X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=e1431a99cc4ac073569830cbb3b7403293a2be5b;hb=6834a636a0b72693041e2f1090c1123f215c9ec1;hp=6a73bd10c6d34d50150067ca095bcbcf7e9ac5b9;hpb=38914ae896884a4b305fda6fea00753c78f8ed12;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 6a73bd1..e1431a9 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -54,11 +54,13 @@ public class Finder extends GFinder
      * @param ap DOCUMENT ME!
      * @param f DOCUMENT ME!
      */
-    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
+    public Finder()
     {
-        this.av = av;
-        this.ap = ap;
-        frame = f;
+      frame = new JInternalFrame();
+      frame.setContentPane(this);
+      frame.setLayer(JLayeredPane.PALETTE_LAYER);
+      Desktop.addInternalFrame(frame, "Find", 340, 110);
+
 
         // all a big pain, but we need to wait until the frame is visible before the textfield can
         // obtain the focus/////////////////////////
@@ -85,6 +87,7 @@ public class Finder extends GFinder
      */
     public void findNext_actionPerformed(ActionEvent e)
     {
+      if (getFocusedViewport())
         doSearch(false);
     }
 
@@ -95,9 +98,25 @@ public class Finder extends GFinder
      */
     public void findAll_actionPerformed(ActionEvent e)
     {
+      if(getFocusedViewport())
+      {
         resIndex = 0;
         seqIndex = 0;
         doSearch(true);
+      }
+    }
+
+    boolean getFocusedViewport()
+    {
+      JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
+
+      if(frame!=null && frame instanceof AlignFrame)
+      {
+        av = ((AlignFrame)frame).viewport;
+        ap = ((AlignFrame)frame).alignPanel;
+        return true;
+      }
+      return false;
     }
 
 
@@ -114,31 +133,29 @@ public class Finder extends GFinder
         panel.add(label, BorderLayout.NORTH);
         panel.add(textinput, BorderLayout.SOUTH);
 
-         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            panel, "New Sequence Feature Name",
-          JOptionPane.OK_CANCEL_OPTION );
 
-         if(reply != JOptionPane.OK_OPTION)
-           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);
+            seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
 
-            SequenceFeature sf = new SequenceFeature(textinput.getText(),
+            features[i] = 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);
+                searchResults.getResultEnd(i),
+               "Search Results");
         }
 
-        ap.alignFrame.showSeqFeatures.setSelected(true);
-        av.setShowSequenceFeatures(true);
-        ap.highlightSearchResults(null);
+        if( ap.seqPanel.seqCanvas.getFeatureRenderer()
+            .createNewFeatures(seqs, features))
+        {
+          ap.alignFrame.showSeqFeatures.setSelected(true);
+          av.setShowSequenceFeatures(true);
+          ap.highlightSearchResults(null);
+        }
     }
 
     /**
@@ -150,7 +167,10 @@ 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;
 
@@ -167,7 +187,7 @@ 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);
             }
@@ -183,16 +203,6 @@ 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);
-
-      //SG  searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
         int end = av.alignment.getHeight();
 
@@ -200,7 +210,7 @@ public class Finder extends GFinder
 
         if (selection != null)
         {
-            if ((selection.getSize() < 1) ||
+            if ((selection.getSize(false) < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -211,7 +221,7 @@ 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;
@@ -219,7 +229,9 @@ 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))