Hidden representatives moved from sequence to viewport

[jalview.git] / src / jalview / gui / Finder.java

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e0ceeef..0e340dc 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -54,27 +54,14 @@ public class Finder extends GFinder
      * @param ap DOCUMENT ME!\r
      * @param f DOCUMENT ME!\r
      */\r
-    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
+    public Finder()\r
     {\r
-        this.av = av;\r
-        this.ap = ap;\r
-        frame = f;\r
+      frame = new JInternalFrame();\r
+      frame.setContentPane(this);\r
+      frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+      Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 \r
-        // all a big pain, but we need to wait until the frame is visible before the textfield can\r
-        // obtain the focus/////////////////////////\r
-        frame.addInternalFrameListener(new InternalFrameAdapter()\r
-            {\r
-                public void internalFrameOpened(InternalFrameEvent evt)\r
-                {\r
-                    SwingUtilities.invokeLater(new Runnable()\r
-                        {\r
-                            public void run()\r
-                            {\r
-                                textfield.requestFocus();\r
-                            }\r
-                        });\r
-                }\r
-            });\r
+      textfield.requestFocus();\r
     }\r
 \r
 \r
@@ -85,6 +72,7 @@ public class Finder extends GFinder
      */\r
     public void findNext_actionPerformed(ActionEvent e)\r
     {\r
+      if (getFocusedViewport())\r
         doSearch(false);\r
     }\r
 \r
@@ -95,9 +83,25 @@ public class Finder extends GFinder
      */\r
     public void findAll_actionPerformed(ActionEvent e)\r
     {\r
+      if(getFocusedViewport())\r
+      {\r
         resIndex = 0;\r
         seqIndex = 0;\r
         doSearch(true);\r
+      }\r
+    }\r
+\r
+    boolean getFocusedViewport()\r
+    {\r
+      JInternalFrame frame = Desktop.desktop.getAllFrames()[1];\r
+\r
+      if(frame!=null && frame instanceof AlignFrame)\r
+      {\r
+        av = ((AlignFrame)frame).viewport;\r
+        ap = ((AlignFrame)frame).alignPanel;\r
+        return true;\r
+      }\r
+      return false;\r
     }\r
 \r
 \r
@@ -114,34 +118,29 @@ public class Finder extends GFinder
         panel.add(label, BorderLayout.NORTH);\r
         panel.add(textinput, BorderLayout.SOUTH);\r
 \r
-         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
-            panel, "New Sequence Feature Name",\r
-          JOptionPane.OK_CANCEL_OPTION );\r
 \r
-         if(reply != JOptionPane.OK_OPTION)\r
-           return;\r
+        SequenceI [] seqs = new SequenceI[searchResults.getSize()];\r
+        SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];\r
+\r
 \r
         for (int i = 0; i < searchResults.getSize(); i ++ )\r
         {\r
-            SequenceI seq = searchResults.getResultSequence(i);\r
+            seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();\r
 \r
-            SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
+            features[i] = new SequenceFeature(textinput.getText(),\r
                 "Search Results", null,\r
                 searchResults.getResultStart(i),\r
-               searchResults.getResultEnd(i),\r
+                searchResults.getResultEnd(i),\r
                "Search Results");\r
-\r
-            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
-                textinput.getText(), new Color(60,160,115),\r
-                    "Search Results");\r
-\r
-            seq.getDatasetSequence().addSequenceFeature(sf);\r
         }\r
 \r
-        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
-        ap.alignFrame.showSeqFeatures.setSelected(true);\r
-        av.setShowSequenceFeatures(true);\r
-        ap.highlightSearchResults(null);\r
+        if( ap.seqPanel.seqCanvas.getFeatureRenderer()\r
+            .createNewFeatures(seqs, features))\r
+        {\r
+          ap.alignFrame.showSeqFeatures.setSelected(true);\r
+          av.setShowSequenceFeatures(true);\r
+          ap.highlightSearchResults(null);\r
+        }\r
     }\r
 \r
     /**\r
@@ -173,7 +172,7 @@ public class Finder extends GFinder
         {\r
             int res = Integer.parseInt(searchString);\r
             found = true;\r
-            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
             {\r
               seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
             }\r
@@ -196,7 +195,7 @@ public class Finder extends GFinder
 \r
         if (selection != null)\r
         {\r
-            if ((selection.getSize(false) < 1) ||\r
+            if ((selection.getSize() < 1) ||\r
                     ((selection.getEndRes() - selection.getStartRes()) < 2))\r
             {\r
                 selection = null;\r
@@ -207,7 +206,7 @@ public class Finder extends GFinder
         {\r
             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
-            if ((selection != null) && !selection.getSequences(false).contains(seq))\r
+            if ((selection != null) && !selection.getSequences(null).contains(seq))\r
             {\r
                 seqIndex++;\r
                 resIndex = 0;\r
@@ -215,7 +214,7 @@ public class Finder extends GFinder
                 continue;\r
             }\r
 \r
-            item = seq.getSequence();\r
+            item = seq.getSequenceAsString();\r
             if(!caseSensitive.isSelected())\r
               item = item.toUpperCase();\r
 \r