X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=e1431a99cc4ac073569830cbb3b7403293a2be5b;hb=f09f33647e90a6376ffcf096d003afa59f2b41fc;hp=e8c16d234f398bce693cd176b1601c56abf6a501;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e8c16d2..e1431a9 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -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;
     }
 
 
@@ -114,34 +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),
+                searchResults.getResultEnd(i),
                "Search Results");
-
-            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-                textinput.getText(), new Color(60,160,115),
-                    "Search Results");
-
-            seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
-        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);
+        }
     }
 
     /**