495c10379c367c9348c9b7d336b82c;hp=5f215edaf44a1e2342720fc6c43b1472491fe646;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5f215ed..e0ceeef 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 +108,39 @@ public class Finder extends GFinder
      */
     public void createNewGroup_actionPerformed(ActionEvent e)
     {
-        Color[] newColors = new Color[24];
+        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);
 
-        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();
+         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),
+               "Search Results");
+
+            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+                textinput.getText(), new Color(60,160,115),
+                    "Search Results");
+
+            seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.av.alignment.addSuperGroup(searchGroup);
+        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+        ap.alignFrame.showSeqFeatures.setSelected(true);
+        av.setShowSequenceFeatures(true);
         ap.highlightSearchResults(null);
     }
 
@@ -149,7 +153,10 @@ public class Finder extends GFinder
     {
         createNewGroup.setEnabled(false);
 
-        String searchString = textfield.getText().toUpperCase().trim();
+        String searchString = textfield.getText().trim();
+        if(!caseSensitive.isSelected())
+          searchString = searchString.toUpperCase();
+
         if(searchString.length()<1)
           return;
 
@@ -166,7 +173,7 @@ public class Finder extends GFinder
         {
             int res = Integer.parseInt(searchString);
             found = true;
-            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
             {
               seq = (Sequence) av.getAlignment().getSequenceAt(0);
             }
@@ -182,16 +189,6 @@ public class Finder extends GFinder
         }
 
         ///////////////////////////////////////////////
-        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);
-
-        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
         int end = av.alignment.getHeight();
 
@@ -199,7 +196,7 @@ public class Finder extends GFinder
 
         if (selection != null)
         {
-            if ((selection.getSize() < 1) ||
+            if ((selection.getSize(false) < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -210,7 +207,7 @@ public class Finder extends GFinder
         {
             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-            if ((selection != null) && !selection.sequences.contains(seq))
+            if ((selection != null) && !selection.getSequences(false).contains(seq))
             {
                 seqIndex++;
                 resIndex = 0;
@@ -218,7 +215,9 @@ public class Finder extends GFinder
                 continue;
             }
 
-            item = seq.getSequence().toUpperCase();
+            item = seq.getSequence();
+            if(!caseSensitive.isSelected())
+              item = item.toUpperCase();
 
             if ((selection != null) &&
                     (selection.getEndRes() < av.alignment.getWidth()-1))