X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ff7646f76e9b245e38e7ad8b9c187b44033c5538;hb=32a72d077d2371f4566688fbd103103d8505b27f;hp=6586a68f3c3f07bd03428c21ce2188812d8a6bd5;hpb=f84a68869b1864eea585ade8ac36939fd88c8a93;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6586a68..ff7646f 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -61,6 +61,9 @@ public class AlignFrame extends Frame implements ActionListener,
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
 
+    viewport.updateConservation(alignPanel);
+    viewport.updateConsensus(alignPanel);
+
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
     seqLimits.setState(viewport.showJVSuffix);
@@ -114,17 +117,6 @@ public class AlignFrame extends Frame implements ActionListener,
    alignPanel.scalePanel.addKeyListener(this);
    alignPanel.annotationPanel.addKeyListener(this);
 
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-     public void propertyChange(java.beans.PropertyChangeEvent evt)
-     {
-       if (evt.getPropertyName().equals("alignment"))
-       {
-         alignmentChanged();
-       }
-     }
-   });
-
 
    if(embedded)
    {
@@ -475,9 +467,9 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==invertColSel)
     { viewport.invertColumnSelection(); alignPanel.repaint(); }
     else if(source==remove2LeftMenuItem)
-            remove2LeftMenuItem_actionPerformed();
+            trimAlignment(true);
     else if(source==remove2RightMenuItem)
-            remove2RightMenuItem_actionPerformed();
+            trimAlignment(false);
     else if(source==removeGappedColumnMenuItem)
             removeGappedColumnMenuItem_actionPerformed();
     else if(source==removeAllGapsMenuItem)
@@ -664,27 +656,73 @@ public void itemStateChanged(ItemEvent evt)
     this.dispose();
   }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
 
+  /**
+   * DOCUMENT ME!
+   */
   void updateEditMenuBar()
   {
+
+    if (viewport.historyList.size() > 0)
+    {
+      undoMenuItem.setEnabled(true);
+      CommandI command = (CommandI) viewport.historyList.peek();
+      undoMenuItem.setLabel("Undo " + command.getDescription());
+    }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setLabel("Undo");
+    }
+
+    if (viewport.redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
+
+      CommandI command = (CommandI) viewport.redoList.peek();
+      redoMenuItem.setLabel("Redo " + command.getDescription());
+    }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setLabel("Redo");
+    }
   }
 
+  public void addHistoryItem(CommandI command)
+  {
+    if(command.getSize()>0)
+    {
+      viewport.historyList.push(command);
+      viewport.redoList.removeAllElements();
+      updateEditMenuBar();
+      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    }
+  }
 
   protected void undoMenuItem_actionPerformed()
   {
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
+    command.undoCommand();
+
+    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    updateEditMenuBar();
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed()
   {
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
+    command.doCommand();
+    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
+    updateEditMenuBar();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
-  // used by undo and redo
-  void restoreHistoryItem(CommandI command)
-  {
-  }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -836,8 +874,6 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-  //  addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-   //                                HistoryItem.PASTE));
     paste(false);
   }
 
@@ -857,26 +893,16 @@ public void itemStateChanged(ItemEvent evt)
         String name = st.nextToken();
         int start = Integer.parseInt(st.nextToken());
         int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
-
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.addElement(sequence);
-        }
+        seqs.addElement(new Sequence(name, st.nextToken(), start, end));
+      }
+      SequenceI[] newSeqs = new SequenceI[seqs.size()];
+      for (int i = 0; i < seqs.size(); i++)
+      {
+        newSeqs[i] = (SequenceI) seqs.elementAt(i);
       }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          newSeqs[i] = (SequenceI) seqs.elementAt(i);
-        }
-
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -905,6 +931,16 @@ 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());
@@ -924,62 +960,62 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-    //                               HistoryItem.HIDE));
-    if (viewport.getSelectionGroup() == null)
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
     {
       return;
     }
 
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if(sg.getSize(false)==viewport.alignment.getHeight())
-          allSequences = true;
-
+    Vector seqs = new Vector();
+    SequenceI seq;
     for (int i = 0; i < sg.getSize(false); i++)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+      seq = sg.getSequenceAt(i);
+      seqs.addElement(seq);
+    }
 
-      // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
-      {
-        viewport.getColumnSelection().removeElements(sg.getStartRes(),
-                                                     sg.getEndRes() + 1);
-      }
 
+   // If the cut affects all sequences, remove highlighted columns
+   if (sg.getSize(false) == viewport.alignment.getHeight())
+   {
+     viewport.getColumnSelection().removeElements(sg.getStartRes(),
+         sg.getEndRes() + 1);
+   }
+
+
+    SequenceI [] cut = new SequenceI[seqs.size()];
+    for(int i=0; i<seqs.size(); i++)
+      cut[i] = (SequenceI)seqs.elementAt(i);
+
+
+    /*
+    //ADD HISTORY ITEM
+    */
+    addHistoryItem(new EditCommand("Cut Sequences",
+                                      EditCommand.CUT,
+                                      cut,
+                                      sg.getStartRes(),
+                                      sg.getEndRes()-sg.getStartRes()+1,
+                                      viewport.alignment));
 
-      if (seq.getSequence().length() < 1)
-      {
-        viewport.getAlignment().deleteSequence(seq);
-      }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
-    }
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+
+    viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+
     if (viewport.getAlignment().getHeight() < 1)
     {
-      try
-      {
         this.setVisible(false);
-      }
-      catch (Exception ex)
-      {}
     }
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-
   }
 
   protected void deleteGroups_actionPerformed()
   {
     viewport.alignment.deleteAllGroups();
+    viewport.sequenceColours=null;
     viewport.setSelectionGroup(null);
 
     alignPanel.repaint();
@@ -995,7 +1031,7 @@ public void itemStateChanged(ItemEvent evt)
     sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1011,7 +1047,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertSequenceMenuItem_actionPerformed()
@@ -1022,83 +1058,143 @@ public void itemStateChanged(ItemEvent evt)
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
-  public void remove2LeftMenuItem_actionPerformed()
+  void trimAlignment(boolean trimLeft)
   {
-  }
+    ColumnSelection colSel = viewport.getColumnSelection();
+    int column;
 
-  public void remove2RightMenuItem_actionPerformed()
-  {
-  }
+    if (colSel.size() > 0)
+    {
+      if(trimLeft)
+        column = colSel.getMin();
+      else
+        column = colSel.getMax();
 
-  public void removeGappedColumnMenuItem_actionPerformed()
-  {
-  }
+      SequenceI [] seqs;
+      if(viewport.getSelectionGroup()!=null)
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      else
+        seqs = viewport.alignment.getSequencesArray();
 
-  public void removeAllGapsMenuItem_actionPerformed()
-  {
+
+      TrimRegionCommand trimRegion;
+      if(trimLeft)
+      {
+        trimRegion = new TrimRegionCommand("Remove Left",
+                                    TrimRegionCommand.TRIM_LEFT,
+                                    seqs,
+                                    column,
+                                    viewport.alignment,
+                                    viewport.colSel,
+                                    viewport.selectionGroup);
+        viewport.setStartRes(0);
+      }
+     else
+     {
+       trimRegion = new TrimRegionCommand("Remove Right",
+                                   TrimRegionCommand.TRIM_RIGHT,
+                                   seqs,
+                                   column,
+                                   viewport.alignment,
+                                   viewport.colSel,
+                                   viewport.selectionGroup);
+     }
+
+     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+      addHistoryItem(trimRegion);
+
+      Vector groups = viewport.alignment.getGroups();
+
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+            || (!trimLeft && !sg.adjustForRemoveRight(column)))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
   }
 
-  public void alignmentChanged()
+
+  public void removeGappedColumnMenuItem_actionPerformed()
   {
-    viewport.alignment.padGaps();
-    if(viewport.autocalculateConsensus)
+    int start = 0, end = viewport.alignment.getWidth()-1;
+
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
     {
-      viewport.updateConsensus();
-      viewport.updateConservation();
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
     }
+    else
+      seqs = viewport.alignment.getSequencesArray();
 
-    resetAllColourSchemes();
-    if(alignPanel.overviewPanel!=null)
-      alignPanel.overviewPanel.updateOverviewImage();
 
-    viewport.alignment.adjustSequenceAnnotations();
-    alignPanel.repaint();
+    RemoveGapColCommand removeGapCols =
+        new RemoveGapColCommand("Remove Gapped Columns",
+                                seqs,
+                                start, end,
+                                viewport.getGapCharacter());
+
+    addHistoryItem(removeGapCols);
+
+    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+   // ShiftList shifts;
+   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+   // edit.alColumnChanges=shifts.getInverse();
+   // if (viewport.hasHiddenColumns)
+   //   viewport.getColumnSelection().compensateForEdits(shifts);
+   viewport.setStartRes(seq.findIndex(startRes)-1);
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
-  void resetAllColourSchemes()
+  public void removeAllGapsMenuItem_actionPerformed()
   {
-    ColourSchemeI cs = viewport.globalColourScheme;
-    if(cs!=null)
+    int start = 0, end = viewport.alignment.getWidth()-1;
+
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
     {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
-            resetClustalX(viewport.alignment.getSequences(),
-                          viewport.alignment.getWidth());
-      }
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequencesArray();
 
-      cs.setConsensus(viewport.hconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) viewport.alignment;
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
 
-        cs.setConservation(c);
-      }
-    }
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+                                           seqs,
+                                           start, end,
+                     viewport.getGapCharacter()));
 
-    int s, sSize = viewport.alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(
-            sg.getSequences(true), sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
-  }
+    viewport.setStartRes(seq.findIndex(startRes)-1);
 
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
+  }
 
   public void findMenuItem_actionPerformed()
   {
@@ -1445,10 +1541,10 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-  //  addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-   //                                HistoryItem.SORT));
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
     alignPanel.repaint();
   }
 
@@ -1772,8 +1868,7 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
     MenuItem findMenuItem = new MenuItem();
-    Menu searchMenu = new Menu();
-    protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
     protected MenuItem nucleotideColour = new MenuItem();
     MenuItem deleteGroups = new MenuItem();
     MenuItem delete = new MenuItem();
@@ -1801,8 +1896,9 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
   Panel embeddedMenu;
   Label embeddedEdit;
-  Label embeddedSearch;
+  Label embeddedSelect;
   Label embeddedView;
+  Label embeddedFormat;
   Label embeddedColour;
   Label embeddedFile;
   Label embeddedHelp;
@@ -1925,9 +2021,7 @@ public void itemStateChanged(ItemEvent evt)
         renderGapsMenuItem.addItemListener(this);
         findMenuItem.setLabel("Find...");
         findMenuItem.addActionListener(this);
-        searchMenu.setLabel("Search");
-
-        abovePIDThreshold.setLabel("Above Identity Threshold");
+    abovePIDThreshold.setLabel("Above Identity Threshold");
         abovePIDThreshold.addItemListener(this);
         nucleotideColour.setLabel("Nucleotide");
         nucleotideColour.addActionListener(this);
@@ -2001,13 +2095,14 @@ public void itemStateChanged(ItemEvent evt)
     showSeqs.addActionListener(this);
     hideColumns.addActionListener(this);
     hideSequences.addActionListener(this);
-
-
+    formatMenu.setLabel("Format");
+    selectMenu.setLabel("Select");
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
-        alignFrameMenuBar.add(searchMenu);
-        alignFrameMenuBar.add(viewMenu);
-        alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(selectMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
+    alignFrameMenuBar.add(colourMenu);
         alignFrameMenuBar.add(calculateMenu);
         alignFrameMenuBar.add(helpMenu);
         fileMenu.add(inputText);
@@ -2023,35 +2118,16 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(copy);
         editMenu.add(pasteMenu);
         editMenu.add(delete);
-        editMenu.addSeparator();
-        editMenu.add(selectAllSequenceMenuItem);
-        editMenu.add(deselectAllSequenceMenuItem);
-        editMenu.add(invertSequenceMenuItem);
-    editMenu.add(invertColSel);
-    editMenu.add(deleteGroups);
-        editMenu.addSeparator();
+    editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
         editMenu.add(removeGappedColumnMenuItem);
         editMenu.add(removeAllGapsMenuItem);
         editMenu.add(removeRedundancyMenuItem);
-        searchMenu.add(findMenuItem);
-        viewMenu.add(font);
-        viewMenu.addSeparator();
     viewMenu.add(menu1);
     viewMenu.add(menu2);
     viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-        viewMenu.add(scaleAbove);
-        viewMenu.add(scaleLeft);
-        viewMenu.add(scaleRight);
-        viewMenu.addSeparator();
-    viewMenu.add(seqLimits);
-    viewMenu.add(viewBoxesMenuItem);
-        viewMenu.add(viewTextMenuItem);
-        viewMenu.add(colourTextMenuItem);
-        viewMenu.add(renderGapsMenuItem);
-        viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
         viewMenu.add(sequenceFeatures);
         viewMenu.add(featureSettings);
@@ -2101,40 +2177,53 @@ public void itemStateChanged(ItemEvent evt)
     menu1.add(showSeqs);
     menu2.add(hideColumns);
     menu2.add(hideSequences);
+    formatMenu.add(font);
+    formatMenu.add(seqLimits);
+    formatMenu.add(wrapMenuItem);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(viewBoxesMenuItem);
+    formatMenu.add(viewTextMenuItem);
+    formatMenu.add(colourTextMenuItem);
+    formatMenu.add(renderGapsMenuItem);
+    selectMenu.add(findMenuItem);
+    selectMenu.addSeparator();
+    selectMenu.add(selectAllSequenceMenuItem);
+    selectMenu.add(deselectAllSequenceMenuItem);
+    selectMenu.add(invertSequenceMenuItem);
+    selectMenu.add(invertColSel);
+    selectMenu.add(deleteGroups);
   }
 
   public void setEmbedded()
   {
 
     embeddedMenu = new Panel();
-    embeddedEdit = new Label();
-    embeddedSearch = new Label();
-    embeddedView = new Label();
-    embeddedColour = new Label();
-    embeddedFile = new Label();
-    embeddedHelp = new Label();
-    embeddedCalculate = new Label();
+    embeddedEdit = new Label("Edit");
+    embeddedSelect = new Label("Select");
+    embeddedView = new Label("View");
+    embeddedFormat = new Label("Label");
+    embeddedColour = new Label("Colour");
+    embeddedFile = new Label("File");
+    embeddedHelp = new Label("Help");
+    embeddedCalculate = new Label("Calculate");
     flowLayout1 = new FlowLayout();
     embeddedMenu.setBackground(Color.lightGray);
     embeddedMenu.setLayout(flowLayout1);
-    embeddedEdit.setText("Edit");
     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedSearch.setText("Search");
-    embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedView.setText("View");
+    embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedColour.setText("Colour");
+    embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedFile.setText("File");
     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedHelp.setText("Help");
     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedCalculate.setText("Calculate");
     embeddedMenu.add(embeddedFile);
     embeddedMenu.add(embeddedEdit);
-    embeddedMenu.add(embeddedSearch);
+    embeddedMenu.add(embeddedSelect);
     embeddedMenu.add(embeddedView);
+    embeddedMenu.add(embeddedFormat);
     embeddedMenu.add(embeddedColour);
     embeddedMenu.add(embeddedCalculate);
     embeddedMenu.add(embeddedHelp);
@@ -2143,8 +2232,9 @@ public void itemStateChanged(ItemEvent evt)
     flowLayout1.setVgap(0);
     embeddedFile.addMouseListener(this);
     embeddedEdit.addMouseListener(this);
-    embeddedSearch.addMouseListener(this);
+    embeddedSelect.addMouseListener(this);
     embeddedView.addMouseListener(this);
+    embeddedFormat.addMouseListener(this);
     embeddedColour.addMouseListener(this);
     embeddedCalculate.addMouseListener(this);
     embeddedHelp.addMouseListener(this);
@@ -2180,6 +2270,8 @@ public void itemStateChanged(ItemEvent evt)
   Menu menu2 = new Menu();
   MenuItem hideColumns = new MenuItem();
   MenuItem hideSequences = new MenuItem();
+  Menu formatMenu = new Menu();
+  Menu selectMenu = new Menu();
 
   public void mousePressed(MouseEvent evt)
   {
@@ -2193,14 +2285,18 @@ public void itemStateChanged(ItemEvent evt)
     {
       popup = editPopup = genPopupMenu(editPopup, editMenu);
     }
-    else if(source==embeddedSearch)
+    else if(source==embeddedSelect)
     {
-      popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
+      popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
     }
     else if(source==embeddedView)
     {
       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
     }
+    else if (source ==embeddedFormat)
+    {
+      popup = viewPopup = genPopupMenu(viewPopup, formatMenu);
+    }
     else if(source==embeddedColour)
     {
       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);