X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=479d77180df9706629d82684060638065275fdcf;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=e99c27f3404ba6f65142339f8da786954b380b63;hpb=6fcda37468514274f893bd4ccf39480ee36ee31d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e99c27f..479d771 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -49,7 +49,8 @@ public class AlignFrame extends Frame implements ActionListener,
                      boolean embedded)
   {
 
-    jalviewServletURL = applet.getParameter("APPLICATION_URL");
+    if (applet != null)
+      jalviewServletURL = applet.getParameter("APPLICATION_URL");
 
     try{
       jbInit();
@@ -208,9 +209,9 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_V:
-        if (evt.isControlDown() || evt.isMetaDown())
+        if (evt.isControlDown())
         {
-          paste(true);
+          paste(evt.isShiftDown());
         }
         break;
       case KeyEvent.VK_A:
@@ -266,8 +267,7 @@ public class AlignFrame extends Frame implements ActionListener,
         {
           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
                                                 || evt.isShiftDown()
-                                                || evt.isAltDown()
-              );
+                                                || evt.isAltDown());
         }
        else
         {
@@ -319,7 +319,6 @@ public class AlignFrame extends Frame implements ActionListener,
          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
        }
-       alignPanel.seqPanel.seqCanvas.repaint();
        break;
 
       case KeyEvent.VK_F:
@@ -328,6 +327,7 @@ public class AlignFrame extends Frame implements ActionListener,
           findMenuItem_actionPerformed();
         }
         break;
+
       case KeyEvent.VK_H:
       {
         boolean toggleSeqs = !evt.isControlDown();
@@ -337,7 +337,7 @@ public class AlignFrame extends Frame implements ActionListener,
 
         if(toggleSeqs)
         {
-          if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+          if (sg != null && sg.getSize() != viewport.alignment.getHeight())
           {
             hide = true;
             viewport.hideAllSelectedSeqs();
@@ -357,10 +357,9 @@ public class AlignFrame extends Frame implements ActionListener,
           else if (!hide)
             viewport.showAllHiddenColumns();
         }
-
-        alignPanel.repaint();
         break;
       }
+
       case KeyEvent.VK_PAGE_UP:
         if (viewport.wrapAlignment)
           alignPanel.scrollUp(true);
@@ -369,6 +368,7 @@ public class AlignFrame extends Frame implements ActionListener,
                                      viewport.startSeq
                                      - viewport.endSeq + viewport.startSeq);
         break;
+
       case KeyEvent.VK_PAGE_DOWN:
         if (viewport.wrapAlignment)
           alignPanel.scrollUp(false);
@@ -377,7 +377,71 @@ public class AlignFrame extends Frame implements ActionListener,
                                      viewport.startSeq
                                      + viewport.endSeq - viewport.startSeq);
         break;
+
+      case KeyEvent.VK_Z:
+        if (evt.isControlDown())
+        {
+          undoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_Y:
+        if (evt.isControlDown())
+        {
+          redoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_L:
+        if (evt.isControlDown())
+        {
+          trimAlignment(true);
+        }
+        break;
+
+      case KeyEvent.VK_R:
+        if (evt.isControlDown())
+        {
+          trimAlignment(false);
+        }
+        break;
+
+      case KeyEvent.VK_E:
+        if (evt.isControlDown())
+        {
+          if (evt.isShiftDown())
+            this.removeAllGapsMenuItem_actionPerformed();
+          else
+            removeGappedColumnMenuItem_actionPerformed();
+        }
+        break;
+      case KeyEvent.VK_I:
+        if (evt.isControlDown())
+        {
+          if (evt.isAltDown())
+            viewport.invertColumnSelection();
+          else
+            this.invertSequenceMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_U:
+        if (evt.isControlDown())
+        {
+          this.deleteGroups_actionPerformed();
+        }
+      break;
+
+    case KeyEvent.VK_T:
+      if (evt.isControlDown())
+      {
+       newView();
+      }
+      break;
+
+
       }
+      alignPanel.repaint();
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -391,21 +455,24 @@ public void itemStateChanged(ItemEvent evt)
     else if(evt.getSource()==wrapMenuItem)
             wrapMenuItem_actionPerformed();
     else if(evt.getSource()==scaleAbove)
-            scaleAbove_actionPerformed();
+            viewport.setScaleAboveWrapped(scaleAbove.getState());
     else if(evt.getSource()==scaleLeft)
-            scaleLeft_actionPerformed();
+            viewport.setScaleLeftWrapped(scaleLeft.getState());
     else if(evt.getSource()==scaleRight)
-            scaleRight_actionPerformed();
+            viewport.setScaleRightWrapped(scaleRight.getState());
      else if(evt.getSource()==seqLimits)
       seqLimits_itemStateChanged();
     else if(evt.getSource()==viewBoxesMenuItem)
-            viewBoxesMenuItem_actionPerformed();
+            viewport.setShowBoxes(viewBoxesMenuItem.getState());
     else if(evt.getSource()==viewTextMenuItem)
-            viewTextMenuItem_actionPerformed();
+            viewport.setShowText(viewTextMenuItem.getState());
     else if(evt.getSource()==renderGapsMenuItem)
-            renderGapsMenuItem_actionPerformed();
+            viewport.setRenderGaps(renderGapsMenuItem.getState());
     else if(evt.getSource()==annotationPanelMenuItem)
-            annotationPanelMenuItem_actionPerformed();
+    {
+      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+    }
       else if(evt.getSource()==sequenceFeatures)
       {
            viewport.showSequenceFeatures(sequenceFeatures.getState());
@@ -415,10 +482,12 @@ public void itemStateChanged(ItemEvent evt)
             conservationMenuItem_actionPerformed();
       else if(evt.getSource()==abovePIDThreshold)
             abovePIDThreshold_actionPerformed();
-          else if(evt.getSource()==applyToAllGroups)
-            applyToAllGroups_actionPerformed();
+      else if(evt.getSource()==applyToAllGroups)
+            viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
       else if(evt.getSource()==autoCalculate)
           viewport.autocalculateConsensus = autoCalculate.getState();
+
+      alignPanel.repaint();
   }
  public void actionPerformed(ActionEvent evt)
  {
@@ -430,6 +499,12 @@ public void itemStateChanged(ItemEvent evt)
       loadTree_actionPerformed();
     else if(source==loadApplication)
       launchFullApplication();
+    else if (source == loadAnnotations)
+      loadAnnotations();
+    else if (source == outputAnnotations)
+      outputAnnotations();
+    else if(source == outputFeatures)
+      outputFeatures(true, "Jalview");
     else if(source==closeMenuItem)
       closeMenuItem_actionPerformed();
     else if(source==copy)
@@ -477,7 +552,9 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==findMenuItem)
             findMenuItem_actionPerformed();
     else if(source==font)
-            font_actionPerformed();
+            new FontChooser(alignPanel);
+    else if (source == newView)
+      newView();
     else if(source==showColumns)
     {
       viewport.showAllHiddenColumns(); alignPanel.repaint();
@@ -495,39 +572,43 @@ public void itemStateChanged(ItemEvent evt)
       viewport.hideAllSelectedSeqs();
     }
     else if(source==featureSettings)
-            featureSettings_actionPerformed();
+            new FeatureSettings(alignPanel);
     else if(source==overviewMenuItem)
             overviewMenuItem_actionPerformed();
     else if(source==noColourmenuItem)
-            noColourmenuItem_actionPerformed();
+            changeColour(null);
     else if(source==clustalColour)
-            clustalColour_actionPerformed();
+    {
+      abovePIDThreshold.setState(false);
+      changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
+                                            viewport.alignment.getWidth()));
+  }
     else if(source==zappoColour)
-            zappoColour_actionPerformed();
+            changeColour(new ZappoColourScheme());
     else if(source==taylorColour)
-            taylorColour_actionPerformed();
+            changeColour(new TaylorColourScheme());
     else if(source==hydrophobicityColour)
-            hydrophobicityColour_actionPerformed();
+            changeColour(new HydrophobicColourScheme());
     else if(source==helixColour)
-            helixColour_actionPerformed();
+            changeColour(new HelixColourScheme());
     else if(source==strandColour)
-            strandColour_actionPerformed();
+            changeColour(new StrandColourScheme());
     else if(source==turnColour)
-            turnColour_actionPerformed();
+            changeColour(new TurnColourScheme());
     else if(source==buriedColour)
-            buriedColour_actionPerformed();
+            changeColour(new BuriedColourScheme());
     else if(source==nucleotideColour)
-            nucleotideColour_actionPerformed();
+            changeColour(new NucleotideColourScheme());
     else if(source==modifyPID)
             modifyPID_actionPerformed();
     else if(source==modifyConservation)
             modifyConservation_actionPerformed();
     else if(source==userDefinedColour)
-            userDefinedColour_actionPerformed();
+            new UserDefinedColours(alignPanel, null);
     else if(source==PIDColour)
-            PIDColour_actionPerformed();
+            changeColour(new PIDColourScheme());
     else if(source==BLOSUM62Colour)
-            BLOSUM62Colour_actionPerformed();
+            changeColour(new Blosum62ColourScheme());
     else if(source==annotationColour)
            new AnnotationColourChooser(viewport, alignPanel);
     else if(source==sortPairwiseMenuItem)
@@ -574,10 +655,61 @@ public void itemStateChanged(ItemEvent evt)
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().getSequences(),
+                                              viewport.getAlignment(),
                                                       viewport.showJVSuffix));
   }
 
+  public void loadAnnotations()
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+    cap.setText("Paste your features / annotations file here.");
+    cap.setAnnotationImport();
+    Frame frame = new Frame();
+    frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
+
+  }
+
+  public void outputAnnotations()
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame,
+                                     "Annotations",
+                                     600, 500);
+    cap.setText( new AnnotationFile().printAnnotations(
+      viewport.alignment.getAlignmentAnnotation() ) );
+  }
+
+  public String outputFeatures(boolean displayTextbox, String format)
+  {
+    String features;
+    if (format.equalsIgnoreCase("Jalview"))
+      features = new FeaturesFile().printJalviewFormat(
+              viewport.alignment.getSequencesArray(),
+              viewport.featuresDisplayed);
+    else
+      features = new FeaturesFile().printGFFFormat(
+             viewport.alignment.getSequencesArray(),
+             viewport.featuresDisplayed);
+
+
+    if(displayTextbox)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       "Features",
+                                       600, 500);
+
+      cap.setText(features);
+    }
+
+    return features;
+  }
+
   void launchFullApplication()
   {
     StringBuffer url = new StringBuffer(jalviewServletURL);
@@ -649,7 +781,10 @@ public void itemStateChanged(ItemEvent evt)
 
   public void closeMenuItem_actionPerformed()
   {
-    PaintRefresher.components.remove(viewport.alignment);
+    PaintRefresher.RemoveComponent(alignPanel);
+    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+
     if(PaintRefresher.components.size()==0 && viewport.applet==null)
       System.exit(0);
 
@@ -707,6 +842,9 @@ public void itemStateChanged(ItemEvent evt)
    */
   protected void undoMenuItem_actionPerformed()
   {
+    if(viewport.historyList.size()<1)
+      return;
+
     CommandI command = (CommandI)viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
@@ -715,7 +853,7 @@ public void itemStateChanged(ItemEvent evt)
 
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,null);
+    originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());
   }
 
   /**
@@ -725,6 +863,9 @@ public void itemStateChanged(ItemEvent evt)
    */
   protected void redoMenuItem_actionPerformed()
   {
+    if(viewport.redoList.size()<1)
+      return;
+
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
@@ -733,19 +874,20 @@ public void itemStateChanged(ItemEvent evt)
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null, null);
+    originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());
   }
 
   AlignViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = viewport;
+    AlignViewport originalSource = null;
     //For sequence removal and addition, we need to fire
    //the property change event FROM the viewport where the
    //original alignment was altered
+   AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
-      AlignmentI al = editCommand.getAlignment();
+      al = editCommand.getAlignment();
       Vector comps = (Vector) PaintRefresher.components
           .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
@@ -760,6 +902,18 @@ public void itemStateChanged(ItemEvent evt)
         }
       }
     }
+
+    if (originalSource == null)
+    {
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+        PaintRefresher.validateSequences(al, viewport.alignment);
+
+      originalSource = viewport;
+    }
+
+
     return originalSource;
   }
 
@@ -776,13 +930,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = 1; i < viewport.alignment.getHeight(); i++)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -796,13 +950,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.getSequences(true).contains(seq))
+        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.getSequences(true).contains(temp))
+        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
         {
           continue;
         }
@@ -827,7 +981,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceGroup sg = viewport.getSelectionGroup();
     copiedSequences = new StringBuffer();
     Hashtable orderedSeqs = new Hashtable();
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.alignment.findIndex(seq);
@@ -856,7 +1010,7 @@ public void itemStateChanged(ItemEvent evt)
       copiedHiddenColumns = null;
 
 
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
         SequenceI seq = null;
 
@@ -900,7 +1054,7 @@ public void itemStateChanged(ItemEvent evt)
         copiedSequences.append(seq.getName() + "\t" +
             startRes + "\t" +
             endRes + "\t" +
-            seq.getSequence(sg.getStartRes(),
+            seq.getSequenceAsString(sg.getStartRes(),
                 sg.getEndRes() + 1) + "\n");
     }
 
@@ -920,6 +1074,7 @@ public void itemStateChanged(ItemEvent evt)
   {
     try
     {
+
       if (copiedSequences == null)
       {
         return;
@@ -970,19 +1125,7 @@ public void itemStateChanged(ItemEvent evt)
       }
       else
       {
-        //!newAlignment
-        addHistoryItem(new EditCommand(
-            "Add sequences",
-            EditCommand.PASTE,
-            newSeqs,
-            0,
-            viewport.alignment.getWidth(),
-            viewport.alignment)
-            );
-
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+        addSequences(newSeqs);
       }
 
     }
@@ -991,6 +1134,30 @@ public void itemStateChanged(ItemEvent evt)
 
   }
 
+  void addSequences(SequenceI[] seqs)
+  {
+    for (int i = 0; i < seqs.length; i++)
+    {
+      viewport.alignment.addSequence(seqs[i]);
+    }
+
+    //!newAlignment
+    addHistoryItem(new EditCommand(
+        "Add sequences",
+        EditCommand.PASTE,
+        seqs,
+        0,
+        viewport.alignment.getWidth(),
+        viewport.alignment)
+        );
+
+    viewport.setEndSeq(viewport.alignment.getHeight());
+    viewport.alignment.getWidth();
+    viewport.firePropertyChange("alignment", null,
+                                viewport.alignment.getSequences());
+
+  }
+
   protected void cut_actionPerformed()
   {
     copy_actionPerformed();
@@ -1008,7 +1175,7 @@ public void itemStateChanged(ItemEvent evt)
 
     Vector seqs = new Vector();
     SequenceI seq;
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
@@ -1016,7 +1183,7 @@ public void itemStateChanged(ItemEvent evt)
 
 
    // If the cut affects all sequences, remove highlighted columns
-   if (sg.getSize(false) == viewport.alignment.getHeight())
+   if (sg.getSize() == viewport.alignment.getHeight())
    {
      viewport.getColumnSelection().removeElements(sg.getStartRes(),
          sg.getEndRes() + 1);
@@ -1114,7 +1281,7 @@ public void itemStateChanged(ItemEvent evt)
 
       SequenceI [] seqs;
       if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       else
         seqs = viewport.alignment.getSequencesArray();
 
@@ -1173,7 +1340,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1212,7 +1379,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1240,10 +1407,53 @@ public void itemStateChanged(ItemEvent evt)
     new Finder(alignPanel);
   }
 
-  public void font_actionPerformed()
+  public void newView()
   {
-    new FontChooser(alignPanel);
-  }
+    AlignmentI newal;
+    if (viewport.hasHiddenRows)
+      newal = new Alignment(viewport.getAlignment().
+                            getHiddenSequences()
+                            .getFullAlignment().
+                            getSequencesArray());
+    else
+      newal = new Alignment(viewport.alignment.getSequencesArray());
+
+    AlignFrame newaf = new AlignFrame(newal,
+                                      viewport.applet,
+                                      "",
+                                      false);
+
+    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel,
+                            newaf.alignPanel.av.getSequenceSetId());
+
+    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
+                            newaf.alignPanel.av.getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
+                            newaf.alignPanel.av.getSequenceSetId());
+
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    int viewSize = -1;
+    for (int i = 0; i < comps.size(); i++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+        viewSize++;
+    }
+
+    String title = new String(this.getTitle());
+    if (title.indexOf("(View") > -1)
+      title = title.substring(0, title.indexOf("(View"));
+
+    title+= "(View "+viewSize+")";
+
+    newaf.setTitle(title.toString());
+
+
+    newaf.viewport.historyList = viewport.historyList;
+    newaf.viewport.redoList = viewport.redoList;
+
+   }
 
 
   public void seqLimits_itemStateChanged()
@@ -1271,53 +1481,6 @@ public void itemStateChanged(ItemEvent evt)
   }
 
 
-  protected void scaleAbove_actionPerformed()
-  {
-    viewport.setScaleAboveWrapped(scaleAbove.getState());
-    alignPanel.repaint();
-  }
-
-  protected void scaleLeft_actionPerformed()
-  {
-    viewport.setScaleLeftWrapped(scaleLeft.getState());
-    alignPanel.repaint();
-  }
-
-  protected void scaleRight_actionPerformed()
-  {
-    viewport.setScaleRightWrapped(scaleRight.getState());
-    alignPanel.repaint();
-  }
-
-  public void viewBoxesMenuItem_actionPerformed()
-  {
-    viewport.setShowBoxes(viewBoxesMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  public void viewTextMenuItem_actionPerformed()
-  {
-    viewport.setShowText(viewTextMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  protected void renderGapsMenuItem_actionPerformed()
-  {
-    viewport.setRenderGaps(renderGapsMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  public void annotationPanelMenuItem_actionPerformed()
-  {
-    viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
-  }
-
-  public void featureSettings_actionPerformed()
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
-
   public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
@@ -1346,62 +1509,6 @@ public void itemStateChanged(ItemEvent evt)
 
   }
 
-  protected void noColourmenuItem_actionPerformed()
-  {
-    changeColour(null);
-  }
-
-  public void clustalColour_actionPerformed()
-  {
-    abovePIDThreshold.setState(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
-                                          viewport.alignment.getWidth()));
-  }
-
-  public void zappoColour_actionPerformed()
-  {
-    changeColour(new ZappoColourScheme());
-  }
-
-  public void taylorColour_actionPerformed()
-  {
-    changeColour(new TaylorColourScheme());
-  }
-
-  public void hydrophobicityColour_actionPerformed()
-  {
-    changeColour(new HydrophobicColourScheme());
-  }
-
-  public void helixColour_actionPerformed()
-  {
-    changeColour(new HelixColourScheme());
-  }
-
-  public void strandColour_actionPerformed()
-  {
-    changeColour(new StrandColourScheme());
-  }
-
-  public void turnColour_actionPerformed()
-  {
-    changeColour(new TurnColourScheme());
-  }
-
-  public void buriedColour_actionPerformed()
-  {
-    changeColour(new BuriedColourScheme());
-  }
-
-  public void nucleotideColour_actionPerformed()
-  {
-    changeColour(new NucleotideColourScheme());
-  }
-
-  protected void applyToAllGroups_actionPerformed()
-  {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
-  }
 
   void changeColour(ColourSchemeI cs)
   {
@@ -1464,7 +1571,9 @@ public void itemStateChanged(ItemEvent evt)
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
+          sg.cs = new ClustalxColourScheme(
+              sg.getSequences(viewport.hiddenRepSequences),
+              sg.getWidth());
         }
         else
         {
@@ -1484,7 +1593,8 @@ public void itemStateChanged(ItemEvent evt)
             || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
         }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -1493,7 +1603,7 @@ public void itemStateChanged(ItemEvent evt)
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true), 0,
+                                            sg.getSequences(viewport.hiddenRepSequences), 0,
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -1563,20 +1673,7 @@ public void itemStateChanged(ItemEvent evt)
     modifyPID_actionPerformed();
   }
 
-  public void userDefinedColour_actionPerformed()
-  {
-    new UserDefinedColours(alignPanel, null);
-  }
-
-  public void PIDColour_actionPerformed()
-  {
-    changeColour(new PIDColourScheme());
-  }
 
-  public void BLOSUM62Colour_actionPerformed()
-  {
-    changeColour(new Blosum62ColourScheme());
-  }
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
@@ -1612,7 +1709,7 @@ public void itemStateChanged(ItemEvent evt)
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
     if (viewport.getSelectionGroup()!=null
-        && viewport.getSelectionGroup().getSize(false) > 1)
+        && viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
@@ -1642,8 +1739,8 @@ public void itemStateChanged(ItemEvent evt)
     }
 
     if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize(false) < 4 &&
-          viewport.getSelectionGroup().getSize(false) > 0)
+          viewport.getSelectionGroup().getSize() < 4 &&
+          viewport.getSelectionGroup().getSize() > 0)
         || viewport.getAlignment().getHeight() < 4)
     {
       return;
@@ -1676,7 +1773,7 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
   void NewTreePanel(String type, String pwType, String title)
@@ -1702,7 +1799,7 @@ public void itemStateChanged(ItemEvent evt)
     }
 
     if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize(false) > 1)
+          viewport.getSelectionGroup().getSize() > 1)
       || (viewport.getSelectionGroup() == null
           && viewport.alignment.getHeight() > 1))
     {
@@ -1720,7 +1817,7 @@ public void itemStateChanged(ItemEvent evt)
   {
       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
       cap.setText("Paste your Newick tree file here.");
-      cap.treeImport = true;
+      cap.setTreeImport();
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
@@ -1858,7 +1955,11 @@ public void itemStateChanged(ItemEvent evt)
     protected MenuBar alignFrameMenuBar = new MenuBar();
     protected Menu fileMenu = new Menu("File");
     protected MenuItem loadApplication = new MenuItem("View in Full Application");
-    protected MenuItem loadTree = new MenuItem("Load Associated Tree");
+    protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+    protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+    protected MenuItem outputFeatures = new MenuItem("Export Features ...");
+    protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
     protected MenuItem closeMenuItem = new MenuItem("Close");
     protected Menu editMenu = new Menu("Edit");
     protected Menu viewMenu = new Menu("View");
@@ -1970,6 +2071,9 @@ public void itemStateChanged(ItemEvent evt)
         loadApplication.addActionListener(this);
 
         loadTree.addActionListener(this);
+        loadAnnotations.addActionListener(this);
+        outputFeatures.addActionListener(this);
+        outputAnnotations.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
         deselectAllSequenceMenuItem.addActionListener(this);
         invertSequenceMenuItem.addActionListener(this);
@@ -2004,7 +2108,6 @@ public void itemStateChanged(ItemEvent evt)
         averageDistanceTreeMenuItem.addActionListener(this);
         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
         neighbourTreeMenuItem.addActionListener(this);
-        alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
         statusBar.setBackground(Color.white);
         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
         statusBar.setText("Status bar");
@@ -2136,6 +2239,8 @@ public void itemStateChanged(ItemEvent evt)
     hideSequences.addActionListener(this);
     formatMenu.setLabel("Format");
     selectMenu.setLabel("Select");
+    newView.setLabel("New View");
+    newView.addActionListener(this);
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -2144,25 +2249,36 @@ public void itemStateChanged(ItemEvent evt)
     alignFrameMenuBar.add(colourMenu);
         alignFrameMenuBar.add(calculateMenu);
         alignFrameMenuBar.add(helpMenu);
+
         fileMenu.add(inputText);
+        fileMenu.add(loadTree);
+        fileMenu.add(loadAnnotations);
+
+        fileMenu.addSeparator();
         fileMenu.add(outputTextboxMenu);
+        fileMenu.add(outputFeatures);
+        fileMenu.add(outputAnnotations);
+
         if(jalviewServletURL!=null)
           fileMenu.add(loadApplication);
+
         fileMenu.addSeparator();
-        fileMenu.add(loadTree);
         fileMenu.add(closeMenuItem);
+
         editMenu.add(undoMenuItem);
         editMenu.add(redoMenuItem);
         editMenu.add(cut);
         editMenu.add(copy);
         editMenu.add(pasteMenu);
         editMenu.add(delete);
-    editMenu.addSeparator();
+        editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
         editMenu.add(removeGappedColumnMenuItem);
         editMenu.add(removeAllGapsMenuItem);
         editMenu.add(removeRedundancyMenuItem);
+    viewMenu.add(newView);
+    viewMenu.addSeparator();
     viewMenu.add(menu1);
     viewMenu.add(menu2);
     viewMenu.addSeparator();
@@ -2242,7 +2358,7 @@ public void itemStateChanged(ItemEvent evt)
     embeddedEdit = new Label("Edit");
     embeddedSelect = new Label("Select");
     embeddedView = new Label("View");
-    embeddedFormat = new Label("Label");
+    embeddedFormat = new Label("Format");
     embeddedColour = new Label("Colour");
     embeddedFile = new Label("File");
     embeddedHelp = new Label("Help");
@@ -2278,14 +2394,12 @@ public void itemStateChanged(ItemEvent evt)
     embeddedCalculate.addMouseListener(this);
     embeddedHelp.addMouseListener(this);
 
-   // setVisible(false);
     fileMenu.remove(closeMenuItem);
     fileMenu.remove(3); // Seperator
 
     viewport.applet.setLayout(new BorderLayout());
     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
     viewport.applet.add(statusBar, BorderLayout.SOUTH);
-   // viewport.applet.validate();
 
     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);
@@ -2298,7 +2412,7 @@ public void itemStateChanged(ItemEvent evt)
 
 
   PopupMenu filePopup, editPopup, searchPopup,
-      viewPopup, colourPopup, calculatePopup, helpPopup;
+      viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
   MenuItem annotationColour = new MenuItem();
@@ -2311,6 +2425,7 @@ public void itemStateChanged(ItemEvent evt)
   MenuItem hideSequences = new MenuItem();
   Menu formatMenu = new Menu();
   Menu selectMenu = new Menu();
+  MenuItem newView = new MenuItem();
 
   public void mousePressed(MouseEvent evt)
   {
@@ -2334,7 +2449,7 @@ public void itemStateChanged(ItemEvent evt)
     }
     else if (source ==embeddedFormat)
     {
-      popup = viewPopup = genPopupMenu(viewPopup, formatMenu);
+      popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
     }
     else if(source==embeddedColour)
     {