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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e8c16d2..e1431a9 100755 (executable)
--- 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!\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
 \r
         // all a big pain, but we need to wait until the frame is visible before the textfield can\r
         // obtain the focus/////////////////////////\r
@@ -85,6 +87,7 @@ public class Finder extends GFinder
      */\r
     public void findNext_actionPerformed(ActionEvent e)\r
     {\r
+      if (getFocusedViewport())\r
         doSearch(false);\r
     }\r
 \r
@@ -95,9 +98,25 @@ 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 +133,29 @@ 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