Feature Settings added to Applet
[jalview.git] / src / jalview / appletgui / AlignFrame.java
index 0670a31..fbe21b5 100755 (executable)
@@ -31,10 +31,11 @@ import java.io.BufferedReader;
 import java.net.URL;\r
 \r
 \r
-public class AlignFrame extends Frame\r
+public class AlignFrame extends Frame implements ActionListener,\r
+    ItemListener, KeyListener, MouseListener\r
 {\r
-  final AlignmentPanel alignPanel;\r
-  public final AlignViewport viewport;\r
+  public AlignmentPanel alignPanel;\r
+  public AlignViewport viewport;\r
   int NEW_WINDOW_WIDTH = 700;\r
   int NEW_WINDOW_HEIGHT = 500;\r
   jalview.bin.JalviewLite applet;\r
@@ -52,8 +53,8 @@ public class AlignFrame extends Frame
     this.applet = applet;\r
     viewport = new AlignViewport(al, applet);\r
     alignPanel = new AlignmentPanel(this, viewport);\r
-    add(alignPanel);\r
-    alignPanel.validate();\r
+\r
+    annotationPanelMenuItem.setState(viewport.showAnnotation);\r
 \r
     if(applet!=null)\r
     {\r
@@ -61,9 +62,9 @@ public class AlignFrame extends Frame
       if (param != null)\r
       {\r
         if (param.equalsIgnoreCase("Id"))\r
-          sortIDMenuItem_actionPerformed(null);\r
+          sortIDMenuItem_actionPerformed();\r
         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
-          sortPairwiseMenuItem_actionPerformed(null);\r
+          sortPairwiseMenuItem_actionPerformed();\r
       }\r
 \r
       param = applet.getParameter("wrap");\r
@@ -72,7 +73,7 @@ public class AlignFrame extends Frame
         if (param.equalsIgnoreCase("true"))\r
         {\r
           wrapMenuItem.setState(true);\r
-          wrapMenuItem_actionPerformed(null);\r
+          wrapMenuItem_actionPerformed();\r
         }\r
       }\r
 \r
@@ -96,20 +97,11 @@ public class AlignFrame extends Frame
 \r
     }\r
 \r
-   MyKeyAdapter keyAdapter = new MyKeyAdapter();\r
    //Some JVMS send keyevents to Top frame or lowest panel,\r
    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
-   this.addKeyListener(keyAdapter);\r
-   alignPanel.seqPanel.seqCanvas.addKeyListener(keyAdapter);\r
-   alignPanel.idPanel.idCanvas.addKeyListener(keyAdapter);\r
-\r
-    this.addWindowListener(new WindowAdapter()\r
-    {\r
-      public void windowClosing(WindowEvent e)\r
-          {\r
-            closeMenuItem_actionPerformed(null);\r
-          }\r
-    });\r
+   this.addKeyListener(this);\r
+   alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+   alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 \r
     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
     {\r
@@ -122,11 +114,13 @@ public class AlignFrame extends Frame
      }\r
    });\r
 \r
-   jalview.bin.JalviewLite.addFrame(this, title,\r
-                                    NEW_WINDOW_WIDTH,\r
-                                    NEW_WINDOW_HEIGHT);\r
-  }\r
 \r
+   add(alignPanel, BorderLayout.CENTER);\r
+   jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+\r
+   alignPanel.validate();\r
+   alignPanel.repaint();\r
+  }\r
   public AlignViewport getAlignViewport()\r
   {\r
     return viewport;\r
@@ -209,6 +203,10 @@ public class AlignFrame extends Frame
       }\r
 \r
       viewport.showSequenceFeatures = true;\r
+      viewMenu.addSeparator();\r
+      viewMenu.add(sequenceFeatures);\r
+      viewMenu.add(featureSettings);\r
+\r
 \r
       alignPanel.repaint();\r
 \r
@@ -219,64 +217,205 @@ public class AlignFrame extends Frame
     }\r
   }\r
 \r
-\r
-  class MyKeyAdapter extends KeyAdapter\r
+  public void keyPressed(KeyEvent evt)\r
   {\r
-\r
-    public void keyPressed(KeyEvent evt)\r
+    switch (evt.getKeyCode())\r
     {\r
-      switch (evt.getKeyCode())\r
-      {\r
-        case 27: // escape key\r
-          deselectAllSequenceMenuItem_actionPerformed(null);\r
-          break;\r
-        case KeyEvent.VK_X:\r
-          if (evt.isControlDown() || evt.isMetaDown())\r
-          {\r
-            cut_actionPerformed(null);\r
-          }\r
-          break;\r
-        case KeyEvent.VK_C:\r
-          if (evt.isControlDown() || evt.isMetaDown())\r
-          {\r
-            copy_actionPerformed(null);\r
-          }\r
-          break;\r
-        case KeyEvent.VK_V:\r
-          if (evt.isControlDown() || evt.isMetaDown())\r
-          {\r
-            paste(true);\r
-          }\r
-          break;\r
-        case KeyEvent.VK_A:\r
-          if (evt.isControlDown() || evt.isMetaDown())\r
-          {\r
-            selectAllSequenceMenuItem_actionPerformed(null);\r
-          }\r
-          break;\r
-        case KeyEvent.VK_DOWN:\r
-          moveSelectedSequences(false);\r
-          break;\r
-        case KeyEvent.VK_UP:\r
-          moveSelectedSequences(true);\r
-          break;\r
-        case KeyEvent.VK_F:\r
-          if (evt.isControlDown())\r
-          {\r
-            findMenuItem_actionPerformed(null);\r
-          }\r
-          break;\r
-        case KeyEvent.VK_BACK_SPACE:\r
-        case KeyEvent.VK_DELETE:\r
-          cut_actionPerformed(null);\r
-          break;\r
-\r
-      }\r
+      case 27: // escape key\r
+        deselectAllSequenceMenuItem_actionPerformed();\r
+        break;\r
+      case KeyEvent.VK_X:\r
+        if (evt.isControlDown() || evt.isMetaDown())\r
+        {\r
+          cut_actionPerformed();\r
+        }\r
+        break;\r
+      case KeyEvent.VK_C:\r
+        if (evt.isControlDown() || evt.isMetaDown())\r
+        {\r
+          copy_actionPerformed();\r
+        }\r
+        break;\r
+      case KeyEvent.VK_V:\r
+        if (evt.isControlDown() || evt.isMetaDown())\r
+        {\r
+          paste(true);\r
+        }\r
+        break;\r
+      case KeyEvent.VK_A:\r
+        if (evt.isControlDown() || evt.isMetaDown())\r
+        {\r
+          selectAllSequenceMenuItem_actionPerformed();\r
+        }\r
+        break;\r
+      case KeyEvent.VK_DOWN:\r
+        moveSelectedSequences(false);\r
+        break;\r
+      case KeyEvent.VK_UP:\r
+        moveSelectedSequences(true);\r
+        break;\r
+      case KeyEvent.VK_F:\r
+        if (evt.isControlDown())\r
+        {\r
+          findMenuItem_actionPerformed();\r
+        }\r
+        break;\r
+      case KeyEvent.VK_BACK_SPACE:\r
+      case KeyEvent.VK_DELETE:\r
+        cut_actionPerformed();\r
+        break;\r
     }\r
   }\r
-\r
-\r
-  public void inputText_actionPerformed(ActionEvent e)\r
+  public void keyReleased(KeyEvent evt)\r
+  {}\r
+  public void keyTyped(KeyEvent evt)\r
+  {}\r
+\r
+public void itemStateChanged(ItemEvent evt)\r
+  {\r
+    if(evt.getSource()==colourTextMenuItem)\r
+            colourTextMenuItem_actionPerformed();\r
+    else if(evt.getSource()==wrapMenuItem)\r
+            wrapMenuItem_actionPerformed();\r
+    else if(evt.getSource()==scaleAbove)\r
+            scaleAbove_actionPerformed();\r
+    else if(evt.getSource()==scaleLeft)\r
+            scaleLeft_actionPerformed();\r
+    else if(evt.getSource()==scaleRight)\r
+            scaleRight_actionPerformed();\r
+     else if(evt.getSource()==seqLimits)\r
+      seqLimits_itemStateChanged();\r
+    else if(evt.getSource()==viewBoxesMenuItem)\r
+            viewBoxesMenuItem_actionPerformed();\r
+    else if(evt.getSource()==viewTextMenuItem)\r
+            viewTextMenuItem_actionPerformed();\r
+    else if(evt.getSource()==renderGapsMenuItem)\r
+            renderGapsMenuItem_actionPerformed();\r
+    else if(evt.getSource()==annotationPanelMenuItem)\r
+            annotationPanelMenuItem_actionPerformed();\r
+      else if(evt.getSource()==sequenceFeatures)\r
+       {     viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+            alignPanel.seqPanel.seqCanvas.repaint();\r
+        }\r
+      else if(evt.getSource()==conservationMenuItem)\r
+            conservationMenuItem_actionPerformed();\r
+      else if(evt.getSource()==abovePIDThreshold)\r
+            abovePIDThreshold_actionPerformed();\r
+          else if(evt.getSource()==applyToAllGroups)\r
+            applyToAllGroups_actionPerformed();\r
+  }\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+    if(evt.getSource()==inputText)\r
+      inputText_actionPerformed();\r
+    else if(evt.getSource()==closeMenuItem)\r
+      closeMenuItem_actionPerformed();\r
+    else if(evt.getSource()==copy)\r
+      copy_actionPerformed();\r
+    else if(evt.getSource()==undoMenuItem)\r
+      undoMenuItem_actionPerformed();\r
+    else if(evt.getSource()==redoMenuItem)\r
+      redoMenuItem_actionPerformed();\r
+    else if(evt.getSource()==inputText)\r
+            inputText_actionPerformed();\r
+    else if(evt.getSource()==closeMenuItem)\r
+            closeMenuItem_actionPerformed();\r
+    else if(evt.getSource()==undoMenuItem)\r
+            undoMenuItem_actionPerformed();\r
+    else if(evt.getSource()==redoMenuItem)\r
+            redoMenuItem_actionPerformed();\r
+    else if(evt.getSource()==copy)\r
+            copy_actionPerformed();\r
+    else if(evt.getSource()==pasteNew)\r
+            pasteNew_actionPerformed();\r
+    else if(evt.getSource()==pasteThis)\r
+            pasteThis_actionPerformed();\r
+    else if(evt.getSource()==cut)\r
+            cut_actionPerformed();\r
+    else if(evt.getSource()==delete)\r
+            delete_actionPerformed();\r
+    else if(evt.getSource()==deleteGroups)\r
+            deleteGroups_actionPerformed();\r
+    else if(evt.getSource()==selectAllSequenceMenuItem)\r
+            selectAllSequenceMenuItem_actionPerformed();\r
+    else if(evt.getSource()==deselectAllSequenceMenuItem)\r
+            deselectAllSequenceMenuItem_actionPerformed();\r
+    else if(evt.getSource()==invertSequenceMenuItem)\r
+            invertSequenceMenuItem_actionPerformed();\r
+    else if(evt.getSource()==remove2LeftMenuItem)\r
+            remove2LeftMenuItem_actionPerformed();\r
+    else if(evt.getSource()==remove2RightMenuItem)\r
+            remove2RightMenuItem_actionPerformed();\r
+    else if(evt.getSource()==removeGappedColumnMenuItem)\r
+            removeGappedColumnMenuItem_actionPerformed();\r
+    else if(evt.getSource()==removeAllGapsMenuItem)\r
+            removeAllGapsMenuItem_actionPerformed();\r
+    else if(evt.getSource()==findMenuItem)\r
+            findMenuItem_actionPerformed();\r
+    else if(evt.getSource()==font)\r
+            font_actionPerformed();\r
+    else if(evt.getSource()==featureSettings)\r
+            featureSettings_actionPerformed();\r
+    else if(evt.getSource()==overviewMenuItem)\r
+            overviewMenuItem_actionPerformed();\r
+    else if(evt.getSource()==noColourmenuItem)\r
+            noColourmenuItem_actionPerformed();\r
+    else if(evt.getSource()==clustalColour)\r
+            clustalColour_actionPerformed();\r
+    else if(evt.getSource()==zappoColour)\r
+            zappoColour_actionPerformed();\r
+    else if(evt.getSource()==taylorColour)\r
+            taylorColour_actionPerformed();\r
+    else if(evt.getSource()==hydrophobicityColour)\r
+            hydrophobicityColour_actionPerformed();\r
+    else if(evt.getSource()==helixColour)\r
+            helixColour_actionPerformed();\r
+    else if(evt.getSource()==strandColour)\r
+            strandColour_actionPerformed();\r
+    else if(evt.getSource()==turnColour)\r
+            turnColour_actionPerformed();\r
+    else if(evt.getSource()==buriedColour)\r
+            buriedColour_actionPerformed();\r
+    else if(evt.getSource()==nucleotideColour)\r
+            nucleotideColour_actionPerformed();\r
+    else if(evt.getSource()==modifyPID)\r
+            modifyPID_actionPerformed();\r
+    else if(evt.getSource()==modifyConservation)\r
+            modifyConservation_actionPerformed();\r
+    else if(evt.getSource()==userDefinedColour)\r
+            userDefinedColour_actionPerformed();\r
+    else if(evt.getSource()==PIDColour)\r
+            PIDColour_actionPerformed();\r
+    else if(evt.getSource()==BLOSUM62Colour)\r
+            BLOSUM62Colour_actionPerformed();\r
+    else if(evt.getSource()==sortPairwiseMenuItem)\r
+            sortPairwiseMenuItem_actionPerformed();\r
+    else if(evt.getSource()==sortIDMenuItem)\r
+            sortIDMenuItem_actionPerformed();\r
+    else if(evt.getSource()==sortGroupMenuItem)\r
+            sortGroupMenuItem_actionPerformed();\r
+    else if(evt.getSource()==removeRedundancyMenuItem)\r
+            removeRedundancyMenuItem_actionPerformed();\r
+    else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
+            pairwiseAlignmentMenuItem_actionPerformed();\r
+    else if(evt.getSource()==PCAMenuItem)\r
+            PCAMenuItem_actionPerformed();\r
+    else if(evt.getSource()==averageDistanceTreeMenuItem)\r
+            averageDistanceTreeMenuItem_actionPerformed();\r
+    else if(evt.getSource()==neighbourTreeMenuItem)\r
+            neighbourTreeMenuItem_actionPerformed();\r
+    else if(evt.getSource()==njTreeBlosumMenuItem)\r
+            njTreeBlosumMenuItem_actionPerformed();\r
+    else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
+            avTreeBlosumMenuItem_actionPerformed();\r
+    else if(evt.getSource()==documentation)\r
+            documentation_actionPerformed();\r
+    else if(evt.getSource()==about)\r
+            about_actionPerformed();\r
+\r
+ }\r
+\r
+  public void inputText_actionPerformed()\r
   {\r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
     Frame frame = new Frame();\r
@@ -297,11 +436,13 @@ public class AlignFrame extends Frame
                                                       viewport.showJVSuffix));\r
   }\r
 \r
-  public void closeMenuItem_actionPerformed(ActionEvent e)\r
+  public void closeMenuItem_actionPerformed()\r
   {\r
     PaintRefresher.components.remove(viewport.alignment);\r
     if(PaintRefresher.components.size()==0 && applet==null)\r
       System.exit(0);\r
+\r
+    this.dispose();\r
   }\r
 \r
   Stack historyList = new Stack();\r
@@ -340,7 +481,7 @@ public class AlignFrame extends Frame
     updateEditMenuBar();\r
   }\r
 \r
-  protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+  protected void undoMenuItem_actionPerformed()\r
   {\r
     HistoryItem hi = (HistoryItem) historyList.pop();\r
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
@@ -349,7 +490,7 @@ public class AlignFrame extends Frame
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
   }\r
 \r
-  protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+  protected void redoMenuItem_actionPerformed()\r
   {\r
     HistoryItem hi = (HistoryItem) redoList.pop();\r
     restoreHistoryItem(hi);\r
@@ -454,7 +595,7 @@ public class AlignFrame extends Frame
   }\r
 \r
   StringBuffer copiedSequences;\r
-  protected void copy_actionPerformed(ActionEvent e)\r
+  protected void copy_actionPerformed()\r
   {\r
     if (viewport.getSelectionGroup() == null)\r
     {\r
@@ -524,12 +665,12 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  protected void pasteNew_actionPerformed(ActionEvent e)\r
+  protected void pasteNew_actionPerformed()\r
   {\r
     paste(true);\r
   }\r
 \r
-  protected void pasteThis_actionPerformed(ActionEvent e)\r
+  protected void pasteThis_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
                                    HistoryItem.PASTE));\r
@@ -599,13 +740,13 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  protected void cut_actionPerformed(ActionEvent e)\r
+  protected void cut_actionPerformed()\r
   {\r
-    copy_actionPerformed(null);\r
-    delete_actionPerformed(null);\r
+    copy_actionPerformed();\r
+    delete_actionPerformed();\r
   }\r
 \r
-  protected void delete_actionPerformed(ActionEvent e)\r
+  protected void delete_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
                                    HistoryItem.HIDE));\r
@@ -660,7 +801,7 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  protected void deleteGroups_actionPerformed(ActionEvent e)\r
+  protected void deleteGroups_actionPerformed()\r
   {\r
     viewport.alignment.deleteAllGroups();\r
     viewport.setSelectionGroup(null);\r
@@ -668,7 +809,7 @@ public class AlignFrame extends Frame
     alignPanel.repaint();\r
   }\r
 \r
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+  public void selectAllSequenceMenuItem_actionPerformed()\r
   {\r
     SequenceGroup sg = new SequenceGroup();\r
     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
@@ -681,17 +822,18 @@ public class AlignFrame extends Frame
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+  public void deselectAllSequenceMenuItem_actionPerformed()\r
   {\r
     viewport.setSelectionGroup(null);\r
     viewport.getColumnSelection().clear();\r
     viewport.setSelectionGroup(null);\r
+    alignPanel.idPanel.idCanvas.searchResults = null;\r
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
     alignPanel.repaint();\r
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+  public void invertSequenceMenuItem_actionPerformed()\r
   {\r
     SequenceGroup sg = viewport.getSelectionGroup();\r
     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
@@ -702,7 +844,7 @@ public class AlignFrame extends Frame
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
-  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+  public void remove2LeftMenuItem_actionPerformed()\r
   {\r
     ColumnSelection colSel = viewport.getColumnSelection();\r
     if (colSel.size() > 0)\r
@@ -731,7 +873,7 @@ public class AlignFrame extends Frame
     }\r
   }\r
 \r
-  public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+  public void remove2RightMenuItem_actionPerformed()\r
   {\r
     ColumnSelection colSel = viewport.getColumnSelection();\r
     if (colSel.size() > 0)\r
@@ -759,7 +901,7 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+  public void removeGappedColumnMenuItem_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
                                    viewport.alignment,\r
@@ -777,7 +919,7 @@ public class AlignFrame extends Frame
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
   }\r
 \r
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+  public void removeAllGapsMenuItem_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
                                    HistoryItem.HIDE));\r
@@ -861,6 +1003,8 @@ public class AlignFrame extends Frame
     resetAllColourSchemes();\r
     if(alignPanel.overviewPanel!=null)\r
       alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+    viewport.alignment.adjustSequenceAnnotations();\r
     alignPanel.repaint();\r
   }\r
 \r
@@ -905,18 +1049,18 @@ public class AlignFrame extends Frame
 \r
 \r
 \r
-  public void findMenuItem_actionPerformed(ActionEvent e)\r
+  public void findMenuItem_actionPerformed()\r
   {\r
     new Finder(alignPanel);\r
   }\r
 \r
-  public void font_actionPerformed(ActionEvent e)\r
+  public void font_actionPerformed()\r
   {\r
     new FontChooser(alignPanel);\r
   }\r
 \r
 \r
-  public void seqLimits_itemStateChanged(ItemEvent e)\r
+  public void seqLimits_itemStateChanged()\r
   {\r
     viewport.setShowJVSuffix(seqLimits.getState());\r
     alignPanel.fontChanged();\r
@@ -924,13 +1068,13 @@ public class AlignFrame extends Frame
   }\r
 \r
 \r
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+  protected void colourTextMenuItem_actionPerformed()\r
   {\r
     viewport.setColourText(colourTextMenuItem.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+  protected void wrapMenuItem_actionPerformed()\r
   {\r
     viewport.setWrapAlignment(wrapMenuItem.getState());\r
     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
@@ -940,49 +1084,54 @@ public class AlignFrame extends Frame
     alignPanel.repaint();\r
   }\r
 \r
-  protected void scaleAbove_actionPerformed(ActionEvent e)\r
+  protected void scaleAbove_actionPerformed()\r
   {\r
     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  protected void scaleLeft_actionPerformed(ActionEvent e)\r
+  protected void scaleLeft_actionPerformed()\r
   {\r
     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  protected void scaleRight_actionPerformed(ActionEvent e)\r
+  protected void scaleRight_actionPerformed()\r
   {\r
     viewport.setScaleRightWrapped(scaleRight.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+  public void viewBoxesMenuItem_actionPerformed()\r
   {\r
     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+  public void viewTextMenuItem_actionPerformed()\r
   {\r
     viewport.setShowText(viewTextMenuItem.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+  protected void renderGapsMenuItem_actionPerformed()\r
   {\r
     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
     alignPanel.repaint();\r
   }\r
 \r
-  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+  public void annotationPanelMenuItem_actionPerformed()\r
   {\r
     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
   }\r
 \r
-  public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+  public void featureSettings_actionPerformed()\r
+  {\r
+    new FeatureSettings(viewport, alignPanel);\r
+  }\r
+\r
+  public void overviewMenuItem_actionPerformed()\r
   {\r
     if (alignPanel.overviewPanel != null)\r
     {\r
@@ -1010,59 +1159,59 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  protected void noColourmenuItem_actionPerformed()\r
   {\r
     changeColour(null);\r
   }\r
 \r
-  public void clustalColour_actionPerformed(ActionEvent e)\r
+  public void clustalColour_actionPerformed()\r
   {\r
     abovePIDThreshold.setState(false);\r
     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
                                           viewport.alignment.getWidth()));\r
   }\r
 \r
-  public void zappoColour_actionPerformed(ActionEvent e)\r
+  public void zappoColour_actionPerformed()\r
   {\r
     changeColour(new ZappoColourScheme());\r
   }\r
 \r
-  public void taylorColour_actionPerformed(ActionEvent e)\r
+  public void taylorColour_actionPerformed()\r
   {\r
     changeColour(new TaylorColourScheme());\r
   }\r
 \r
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+  public void hydrophobicityColour_actionPerformed()\r
   {\r
     changeColour(new HydrophobicColourScheme());\r
   }\r
 \r
-  public void helixColour_actionPerformed(ActionEvent e)\r
+  public void helixColour_actionPerformed()\r
   {\r
     changeColour(new HelixColourScheme());\r
   }\r
 \r
-  public void strandColour_actionPerformed(ActionEvent e)\r
+  public void strandColour_actionPerformed()\r
   {\r
     changeColour(new StrandColourScheme());\r
   }\r
 \r
-  public void turnColour_actionPerformed(ActionEvent e)\r
+  public void turnColour_actionPerformed()\r
   {\r
     changeColour(new TurnColourScheme());\r
   }\r
 \r
-  public void buriedColour_actionPerformed(ActionEvent e)\r
+  public void buriedColour_actionPerformed()\r
   {\r
     changeColour(new BuriedColourScheme());\r
   }\r
 \r
-  public void nucleotideColour_actionPerformed(ActionEvent e)\r
+  public void nucleotideColour_actionPerformed()\r
   {\r
     changeColour(new NucleotideColourScheme());\r
   }\r
 \r
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+  protected void applyToAllGroups_actionPerformed()\r
   {\r
     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
   }\r
@@ -1183,7 +1332,7 @@ public class AlignFrame extends Frame
 \r
 \r
 \r
-  protected void modifyPID_actionPerformed(ActionEvent e)\r
+  protected void modifyPID_actionPerformed()\r
   {\r
     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
     {\r
@@ -1193,7 +1342,7 @@ public class AlignFrame extends Frame
     }\r
   }\r
 \r
-  protected void modifyConservation_actionPerformed(ActionEvent e)\r
+  protected void modifyConservation_actionPerformed()\r
   {\r
     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
     {\r
@@ -1203,7 +1352,7 @@ public class AlignFrame extends Frame
     }\r
   }\r
 \r
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+  protected void conservationMenuItem_actionPerformed()\r
   {\r
     viewport.setConservationSelected(conservationMenuItem.getState());\r
 \r
@@ -1212,10 +1361,10 @@ public class AlignFrame extends Frame
 \r
     changeColour(viewport.getGlobalColourScheme());\r
 \r
-    modifyConservation_actionPerformed(null);\r
+    modifyConservation_actionPerformed();\r
   }\r
 \r
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+  public void abovePIDThreshold_actionPerformed()\r
   {\r
     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 \r
@@ -1224,25 +1373,25 @@ public class AlignFrame extends Frame
 \r
     changeColour(viewport.getGlobalColourScheme());\r
 \r
-    modifyPID_actionPerformed(null);\r
+    modifyPID_actionPerformed();\r
   }\r
 \r
-  public void userDefinedColour_actionPerformed(ActionEvent e)\r
+  public void userDefinedColour_actionPerformed()\r
   {\r
     new UserDefinedColours(alignPanel, null);\r
   }\r
 \r
-  public void PIDColour_actionPerformed(ActionEvent e)\r
+  public void PIDColour_actionPerformed()\r
   {\r
     changeColour(new PIDColourScheme());\r
   }\r
 \r
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  public void BLOSUM62Colour_actionPerformed()\r
   {\r
     changeColour(new Blosum62ColourScheme());\r
   }\r
 \r
-  public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+  public void sortPairwiseMenuItem_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
@@ -1251,7 +1400,7 @@ public class AlignFrame extends Frame
     alignPanel.repaint();\r
   }\r
 \r
-  public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+  public void sortIDMenuItem_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
@@ -1259,7 +1408,7 @@ public class AlignFrame extends Frame
     alignPanel.repaint();\r
   }\r
 \r
-  public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+  public void sortGroupMenuItem_actionPerformed()\r
   {\r
     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
@@ -1268,7 +1417,7 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+  public void removeRedundancyMenuItem_actionPerformed()\r
   {\r
     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
     Frame frame = new Frame();\r
@@ -1278,7 +1427,7 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+  public void pairwiseAlignmentMenuItem_actionPerformed()\r
   {\r
     if (viewport.getSelectionGroup().getSize() > 1)\r
     {\r
@@ -1288,7 +1437,7 @@ public class AlignFrame extends Frame
     }\r
   }\r
 \r
-  public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+  public void PCAMenuItem_actionPerformed()\r
   {\r
     //are the sequences aligned?\r
     if (!viewport.alignment.isAligned())\r
@@ -1327,22 +1476,22 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+  public void averageDistanceTreeMenuItem_actionPerformed()\r
   {\r
     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
   }\r
 \r
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+  public void neighbourTreeMenuItem_actionPerformed()\r
   {\r
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
   }\r
 \r
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+  protected void njTreeBlosumMenuItem_actionPerformed()\r
   {\r
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
   }\r
 \r
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+  protected void avTreeBlosumMenuItem_actionPerformed()\r
   {\r
     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
   }\r
@@ -1394,7 +1543,7 @@ public class AlignFrame extends Frame
     sortByTreeMenu.add(item);\r
     item.addActionListener(new java.awt.event.ActionListener()\r
     {\r
-      public void actionPerformed(ActionEvent e)\r
+      public void actionPerformed(ActionEvent evt)\r
       {\r
         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
                                        HistoryItem.SORT));\r
@@ -1412,12 +1561,12 @@ public class AlignFrame extends Frame
     });\r
   }\r
 \r
-  protected void documentation_actionPerformed(ActionEvent e)\r
+  protected void documentation_actionPerformed()\r
   {\r
-    showURL("http://www.jalview.org/help.html");\r
+    showURL("http://www.jalview.org/help.html", "HELP");\r
   }\r
 \r
-  protected void about_actionPerformed(ActionEvent e)\r
+  protected void about_actionPerformed()\r
   {\r
 \r
     class AboutPanel extends Canvas\r
@@ -1482,17 +1631,6 @@ public class AlignFrame extends Frame
 \r
   }\r
 \r
-  /**\r
-   * Displays the given URL in a new browser window\r
-   *\r
-   * @param url URL to display in browser window.\r
-   * <br>New window will be named "HELP_WINDOW"\r
-   */\r
-  public void showURL(String url)\r
-  {\r
-    showURL(url, "HELP");\r
-  }\r
-\r
   public void showURL(String url, String target)\r
   {\r
     if (applet == null)\r
@@ -1574,7 +1712,7 @@ public class AlignFrame extends Frame
     MenuItem delete = new MenuItem();\r
     MenuItem copy = new MenuItem();\r
     MenuItem cut = new MenuItem();\r
-    Menu Menu1 = new Menu();\r
+    Menu pasteMenu = new Menu();\r
     MenuItem pasteNew = new MenuItem();\r
     MenuItem pasteThis = new MenuItem();\r
     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
@@ -1592,8 +1730,17 @@ public class AlignFrame extends Frame
     MenuItem documentation = new MenuItem();\r
     MenuItem about = new MenuItem();\r
     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
-\r
-    private void jbInit() throws Exception {\r
+  Panel embeddedMenu;\r
+  Label embeddedEdit;\r
+  Label embeddedSearch;\r
+  Label embeddedView;\r
+  Label embeddedColour;\r
+  Label embeddedFile;\r
+  Label embeddedHelp;\r
+  Label embeddedCalculate;\r
+  FlowLayout flowLayout1;\r
+\r
+  private void jbInit() throws Exception {\r
 \r
       setMenuBar(alignFrameMenuBar);\r
 \r
@@ -1617,123 +1764,50 @@ public class AlignFrame extends Frame
         outputTextboxMenu.add(item);\r
       }\r
 \r
-\r
         fileMenu.setLabel("File");\r
         closeMenuItem.setLabel("Close");\r
-        closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    closeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        closeMenuItem.addActionListener(this);\r
         editMenu.setLabel("Edit");\r
         viewMenu.setLabel("View");\r
         colourMenu.setLabel("Colour");\r
         calculateMenu.setLabel("Calculate");\r
         selectAllSequenceMenuItem.setLabel("Select all");\r
-        selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    selectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        selectAllSequenceMenuItem.addActionListener(this);\r
         deselectAllSequenceMenuItem.setLabel("Deselect All");\r
-        deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    deselectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        deselectAllSequenceMenuItem.addActionListener(this);\r
         invertSequenceMenuItem.setLabel("Invert Selection");\r
-        invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    invertSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        invertSequenceMenuItem.addActionListener(this);\r
         remove2LeftMenuItem.setLabel("Remove Left");\r
-        remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2LeftMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        remove2LeftMenuItem.addActionListener(this);\r
         remove2RightMenuItem.setLabel("Remove Right");\r
-        remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2RightMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        remove2RightMenuItem.addActionListener(this);\r
         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
-        removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeGappedColumnMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        removeGappedColumnMenuItem.addActionListener(this);\r
         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
-        removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeAllGapsMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        removeAllGapsMenuItem.addActionListener(this);\r
         viewBoxesMenuItem.setLabel("Boxes");\r
         viewBoxesMenuItem.setState(true);\r
-        viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    viewBoxesMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        viewBoxesMenuItem.addItemListener(this);\r
         viewTextMenuItem.setLabel("Text");\r
         viewTextMenuItem.setState(true);\r
-        viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    viewTextMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        viewTextMenuItem.addItemListener(this);\r
         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
-        sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortPairwiseMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        sortPairwiseMenuItem.addActionListener(this);\r
         sortIDMenuItem.setLabel("by ID");\r
-        sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortIDMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        sortIDMenuItem.addActionListener(this);\r
         sortGroupMenuItem.setLabel("by Group");\r
-        sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortGroupMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        sortGroupMenuItem.addActionListener(this);\r
         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
-        removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeRedundancyMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        removeRedundancyMenuItem.addActionListener(this);\r
         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
-        pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pairwiseAlignmentMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        pairwiseAlignmentMenuItem.addActionListener(this);\r
         PCAMenuItem.setLabel("Principal Component Analysis");\r
-        PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PCAMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        PCAMenuItem.addActionListener(this);\r
         averageDistanceTreeMenuItem.setLabel(\r
             "Average Distance Using % Identity");\r
-        averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    averageDistanceTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        averageDistanceTreeMenuItem.addActionListener(this);\r
         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
-        neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    neighbourTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        neighbourTreeMenuItem.addActionListener(this);\r
         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
         statusBar.setBackground(Color.white);\r
         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
@@ -1741,281 +1815,115 @@ public class AlignFrame extends Frame
         outputTextboxMenu.setLabel("Output to Textbox");\r
         clustalColour.setLabel("Clustalx");\r
 \r
-        clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    clustalColour_actionPerformed(e);\r
-                }\r
-            });\r
+        clustalColour.addActionListener(this);\r
         zappoColour.setLabel("Zappo");\r
-        zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    zappoColour_actionPerformed(e);\r
-                }\r
-            });\r
+        zappoColour.addActionListener(this);\r
         taylorColour.setLabel("Taylor");\r
-        taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    taylorColour_actionPerformed(e);\r
-                }\r
-            });\r
+        taylorColour.addActionListener(this);\r
         hydrophobicityColour.setLabel("Hydrophobicity");\r
-        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    hydrophobicityColour_actionPerformed(e);\r
-                }\r
-            });\r
+        hydrophobicityColour.addActionListener(this);\r
         helixColour.setLabel("Helix Propensity");\r
-        helixColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    helixColour_actionPerformed(e);\r
-                }\r
-            });\r
+        helixColour.addActionListener(this);\r
         strandColour.setLabel("Strand Propensity");\r
-        strandColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    strandColour_actionPerformed(e);\r
-                }\r
-            });\r
+        strandColour.addActionListener(this);\r
         turnColour.setLabel("Turn Propensity");\r
-        turnColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    turnColour_actionPerformed(e);\r
-                }\r
-            });\r
+        turnColour.addActionListener(this);\r
         buriedColour.setLabel("Buried Index");\r
-        buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    buriedColour_actionPerformed(e);\r
-                }\r
-            });\r
+        buriedColour.addActionListener(this);\r
         userDefinedColour.setLabel("User Defined...");\r
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    userDefinedColour_actionPerformed(e);\r
-                }\r
-            });\r
+        userDefinedColour.addActionListener(this);\r
         PIDColour.setLabel("Percentage Identity");\r
-        PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PIDColour_actionPerformed(e);\r
-                }\r
-            });\r
+        PIDColour.addActionListener(this);\r
         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    BLOSUM62Colour_actionPerformed(e);\r
-                }\r
-            });\r
+        BLOSUM62Colour.addActionListener(this);\r
         avDistanceTreeBlosumMenuItem.setLabel(\r
             "Average Distance Using BLOSUM62");\r
-        avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    avTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        avDistanceTreeBlosumMenuItem.addActionListener(this);\r
         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
-        njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    njTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        annotationPanelMenuItem.setActionCommand("");\r
-        annotationPanelMenuItem.setState(true);\r
+        njTreeBlosumMenuItem.addActionListener(this);\r
         annotationPanelMenuItem.setLabel("Show Annotations");\r
-        annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    annotationPanelMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        annotationPanelMenuItem.addItemListener(this);\r
         colourTextMenuItem.setLabel("Colour Text");\r
-        colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    colourTextMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        colourTextMenuItem.addItemListener(this);\r
         overviewMenuItem.setLabel("Overview Window");\r
-        overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    overviewMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        overviewMenuItem.addActionListener(this);\r
         undoMenuItem.setEnabled(false);\r
         undoMenuItem.setLabel("Undo");\r
-        undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    undoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        undoMenuItem.addActionListener(this);\r
         redoMenuItem.setEnabled(false);\r
         redoMenuItem.setLabel("Redo");\r
-        redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    redoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        redoMenuItem.addActionListener(this);\r
         conservationMenuItem.setLabel("by Conservation");\r
-        conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    conservationMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        conservationMenuItem.addItemListener(this);\r
         noColourmenuItem.setLabel("None");\r
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    noColourmenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        noColourmenuItem.addActionListener(this);\r
         wrapMenuItem.setLabel("Wrap");\r
-        wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    wrapMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        wrapMenuItem.addItemListener(this);\r
         renderGapsMenuItem.setLabel("Show Gaps");\r
         renderGapsMenuItem.setState(true);\r
-        renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    renderGapsMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
+        renderGapsMenuItem.addItemListener(this);\r
         findMenuItem.setLabel("Find...");\r
-        findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    findMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
+        findMenuItem.addActionListener(this);\r
         searchMenu.setLabel("Search");\r
 \r
         abovePIDThreshold.setLabel("Above Identity Threshold");\r
-        abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    abovePIDThreshold_actionPerformed(null);\r
-                }\r
-            });\r
+        abovePIDThreshold.addItemListener(this);\r
         nucleotideColour.setLabel("Nucleotide");\r
-        nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    nucleotideColour_actionPerformed(e);\r
-                }\r
-            });\r
+        nucleotideColour.addActionListener(this);\r
         deleteGroups.setLabel("Undefine Groups");\r
-        deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    deleteGroups_actionPerformed(e);\r
-                }\r
-            });\r
+        deleteGroups.addActionListener(this);\r
         copy.setLabel("Copy");\r
-        copy.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    copy_actionPerformed(e);\r
-                }\r
-            });\r
+        copy.addActionListener(this);\r
         cut.setLabel("Cut");\r
-        cut.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cut_actionPerformed(e);\r
-                }\r
-            });\r
+        cut.addActionListener(this);\r
         delete.setLabel("Delete");\r
-        delete.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    delete_actionPerformed(e);\r
-                }\r
-            });\r
-        Menu1.setLabel("Paste");\r
+        delete.addActionListener(this);\r
+        pasteMenu.setLabel("Paste");\r
         pasteNew.setLabel("To New Alignment");\r
-        pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteNew_actionPerformed(e);\r
-                }\r
-            });\r
+        pasteNew.addActionListener(this);\r
         pasteThis.setLabel("Add To This Alignment");\r
-        pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteThis_actionPerformed(e);\r
-                }\r
-            });\r
+        pasteThis.addActionListener(this);\r
         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
         applyToAllGroups.setState(true);\r
-        applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    applyToAllGroups_actionPerformed(null);\r
-                }\r
-            });\r
+        applyToAllGroups.addItemListener(this);\r
         font.setLabel("Font...");\r
-        font.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    font_actionPerformed(e);\r
-                }\r
-            });\r
+        font.addActionListener(this);\r
         scaleAbove.setLabel("Scale Above");\r
         scaleAbove.setState(true);\r
-        scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleAbove_actionPerformed(null);\r
-                }\r
-            });\r
+        scaleAbove.setEnabled(false);\r
+        scaleAbove.addItemListener(this);\r
         scaleLeft.setEnabled(false);\r
         scaleLeft.setState(true);\r
         scaleLeft.setLabel("Scale Left");\r
-        scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleLeft_actionPerformed(null);\r
-                }\r
-            });\r
+        scaleLeft.addItemListener(this);\r
         scaleRight.setEnabled(false);\r
         scaleRight.setState(true);\r
         scaleRight.setLabel("Scale Right");\r
-        scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleRight_actionPerformed(null);\r
-                }\r
-            });\r
+        scaleRight.addItemListener(this);\r
         modifyPID.setLabel("Modify Identity Threshold...");\r
-        modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyPID_actionPerformed(e);\r
-                }\r
-            });\r
+        modifyPID.addActionListener(this);\r
         modifyConservation.setLabel("Modify Conservation Threshold...");\r
-        modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyConservation_actionPerformed(e);\r
-                }\r
-            });\r
+        modifyConservation.addActionListener(this);\r
         sortByTreeMenu.setLabel("By Tree Order");\r
         sort.setLabel("Sort");\r
         calculate.setLabel("Calculate Tree");\r
         inputText.setLabel("Input from textbox");\r
-        inputText.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    inputText_actionPerformed(e);\r
-                }\r
-            });\r
+        inputText.addActionListener(this);\r
 \r
         helpMenu.setLabel("Help");\r
         documentation.setLabel("Documentation");\r
-        documentation.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    documentation_actionPerformed(e);\r
-                }\r
-            });\r
+        documentation.addActionListener(this);\r
 \r
         about.setLabel("About...");\r
-        about.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    about_actionPerformed(e);\r
-                }\r
-            });\r
+        about.addActionListener(this);\r
           seqLimits.setState(true);\r
     seqLimits.setLabel("Show Sequence Limits");\r
-    seqLimits.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent e)\r
-      {\r
-        seqLimits_itemStateChanged(e);\r
-      }\r
-    });\r
+    seqLimits.addItemListener(this);\r
+    featureSettings.setLabel("Feature Settings...");\r
+    featureSettings.addActionListener(this);\r
+    sequenceFeatures.setLabel("Sequence Features");\r
+    sequenceFeatures.addItemListener(this);\r
+    sequenceFeatures.setState(true);\r
 \r
     alignFrameMenuBar.add(fileMenu);\r
         alignFrameMenuBar.add(editMenu);\r
@@ -2032,7 +1940,7 @@ public class AlignFrame extends Frame
         editMenu.add(redoMenuItem);\r
         editMenu.add(cut);\r
         editMenu.add(copy);\r
-        editMenu.add(Menu1);\r
+        editMenu.add(pasteMenu);\r
         editMenu.add(delete);\r
         editMenu.addSeparator();\r
         editMenu.add(selectAllSequenceMenuItem);\r
@@ -2048,7 +1956,7 @@ public class AlignFrame extends Frame
         searchMenu.add(findMenuItem);\r
         viewMenu.add(font);\r
         viewMenu.addSeparator();\r
-        viewMenu.add(seqLimits);\r
+    viewMenu.add(seqLimits);\r
         viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
         viewMenu.add(scaleAbove);\r
@@ -2060,7 +1968,7 @@ public class AlignFrame extends Frame
         viewMenu.add(colourTextMenuItem);\r
         viewMenu.add(renderGapsMenuItem);\r
         viewMenu.add(annotationPanelMenuItem);\r
-        viewMenu.addSeparator();\r
+    viewMenu.addSeparator();\r
         viewMenu.add(overviewMenuItem);\r
         colourMenu.add(applyToAllGroups);\r
         colourMenu.addSeparator();\r
@@ -2088,8 +1996,8 @@ public class AlignFrame extends Frame
         calculateMenu.add(pairwiseAlignmentMenuItem);\r
         calculateMenu.add(PCAMenuItem);\r
         this.add(statusBar, BorderLayout.SOUTH);\r
-        Menu1.add(pasteNew);\r
-        Menu1.add(pasteThis);\r
+        pasteMenu.add(pasteNew);\r
+        pasteMenu.add(pasteThis);\r
         sort.add(sortIDMenuItem);\r
         sort.add(sortByTreeMenu);\r
         sort.add(sortGroupMenuItem);\r
@@ -2100,6 +2008,142 @@ public class AlignFrame extends Frame
         calculate.add(njTreeBlosumMenuItem);\r
         helpMenu.add(documentation);\r
         helpMenu.add(about);\r
+  }\r
+\r
+  public void setEmbedded()\r
+  {\r
+\r
+    embeddedMenu = new Panel();\r
+    embeddedEdit = new Label();\r
+    embeddedSearch = new Label();\r
+    embeddedView = new Label();\r
+    embeddedColour = new Label();\r
+    embeddedFile = new Label();\r
+    embeddedHelp = new Label();\r
+    embeddedCalculate = new Label();\r
+    flowLayout1 = new FlowLayout();\r
+    embeddedMenu.setBackground(Color.lightGray);\r
+    embeddedMenu.setLayout(flowLayout1);\r
+    embeddedEdit.setText("Edit");\r
+    embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedSearch.setText("Search");\r
+    embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedView.setText("View");\r
+    embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedColour.setText("Colour");\r
+    embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedFile.setText("File");\r
+    embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedHelp.setText("Help");\r
+    embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+    embeddedCalculate.setText("Calculate");\r
+    embeddedMenu.add(embeddedFile);\r
+    embeddedMenu.add(embeddedEdit);\r
+    embeddedMenu.add(embeddedSearch);\r
+    embeddedMenu.add(embeddedView);\r
+    embeddedMenu.add(embeddedColour);\r
+    embeddedMenu.add(embeddedCalculate);\r
+    embeddedMenu.add(embeddedHelp);\r
+    flowLayout1.setAlignment(FlowLayout.LEFT);\r
+    flowLayout1.setHgap(2);\r
+    flowLayout1.setVgap(0);\r
+    embeddedFile.addMouseListener(this);\r
+    embeddedEdit.addMouseListener(this);\r
+    embeddedSearch.addMouseListener(this);\r
+    embeddedView.addMouseListener(this);\r
+    embeddedColour.addMouseListener(this);\r
+    embeddedCalculate.addMouseListener(this);\r
+    embeddedHelp.addMouseListener(this);\r
+\r
+    setVisible(false);\r
+    fileMenu.remove(closeMenuItem);\r
+    fileMenu.remove(2); // Seperator\r
+\r
+    applet.setLayout(new BorderLayout());\r
+    applet.add(embeddedMenu, BorderLayout.NORTH);\r
+    applet.add(statusBar, BorderLayout.SOUTH);\r
+    applet.validate();\r
+\r
+\r
+    alignPanel.setSize(applet.size().width, applet.size().height\r
+                       - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
+\r
+     applet.add(alignPanel, BorderLayout.CENTER);\r
+     applet.validate();\r
+  }\r
+\r
+\r
+\r
+  PopupMenu filePopup, editPopup, searchPopup,\r
+      viewPopup, colourPopup, calculatePopup, helpPopup;\r
+  MenuItem featureSettings = new MenuItem();\r
+  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+\r
+  public void mousePressed(MouseEvent evt)\r
+  {\r
+    PopupMenu popup = null;\r
+    Label source = (Label)evt.getSource();\r
+    if(source==embeddedFile)\r
+    {\r
+      popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
     }\r
+    else if(source==embeddedEdit)\r
+    {\r
+      popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+    }\r
+    else if(source==embeddedSearch)\r
+    {\r
+      popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
+    }\r
+    else if(source==embeddedView)\r
+    {\r
+      popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+    }\r
+    else if(source==embeddedColour)\r
+    {\r
+      popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+    }\r
+    else if(source==embeddedCalculate)\r
+    {\r
+      popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+    }\r
+    else if(source==embeddedHelp)\r
+    {\r
+      popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+    }\r
+\r
+    embeddedMenu.add(popup);\r
+    popup.show(embeddedMenu,\r
+               source.getBounds().x,\r
+               source.getBounds().y + source.getBounds().getSize().height);\r
+  }\r
+\r
+  PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+  {\r
+    if(popup!=null)\r
+    {\r
+      return popup;\r
+    }\r
+    popup = new PopupMenu();\r
+    int m, mSize = original.getItemCount();\r
+    for(m=0; m<mSize; m++)\r
+    {\r
+      popup.add(original.getItem(m));\r
+      mSize--;\r
+      m--;\r
+    }\r
+\r
+    return popup;\r
+  }\r
+  public void mouseClicked(MouseEvent evt)\r
+  {}\r
+  public void mouseReleased(MouseEvent evt)\r
+  {}\r
+  public void mouseEntered(MouseEvent evt)\r
+  {}\r
+  public void mouseExited(MouseEvent evt)\r
+  {}\r
+\r
 }\r
 \r