javadoc and informative error message when external binding to PDB fails
authorjprocter <Jim Procter>
Thu, 5 May 2011 13:55:16 +0000 (13:55 +0000)
committerjprocter <Jim Procter>
Thu, 5 May 2011 13:55:16 +0000 (13:55 +0000)
src/jalview/appletgui/AlignFrame.java

index f7cfba0..4634142 100755 (executable)
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- */
-package jalview.appletgui;
-
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.JalviewLite;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.structure.StructureSelectionManager;
-
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
-        ItemListener, KeyListener
-{
-  public AlignmentPanel alignPanel;
-
-  public AlignViewport viewport;
-
-  int DEFAULT_WIDTH = 700;
-
-  int DEFAULT_HEIGHT = 500;
-
-  String jalviewServletURL;
-
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
-          String title, boolean embedded)
-  {
-
-    if (applet != null)
-    {
-      jalviewServletURL = applet.getParameter("APPLICATION_URL");
-    }
-
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    viewport = new AlignViewport(al, applet);
-    alignPanel = new AlignmentPanel(this, viewport);
-
-    viewport.updateConservation(alignPanel);
-    viewport.updateConsensus(alignPanel);
-
-    annotationPanelMenuItem.setState(viewport.showAnnotation);
-    displayNonconservedMenuItem.setState(viewport.getShowunconserved());
-    followMouseOverFlag.setState(viewport.getFollowHighlight());
-    showGroupConsensus.setState(viewport.showGroupConsensus);
-    showGroupConservation.setState(viewport.showGroupConservation);
-    showConsensusHistogram.setState(viewport.showConsensusHistogram);
-    showSequenceLogo.setState(viewport.showSequenceLogo);
-
-    seqLimits.setState(viewport.showJVSuffix);
-
-    if (applet != null)
-    {
-      String param = applet.getParameter("sortBy");
-      if (param != null)
-      {
-        if (param.equalsIgnoreCase("Id"))
-        {
-          sortIDMenuItem_actionPerformed();
-        }
-        else if (param.equalsIgnoreCase("Pairwise Identity"))
-        {
-          sortPairwiseMenuItem_actionPerformed();
-        }
-        else if (param.equalsIgnoreCase("Length"))
-        {
-          sortLengthMenuItem_actionPerformed();
-        }
-      }
-
-      param = applet.getParameter("wrap");
-      if (param != null)
-      {
-        if (param.equalsIgnoreCase("true"))
-        {
-          wrapMenuItem.setState(true);
-          wrapMenuItem_actionPerformed();
-        }
-      }
-      param = applet.getParameter("centrecolumnlabels");
-      if (param != null)
-      {
-        centreColumnLabelFlag.setState(true);
-        centreColumnLabelFlag_stateChanged();
-      }
-      try
-      {
-        param = applet.getParameter("windowWidth");
-        if (param != null)
-        {
-          int width = Integer.parseInt(param);
-          DEFAULT_WIDTH = width;
-        }
-        param = applet.getParameter("windowHeight");
-        if (param != null)
-        {
-          int height = Integer.parseInt(param);
-          DEFAULT_HEIGHT = height;
-        }
-      } catch (Exception ex)
-      {
-      }
-
-    }
-
-    // Some JVMS send keyevents to Top frame or lowest panel,
-    // Havent worked out why yet. So add to both this frame and seqCanvas for
-    // now
-    this.addKeyListener(this);
-    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
-    alignPanel.idPanel.idCanvas.addKeyListener(this);
-    alignPanel.scalePanel.addKeyListener(this);
-    alignPanel.annotationPanel.addKeyListener(this);
-    alignPanel.annotationPanelHolder.addKeyListener(this);
-    alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
-    alignPanel.alabels.addKeyListener(this);
-    createAlignFrameWindow(embedded, title);
-    alignPanel.validate();
-    alignPanel.paintAlignment(true);
-  }
-
-  public AlignViewport getAlignViewport()
-  {
-    return viewport;
-  }
-
-  public SeqCanvas getSeqcanvas()
-  {
-    return alignPanel.seqPanel.seqCanvas;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param String
-   *          DOCUMENT ME!
-   */
-
-  public void parseFeaturesFile(String file, String type)
-  {
-    Hashtable featureLinks = new Hashtable();
-    boolean featuresFile = false;
-    try
-    {
-      featuresFile = new jalview.io.FeaturesFile(file, type)
-              .parse(viewport.alignment,
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
-                      featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    if (featuresFile)
-    {
-      if (featureLinks.size() > 0)
-      {
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
-      }
-      viewport.showSequenceFeatures = true;
-      sequenceFeatures.setState(true);
-      if (viewport.featureSettings != null)
-      {
-        viewport.featureSettings.refreshTable();
-      }
-      alignPanel.paintAlignment(true);
-    }
-
-  }
-
-  public void keyPressed(KeyEvent evt)
-  {
-    if (viewport.cursorMode
-            && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
-                    .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
-                    .getKeyCode() <= KeyEvent.VK_NUMPAD9))
-            && Character.isDigit(evt.getKeyChar()))
-      alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
-    switch (evt.getKeyCode())
-    {
-    case 27: // escape key
-      deselectAllSequenceMenuItem_actionPerformed();
-      
-      alignPanel.alabels.cancelDrag(); 
-      break;
-    case KeyEvent.VK_X:
-      if (evt.isControlDown() || evt.isMetaDown())
-      {
-        cut_actionPerformed();
-      }
-      break;
-    case KeyEvent.VK_C:
-      if (viewport.cursorMode && !evt.isControlDown())
-      {
-        alignPanel.seqPanel.setCursorColumn();
-      }
-      if (evt.isControlDown() || evt.isMetaDown())
-      {
-        copy_actionPerformed();
-      }
-      break;
-    case KeyEvent.VK_V:
-      if (evt.isControlDown())
-      {
-        paste(evt.isShiftDown());
-      }
-      break;
-    case KeyEvent.VK_A:
-      if (evt.isControlDown() || evt.isMetaDown())
-      {
-        selectAllSequenceMenuItem_actionPerformed();
-      }
-      break;
-    case KeyEvent.VK_DOWN:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.moveCursor(0, 1);
-      }
-      else
-      {
-        moveSelectedSequences(false);
-      }
-      break;
-
-    case KeyEvent.VK_UP:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.moveCursor(0, -1);
-      }
-      else
-      {
-        moveSelectedSequences(true);
-      }
-      break;
-
-    case KeyEvent.VK_LEFT:
-      if (evt.isAltDown() || !viewport.cursorMode)
-        slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
-      else
-        alignPanel.seqPanel.moveCursor(-1, 0);
-      break;
-
-    case KeyEvent.VK_RIGHT:
-      if (evt.isAltDown() || !viewport.cursorMode)
-        slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
-      else
-        alignPanel.seqPanel.moveCursor(1, 0);
-      break;
-
-    case KeyEvent.VK_SPACE:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
-                || evt.isShiftDown() || evt.isAltDown());
-      }
-      break;
-
-    case KeyEvent.VK_DELETE:
-    case KeyEvent.VK_BACK_SPACE:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
-                || evt.isShiftDown() || evt.isAltDown());
-      }
-      else
-      {
-        cut_actionPerformed();
-        alignPanel.seqPanel.seqCanvas.repaint();
-      }
-      break;
-
-    case KeyEvent.VK_S:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.setCursorRow();
-      }
-      break;
-    case KeyEvent.VK_P:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.setCursorPosition();
-      }
-      break;
-
-    case KeyEvent.VK_ENTER:
-    case KeyEvent.VK_COMMA:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.setCursorRowAndColumn();
-      }
-      break;
-
-    case KeyEvent.VK_Q:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.setSelectionAreaAtCursor(true);
-      }
-      break;
-    case KeyEvent.VK_M:
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.setSelectionAreaAtCursor(false);
-      }
-      break;
-
-    case KeyEvent.VK_F2:
-      viewport.cursorMode = !viewport.cursorMode;
-      statusBar.setText("Keyboard editing mode is "
-              + (viewport.cursorMode ? "on" : "off"));
-      if (viewport.cursorMode)
-      {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
-      }
-      break;
-
-    case KeyEvent.VK_F:
-      if (evt.isControlDown())
-      {
-        findMenuItem_actionPerformed();
-      }
-      break;
-
-    case KeyEvent.VK_H:
-    {
-      boolean toggleSeqs = !evt.isControlDown();
-      boolean toggleCols = !evt.isShiftDown();
-      toggleHiddenRegions(toggleSeqs, toggleCols);
-      break;
-    }
-
-    case KeyEvent.VK_PAGE_UP:
-      if (viewport.wrapAlignment)
-      {
-        alignPanel.scrollUp(true);
-      }
-      else
-      {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
-      }
-      break;
-
-    case KeyEvent.VK_PAGE_DOWN:
-      if (viewport.wrapAlignment)
-      {
-        alignPanel.scrollUp(false);
-      }
-      else
-      {
-        alignPanel.setScrollValues(viewport.startRes, 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())
-        {
-          invertColSel_actionPerformed();
-        }
-        else
-        {
-          invertSequenceMenuItem_actionPerformed();
-        }
-      }
-      break;
-
-    case KeyEvent.VK_U:
-      if (evt.isControlDown())
-      {
-        this.deleteGroups_actionPerformed();
-      }
-      break;
-
-    case KeyEvent.VK_T:
-      if (evt.isControlDown())
-      {
-        newView(null);
-      }
-      break;
-
-    }
-    alignPanel.paintAlignment(true);
-  }
-
-  /**
-   * called by key handler and the hide all/show all menu items
-   * 
-   * @param toggleSeqs
-   * @param toggleCols
-   */
-  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
-  {
-    boolean hide = false;
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (!toggleSeqs && !toggleCols)
-    {
-      // Hide everything by the current selection - this is a hack - we do the
-      // invert and then hide
-      // first check that there will be visible columns after the invert.
-      if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
-              .getSelected().size() > 0)
-              || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
-                      .getEndRes()))
-      {
-        // now invert the sequence set, if required - empty selection implies
-        // that no hiding is required.
-        if (sg != null)
-        {
-          invertSequenceMenuItem_actionPerformed();
-          sg = viewport.getSelectionGroup();
-          toggleSeqs = true;
-
-        }
-        viewport.expandColSelection(sg, true);
-        // finally invert the column selection and get the new sequence
-        // selection and indicate it should be hidden.
-        invertColSel_actionPerformed();
-        toggleCols = true;
-      }
-    }
-
-    if (toggleSeqs)
-    {
-      if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-      {
-        hide = true;
-        viewport.hideAllSelectedSeqs();
-      }
-      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
-      {
-        viewport.showAllHiddenSeqs();
-      }
-    }
-
-    if (toggleCols)
-    {
-      if (viewport.colSel.getSelected().size() > 0)
-      {
-        viewport.hideSelectedColumns();
-        if (!toggleSeqs)
-        {
-          viewport.selectionGroup = sg;
-        }
-      }
-      else if (!hide)
-      {
-        viewport.showAllHiddenColumns();
-      }
-    }
-  }
-
-  public void keyReleased(KeyEvent evt)
-  {
-  }
-
-  public void keyTyped(KeyEvent evt)
-  {
-  }
-
-  public void itemStateChanged(ItemEvent evt)
-  {
-    if (evt.getSource() == displayNonconservedMenuItem)
-    {
-      displayNonconservedMenuItem_actionPerformed();
-    }
-    else if (evt.getSource() == colourTextMenuItem)
-    {
-      colourTextMenuItem_actionPerformed();
-    }
-    else if (evt.getSource() == wrapMenuItem)
-    {
-      wrapMenuItem_actionPerformed();
-    }
-    else if (evt.getSource() == scaleAbove)
-    {
-      viewport.setScaleAboveWrapped(scaleAbove.getState());
-    }
-    else if (evt.getSource() == scaleLeft)
-    {
-      viewport.setScaleLeftWrapped(scaleLeft.getState());
-    }
-    else if (evt.getSource() == scaleRight)
-    {
-      viewport.setScaleRightWrapped(scaleRight.getState());
-    }
-    else if (evt.getSource() == seqLimits)
-    {
-      seqLimits_itemStateChanged();
-    }
-    else if (evt.getSource() == viewBoxesMenuItem)
-    {
-      viewport.setShowBoxes(viewBoxesMenuItem.getState());
-    }
-    else if (evt.getSource() == viewTextMenuItem)
-    {
-      viewport.setShowText(viewTextMenuItem.getState());
-    }
-    else if (evt.getSource() == renderGapsMenuItem)
-    {
-      viewport.setRenderGaps(renderGapsMenuItem.getState());
-    }
-    else if (evt.getSource() == annotationPanelMenuItem)
-    {
-      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
-    }
-    else if (evt.getSource() == sequenceFeatures)
-    {
-      viewport.showSequenceFeatures(sequenceFeatures.getState());
-      alignPanel.seqPanel.seqCanvas.repaint();
-    }
-    else if (evt.getSource() == conservationMenuItem)
-    {
-      conservationMenuItem_actionPerformed();
-    }
-    else if (evt.getSource() == abovePIDThreshold)
-    {
-      abovePIDThreshold_actionPerformed();
-    }
-    else if (evt.getSource() == applyToAllGroups)
-    {
-      viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
-    }
-    else if (evt.getSource() == autoCalculate)
-    {
-      viewport.autocalculateConsensus = autoCalculate.getState();
-    }
-    else if (evt.getSource() == this.centreColumnLabelFlag)
-    {
-      centreColumnLabelFlag_stateChanged();
-    }
-    else if (evt.getSource() == this.followMouseOverFlag)
-    {
-      mouseOverFlag_stateChanged();
-    }
-    else if (evt.getSource() == showGroupConsensus)
-    {
-      showGroupConsensus_actionPerformed();
-    }
-    else if (evt.getSource() == showGroupConservation)
-    {
-      showGroupConservation_actionPerformed();
-    }
-    else if (evt.getSource() == showSequenceLogo)
-    {
-      showSequenceLogo_actionPerformed();
-    }
-    else if (evt.getSource() == showConsensusHistogram)
-    {
-      showConsensusHistogram_actionPerformed();
-    }
-    else if (evt.getSource() == applyAutoAnnotationSettings)
-    {
-      applyAutoAnnotationSettings_actionPerformed();
-    }
-    alignPanel.paintAlignment(true);
-  }
-
-  private void mouseOverFlag_stateChanged()
-  {
-    viewport.followHighlight = followMouseOverFlag.getState();
-    // TODO: could kick the scrollTo mechanism to reset view for current
-    // searchresults.
-  }
-
-  private void centreColumnLabelFlag_stateChanged()
-  {
-    viewport.centreColumnLabels = centreColumnLabelFlag.getState();
-    this.alignPanel.annotationPanel.repaint();
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    Object source = evt.getSource();
-
-    if (source == inputText)
-    {
-      inputText_actionPerformed();
-    }
-    else if (source == loadTree)
-    {
-      loadTree_actionPerformed();
-    }
-    else if (source == loadApplication)
-    {
-      launchFullApplication();
-    }
-    else if (source == loadAnnotations)
-    {
-      loadAnnotations();
-    }
-    else if (source == outputAnnotations)
-    {
-      outputAnnotations(true);
-    }
-    else if (source == outputFeatures)
-    {
-      outputFeatures(true, "Jalview");
-    }
-    else if (source == closeMenuItem)
-    {
-      closeMenuItem_actionPerformed();
-    }
-    else if (source == copy)
-    {
-      copy_actionPerformed();
-    }
-    else if (source == undoMenuItem)
-    {
-      undoMenuItem_actionPerformed();
-    }
-    else if (source == redoMenuItem)
-    {
-      redoMenuItem_actionPerformed();
-    }
-    else if (source == inputText)
-    {
-      inputText_actionPerformed();
-    }
-    else if (source == closeMenuItem)
-    {
-      closeMenuItem_actionPerformed();
-    }
-    else if (source == undoMenuItem)
-    {
-      undoMenuItem_actionPerformed();
-    }
-    else if (source == redoMenuItem)
-    {
-      redoMenuItem_actionPerformed();
-    }
-    else if (source == copy)
-    {
-      copy_actionPerformed();
-    }
-    else if (source == pasteNew)
-    {
-      pasteNew_actionPerformed();
-    }
-    else if (source == pasteThis)
-    {
-      pasteThis_actionPerformed();
-    }
-    else if (source == cut)
-    {
-      cut_actionPerformed();
-    }
-    else if (source == delete)
-    {
-      delete_actionPerformed();
-    }
-    else if (source == grpsFromSelection)
-    {
-      makeGrpsFromSelection_actionPerformed();
-    }
-    else if (source == deleteGroups)
-    {
-      deleteGroups_actionPerformed();
-    }
-    else if (source == selectAllSequenceMenuItem)
-    {
-      selectAllSequenceMenuItem_actionPerformed();
-    }
-    else if (source == deselectAllSequenceMenuItem)
-    {
-      deselectAllSequenceMenuItem_actionPerformed();
-    }
-    else if (source == invertSequenceMenuItem)
-    {
-      invertSequenceMenuItem_actionPerformed();
-    }
-    else if (source == invertColSel)
-    {
-      viewport.invertColumnSelection();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == remove2LeftMenuItem)
-    {
-      trimAlignment(true);
-    }
-    else if (source == remove2RightMenuItem)
-    {
-      trimAlignment(false);
-    }
-    else if (source == removeGappedColumnMenuItem)
-    {
-      removeGappedColumnMenuItem_actionPerformed();
-    }
-    else if (source == removeAllGapsMenuItem)
-    {
-      removeAllGapsMenuItem_actionPerformed();
-    }
-    else if (source == findMenuItem)
-    {
-      findMenuItem_actionPerformed();
-    }
-    else if (source == font)
-    {
-      new FontChooser(alignPanel);
-    }
-    else if (source == newView)
-    {
-      newView(null);
-    }
-    else if (source == showColumns)
-    {
-      viewport.showAllHiddenColumns();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == showSeqs)
-    {
-      viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == hideColumns)
-    {
-      viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == hideSequences
-            && viewport.getSelectionGroup() != null)
-    {
-      viewport.hideAllSelectedSeqs();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == hideAllButSelection)
-    {
-      toggleHiddenRegions(false, false);
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == hideAllSelection)
-    {
-      SequenceGroup sg = viewport.getSelectionGroup();
-      viewport.expandColSelection(sg, false);
-      viewport.hideAllSelectedSeqs();
-      viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == showAllHidden)
-    {
-      viewport.showAllHiddenColumns();
-      viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
-    }
-    else if (source == showGroupConsensus)
-    {
-      showGroupConsensus_actionPerformed();
-    }
-    else if (source == showGroupConservation)
-    {
-      showGroupConservation_actionPerformed();
-    }
-    else if (source == showSequenceLogo)
-    {
-      showSequenceLogo_actionPerformed();
-    }
-    else if (source == showConsensusHistogram)
-    {
-      showConsensusHistogram_actionPerformed();
-    }
-    else if (source == applyAutoAnnotationSettings)
-    {
-      applyAutoAnnotationSettings_actionPerformed();
-    }
-    else if (source == featureSettings)
-    {
-      new FeatureSettings(alignPanel);
-    }
-    else if (source == alProperties)
-    {
-      StringBuffer contents = new jalview.io.AlignmentProperties(
-              viewport.alignment).formatAsString();
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
-      cap.setText(contents.toString());
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
-              + getTitle(), 400, 250);
-    }
-    else if (source == overviewMenuItem)
-    {
-      overviewMenuItem_actionPerformed();
-    }
-    else if (source == noColourmenuItem)
-    {
-      changeColour(null);
-    }
-    else if (source == clustalColour)
-    {
-      abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(
-              viewport.alignment.getSequences(),
-              viewport.alignment.getWidth()));
-    }
-    else if (source == zappoColour)
-    {
-      changeColour(new ZappoColourScheme());
-    }
-    else if (source == taylorColour)
-    {
-      changeColour(new TaylorColourScheme());
-    }
-    else if (source == hydrophobicityColour)
-    {
-      changeColour(new HydrophobicColourScheme());
-    }
-    else if (source == helixColour)
-    {
-      changeColour(new HelixColourScheme());
-    }
-    else if (source == strandColour)
-    {
-      changeColour(new StrandColourScheme());
-    }
-    else if (source == turnColour)
-    {
-      changeColour(new TurnColourScheme());
-    }
-    else if (source == buriedColour)
-    {
-      changeColour(new BuriedColourScheme());
-    }
-    else if (source == nucleotideColour)
-    {
-      changeColour(new NucleotideColourScheme());
-    }
-    else if (source == modifyPID)
-    {
-      modifyPID_actionPerformed();
-    }
-    else if (source == modifyConservation)
-    {
-      modifyConservation_actionPerformed();
-    }
-    else if (source == userDefinedColour)
-    {
-      new UserDefinedColours(alignPanel, null);
-    }
-    else if (source == PIDColour)
-    {
-      changeColour(new PIDColourScheme());
-    }
-    else if (source == BLOSUM62Colour)
-    {
-      changeColour(new Blosum62ColourScheme());
-    }
-    else if (source == annotationColour)
-    {
-      new AnnotationColourChooser(viewport, alignPanel);
-    }
-    else if (source == sortPairwiseMenuItem)
-    {
-      sortPairwiseMenuItem_actionPerformed();
-    }
-    else if (source == sortIDMenuItem)
-    {
-      sortIDMenuItem_actionPerformed();
-    }
-    else if (source == sortLengthMenuItem)
-    {
-      sortLengthMenuItem_actionPerformed();
-    }
-    else if (source == sortGroupMenuItem)
-    {
-      sortGroupMenuItem_actionPerformed();
-    }
-    else if (source == removeRedundancyMenuItem)
-    {
-      removeRedundancyMenuItem_actionPerformed();
-    }
-    else if (source == pairwiseAlignmentMenuItem)
-    {
-      pairwiseAlignmentMenuItem_actionPerformed();
-    }
-    else if (source == PCAMenuItem)
-    {
-      PCAMenuItem_actionPerformed();
-    }
-    else if (source == averageDistanceTreeMenuItem)
-    {
-      averageDistanceTreeMenuItem_actionPerformed();
-    }
-    else if (source == neighbourTreeMenuItem)
-    {
-      neighbourTreeMenuItem_actionPerformed();
-    }
-    else if (source == njTreeBlosumMenuItem)
-    {
-      njTreeBlosumMenuItem_actionPerformed();
-    }
-    else if (source == avDistanceTreeBlosumMenuItem)
-    {
-      avTreeBlosumMenuItem_actionPerformed();
-    }
-    else if (source == documentation)
-    {
-      documentation_actionPerformed();
-    }
-    else if (source == about)
-    {
-      about_actionPerformed();
-    }
-
-  }
-
-  public void inputText_actionPerformed()
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
-  }
-
-  protected void outputText_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-            "Alignment output - " + e.getActionCommand(), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
-            e.getActionCommand(), 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 String outputAnnotations(boolean displayTextbox)
-  {
-    String annotation = new AnnotationFile().printAnnotations(
-            viewport.showAnnotation ? viewport.alignment
-                    .getAlignmentAnnotation() : null, viewport.alignment
-                    .getGroups(),
-            ((Alignment) viewport.alignment).alignmentProperties);
-
-    if (displayTextbox)
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
-      cap.setText(annotation);
-    }
-
-    return annotation;
-  }
-
-  private Hashtable getDisplayedFeatureCols()
-  {
-    if (alignPanel.getFeatureRenderer() != null)
-    {
-      FeatureRenderer fr = alignPanel.getFeatureRenderer();
-      Hashtable fcols = new Hashtable();
-      Enumeration en = viewport.featuresDisplayed.keys();
-      while (en.hasMoreElements())
-      {
-        Object col = en.nextElement();
-        fcols.put(col, fr.featureColours.get(col));
-      }
-      return fcols;
-    }
-    return null;
-  }
-
-  public String outputFeatures(boolean displayTextbox, String format)
-  {
-    String features;
-    if (format.equalsIgnoreCase("Jalview"))
-    {
-      features = new FeaturesFile().printJalviewFormat(
-              viewport.alignment.getSequencesArray(),
-              getDisplayedFeatureCols());
-    }
-    else
-    {
-      features = new FeaturesFile().printGFFFormat(
-              viewport.alignment.getSequencesArray(),
-              getDisplayedFeatureCols());
-    }
-
-    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);
-
-    url.append("?open="
-            + appendProtocol(viewport.applet.getParameter("file")));
-
-    if (viewport.applet.getParameter("features") != null)
-    {
-      url.append("&features=");
-      url.append(appendProtocol(viewport.applet.getParameter("features")));
-    }
-
-    if (viewport.applet.getParameter("annotations") != null)
-    {
-      url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
-    }
-
-    if (viewport.applet.getParameter("jnetfile") != null)
-    {
-      url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
-    }
-
-    if (viewport.applet.getParameter("defaultColour") != null)
-    {
-      url.append("&colour="
-              + removeWhiteSpace(viewport.applet
-                      .getParameter("defaultColour")));
-    }
-
-    if (viewport.applet.getParameter("userDefinedColour") != null)
-    {
-      url.append("&colour="
-              + removeWhiteSpace(viewport.applet
-                      .getParameter("userDefinedColour")));
-    }
-    if (viewport.applet.getParameter("tree") != null)
-    {
-      url.append("&tree="
-              + appendProtocol(viewport.applet.getParameter("tree")));
-    }
-    if (viewport.applet.getParameter("treeFile") != null)
-    {
-      url.append("&tree="
-              + appendProtocol(viewport.applet.getParameter("treeFile")));
-    }
-
-    showURL(url.toString(), "FULL_APP");
-  }
-
-  String removeWhiteSpace(String colour)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < colour.length(); i++)
-    {
-      if (Character.isWhitespace(colour.charAt(i)))
-      {
-        sb.append("%20");
-      }
-      else
-      {
-        sb.append(colour.charAt(i));
-      }
-    }
-
-    return sb.toString();
-  }
-
-  String appendProtocol(String url)
-  {
-    try
-    {
-      new URL(url);
-      url = URLEncoder.encode(url);
-    }
-    /*
-     * When we finally deprecate 1.1 compatibility, we can start to use
-     * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
-     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
-     * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
-     * ex.printStackTrace(); }
-     */
-    catch (java.net.MalformedURLException ex)
-    {
-      url = viewport.applet.getCodeBase() + url;
-    }
-    return url;
-  }
-
-  public void closeMenuItem_actionPerformed()
-  {
-    PaintRefresher.RemoveComponent(alignPanel);
-    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
-    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
-
-    if (PaintRefresher.components.size() == 0 && viewport.applet == null)
-    {
-      System.exit(0);
-    }
-
-    this.dispose();
-  }
-
-  /**
-   * 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;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void undoMenuItem_actionPerformed()
-  {
-    if (viewport.historyList.size() < 1)
-    {
-      return;
-    }
-
-    CommandI command = (CommandI) viewport.historyList.pop();
-    viewport.redoList.push(command);
-    command.undoCommand(null);
-
-    AlignViewport originalSource = getOriginatingSource(command);
-
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-    updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.alignment.getSequences());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void redoMenuItem_actionPerformed()
-  {
-    if (viewport.redoList.size() < 1)
-    {
-      return;
-    }
-
-    CommandI command = (CommandI) viewport.redoList.pop();
-    viewport.historyList.push(command);
-    command.doCommand(null);
-
-    AlignViewport originalSource = getOriginatingSource(command);
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-
-    updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.alignment.getSequences());
-  }
-
-  AlignViewport getOriginatingSource(CommandI command)
-  {
-    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;
-      al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components.get(viewport
-              .getSequenceSetId());
-      for (int i = 0; i < comps.size(); i++)
-      {
-        if (comps.elementAt(i) instanceof AlignmentPanel)
-        {
-          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
-          {
-            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
-            break;
-          }
-        }
-      }
-    }
-
-    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;
-  }
-
-  public void moveSelectedSequences(boolean up)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg == null)
-    {
-      return;
-    }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
-    alignPanel.paintAlignment(true);
-  }
-
-  synchronized void slideSequences(boolean right, int size)
-  {
-    Vector sg = new Vector();
-    if (viewport.cursorMode)
-    {
-      sg.addElement(viewport.alignment
-              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
-    }
-    else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport.alignment
-                    .getHeight())
-    {
-      sg = viewport.getSelectionGroup().getSequences(
-              viewport.hiddenRepSequences);
-    }
-
-    if (sg.size() < 1)
-    {
-      return;
-    }
-
-    Vector invertGroup = new Vector();
-
-    for (int i = 0; i < viewport.alignment.getHeight(); i++)
-    {
-      if (!sg.contains(viewport.alignment.getSequenceAt(i)))
-        invertGroup.addElement(viewport.alignment.getSequenceAt(i));
-    }
-
-    SequenceI[] seqs1 = new SequenceI[sg.size()];
-    for (int i = 0; i < sg.size(); i++)
-      seqs1[i] = (SequenceI) sg.elementAt(i);
-
-    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
-    for (int i = 0; i < invertGroup.size(); i++)
-      seqs2[i] = (SequenceI) invertGroup.elementAt(i);
-
-    SlideSequencesCommand ssc;
-    if (right)
-      ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
-              size, viewport.getGapCharacter());
-    else
-      ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
-              size, viewport.getGapCharacter());
-
-    int groupAdjustment = 0;
-    if (ssc.getGapsInsertedBegin() && right)
-    {
-      if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor(size, 0);
-      else
-        groupAdjustment = size;
-    }
-    else if (!ssc.getGapsInsertedBegin() && !right)
-    {
-      if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor(-size, 0);
-      else
-        groupAdjustment = -size;
-    }
-
-    if (groupAdjustment != 0)
-    {
-      viewport.getSelectionGroup().setStartRes(
-              viewport.getSelectionGroup().getStartRes() + groupAdjustment);
-      viewport.getSelectionGroup().setEndRes(
-              viewport.getSelectionGroup().getEndRes() + groupAdjustment);
-    }
-
-    boolean appendHistoryItem = false;
-    if (viewport.historyList != null && viewport.historyList.size() > 0
-            && viewport.historyList.peek() instanceof SlideSequencesCommand)
-    {
-      appendHistoryItem = ssc
-              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
-                      .peek());
-    }
-
-    if (!appendHistoryItem)
-      addHistoryItem(ssc);
-
-    repaint();
-  }
-
-  static StringBuffer copiedSequences;
-
-  static Vector copiedHiddenColumns;
-
-  protected void copy_actionPerformed()
-  {
-    if (viewport.getSelectionGroup() == null)
-    {
-      return;
-    }
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-    copiedSequences = new StringBuffer();
-    Hashtable orderedSeqs = new Hashtable();
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
-    }
-
-    int index = 0, startRes, endRes;
-    char ch;
-
-    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
-    {
-      copiedHiddenColumns = new Vector();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
-      {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
-
-        copiedHiddenColumns.addElement(new int[]
-        { region[0] - hiddenOffset, region[1] - hiddenOffset });
-      }
-    }
-    else
-    {
-      copiedHiddenColumns = null;
-    }
-
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      SequenceI seq = null;
-
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          break;
-        }
-        else
-        {
-          index++;
-        }
-      }
-
-      // FIND START RES
-      // Returns residue following index if gap
-      startRes = seq.findPosition(sg.getStartRes());
-
-      // FIND END RES
-      // Need to find the residue preceeding index if gap
-      endRes = 0;
-
-      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
-      {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap((ch)))
-        {
-          endRes++;
-        }
-      }
-
-      if (endRes > 0)
-      {
-        endRes += seq.getStart() - 1;
-      }
-
-      copiedSequences.append(seq.getName()
-              + "\t"
-              + startRes
-              + "\t"
-              + endRes
-              + "\t"
-              + seq.getSequenceAsString(sg.getStartRes(),
-                      sg.getEndRes() + 1) + "\n");
-    }
-
-  }
-
-  protected void pasteNew_actionPerformed()
-  {
-    paste(true);
-  }
-
-  protected void pasteThis_actionPerformed()
-  {
-    paste(false);
-  }
-
-  void paste(boolean newAlignment)
-  {
-    try
-    {
-
-      if (copiedSequences == null)
-      {
-        return;
-      }
-
-      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
-      Vector seqs = new Vector();
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        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)
-      {
-        String newtitle = new String("Copied sequences");
-        if (getTitle().startsWith("Copied sequences"))
-        {
-          newtitle = getTitle();
-        }
-        else
-        {
-          newtitle = newtitle.concat("- from " + getTitle());
-        }
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs),
-                viewport.applet, newtitle, false);
-        if (copiedHiddenColumns != null)
-        {
-          for (int i = 0; i < copiedHiddenColumns.size(); i++)
-          {
-            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
-            af.viewport.hideColumns(region[0], region[1]);
-          }
-        }
-
-        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
-                DEFAULT_HEIGHT);
-      }
-      else
-      {
-        addSequences(newSeqs);
-      }
-
-    } catch (Exception ex)
-    {
-    } // could be anything being pasted in here
-
-  }
-
-  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();
-    delete_actionPerformed();
-  }
-
-  protected void delete_actionPerformed()
-  {
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg == null)
-    {
-      return;
-    }
-
-    Vector seqs = new Vector();
-    SequenceI seq;
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      seq = sg.getSequenceAt(i);
-      seqs.addElement(seq);
-    }
-
-    // If the cut affects all sequences, remove highlighted columns
-    if (sg.getSize() == 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));
-
-    viewport.setSelectionGroup(null);
-    viewport.alignment.deleteGroup(sg);
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
-
-    if (viewport.getAlignment().getHeight() < 1)
-    {
-      this.setVisible(false);
-    }
-    viewport.sendSelection();
-  }
-
-  /**
-   * group consensus toggled
-   * 
-   */
-  protected void showGroupConsensus_actionPerformed()
-  {
-    viewport.setShowGroupConsensus(showGroupConsensus.getState());
-    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-
-  }
-
-  /**
-   * group conservation toggled.
-   */
-  protected void showGroupConservation_actionPerformed()
-  {
-    viewport.setShowGroupConservation(showGroupConservation.getState());
-    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
-   * .event.ActionEvent)
-   */
-  protected void showConsensusHistogram_actionPerformed()
-  {
-    viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
-    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-  }
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
-   * .event.ActionEvent)
-   */
-  protected void showSequenceLogo_actionPerformed()
-  {
-    viewport.setShowSequenceLogo(showSequenceLogo.getState());
-    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-  }
-
-  protected void applyAutoAnnotationSettings_actionPerformed()
-  {
-    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-  }
-
-  protected void makeGrpsFromSelection_actionPerformed()
-  {
-    if (viewport.getSelectionGroup() != null)
-    {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()),
-              viewport.alignment.getGroups());
-      viewport.alignment.deleteAllGroups();
-      viewport.sequenceColours = null;
-      viewport.setSelectionGroup(null);
-      // set view properties for each group
-      for (int g = 0; g < gps.length; g++)
-      {
-        // gps[g].setShowunconserved(viewport.getShowUnconserved());
-        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
-        viewport.alignment.addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
-                .hasMoreElements(); viewport.setSequenceColour(
-                (SequenceI) sq.nextElement(), col))
-          ;
-      }
-      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
-      alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
-    }
-  }
-
-  protected void deleteGroups_actionPerformed()
-  {
-    viewport.alignment.deleteAllGroups();
-    viewport.sequenceColours = null;
-    viewport.setSelectionGroup(null);
-
-    alignPanel.paintAlignment(true);
-  }
-
-  public void selectAllSequenceMenuItem_actionPerformed()
-  {
-    SequenceGroup sg = new SequenceGroup();
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
-    sg.setEndRes(viewport.alignment.getWidth() - 1);
-    viewport.setSelectionGroup(sg);
-    alignPanel.paintAlignment(true);
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
-    viewport.sendSelection();
-  }
-
-  public void deselectAllSequenceMenuItem_actionPerformed()
-  {
-    if (viewport.cursorMode)
-    {
-      alignPanel.seqPanel.keyboardNo1 = null;
-      alignPanel.seqPanel.keyboardNo2 = null;
-    }
-    viewport.setSelectionGroup(null);
-    viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
-    alignPanel.idPanel.idCanvas.searchResults = null;
-    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.paintAlignment(true);
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
-    viewport.sendSelection();
-  }
-
-  public void invertSequenceMenuItem_actionPerformed()
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
-    }
-
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
-    viewport.sendSelection();
-  }
-
-  public void invertColSel_actionPerformed()
-  {
-    viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
-    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
-    viewport.sendSelection();
-  }
-
-  void trimAlignment(boolean trimLeft)
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    int column;
-
-    if (colSel.size() > 0)
-    {
-      if (trimLeft)
-      {
-        column = colSel.getMin();
-      }
-      else
-      {
-        column = colSel.getMax();
-      }
-
-      SequenceI[] seqs;
-      if (viewport.getSelectionGroup() != null)
-      {
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(
-                viewport.hiddenRepSequences);
-      }
-      else
-      {
-        seqs = viewport.alignment.getSequencesArray();
-      }
-
-      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 removeGappedColumnMenuItem_actionPerformed()
-  {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
-
-    SequenceI[] seqs;
-    if (viewport.getSelectionGroup() != null)
-    {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
-    }
-    else
-    {
-      seqs = viewport.alignment.getSequencesArray();
-    }
-
-    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
-            "Remove Gapped Columns", seqs, start, end, viewport.alignment);
-
-    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());
-
-  }
-
-  public void removeAllGapsMenuItem_actionPerformed()
-  {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
-
-    SequenceI[] seqs;
-    if (viewport.getSelectionGroup() != null)
-    {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
-    }
-    else
-    {
-      seqs = viewport.alignment.getSequencesArray();
-    }
-
-    // This is to maintain viewport position on first residue
-    // of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.alignment));
-
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
-
-  }
-
-  public void findMenuItem_actionPerformed()
-  {
-    new Finder(alignPanel);
-  }
-
-  /**
-   * create a new view derived from the current view
-   * 
-   * @param viewtitle
-   * @return frame for the new view
-   */
-  public AlignFrame newView(String viewtitle)
-  {
-    AlignmentI newal;
-    if (viewport.hasHiddenRows)
-    {
-      newal = new Alignment(viewport.getAlignment().getHiddenSequences()
-              .getFullAlignment().getSequencesArray());
-    }
-    else
-    {
-      newal = new Alignment(viewport.alignment.getSequencesArray());
-    }
-
-    if (viewport.alignment.getAlignmentAnnotation() != null)
-    {
-      for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
-      {
-        if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
-        {
-          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
-        }
-      }
-    }
-
-    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 (viewtitle != null)
-    {
-      title = viewtitle + " ( " + title + ")";
-    }
-    else
-    {
-      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;
-    return newaf;
-  }
-
-  /**
-   * 
-   * @return list of feature groups on the view
-   */
-  public String[] getFeatureGroups()
-  {
-    FeatureRenderer fr = null;
-    if (alignPanel != null
-            && (fr = alignPanel.getFeatureRenderer()) != null)
-    {
-      return fr.getGroups();
-    }
-    return null;
-  }
-
-  /**
-   * get sequence feature groups that are hidden or shown
-   * 
-   * @param visible
-   *          true is visible
-   * @return list
-   */
-  public String[] getFeatureGroupsOfState(boolean visible)
-  {
-    FeatureRenderer fr = null;
-    if (alignPanel != null
-            && (fr = alignPanel.getFeatureRenderer()) != null)
-    {
-      return fr.getGroups(visible);
-    }
-    return null;
-  }
-
-  /**
-   * Change the display state for the given feature groups
-   * 
-   * @param groups
-   *          list of group strings
-   * @param state
-   *          visible or invisible
-   */
-  public void setFeatureGroupState(String[] groups, boolean state)
-  {
-    FeatureRenderer fr = null;
-    this.sequenceFeatures.setState(true);
-    viewport.showSequenceFeatures(true);
-    if (alignPanel != null
-            && (fr = alignPanel.getFeatureRenderer()) != null)
-    {
-      fr.setGroupState(groups, state);
-      alignPanel.seqPanel.seqCanvas.repaint();
-      if (alignPanel.overviewPanel != null)
-      {
-        alignPanel.overviewPanel.updateOverviewImage();
-      }
-    }
-  }
-
-  public void seqLimits_itemStateChanged()
-  {
-    viewport.setShowJVSuffix(seqLimits.getState());
-    alignPanel.fontChanged();
-    alignPanel.paintAlignment(true);
-  }
-
-  protected void colourTextMenuItem_actionPerformed()
-  {
-    viewport.setColourText(colourTextMenuItem.getState());
-    alignPanel.paintAlignment(true);
-  }
-
-  protected void displayNonconservedMenuItem_actionPerformed()
-  {
-    viewport.setShowunconserved(displayNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
-  }
-
-  protected void wrapMenuItem_actionPerformed()
-  {
-    viewport.setWrapAlignment(wrapMenuItem.getState());
-    alignPanel.setWrapAlignment(wrapMenuItem.getState());
-    scaleAbove.setEnabled(wrapMenuItem.getState());
-    scaleLeft.setEnabled(wrapMenuItem.getState());
-    scaleRight.setEnabled(wrapMenuItem.getState());
-    alignPanel.paintAlignment(true);
-  }
-
-  public void overviewMenuItem_actionPerformed()
-  {
-    if (alignPanel.overviewPanel != null)
-    {
-      return;
-    }
-
-    Frame frame = new Frame();
-    OverviewPanel overview = new OverviewPanel(alignPanel);
-    frame.add(overview);
-    // +50 must allow for applet frame window
-    jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
-            overview.getPreferredSize().width,
-            overview.getPreferredSize().height + 50);
-
-    frame.pack();
-    frame.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent e)
-      {
-        alignPanel.setOverviewPanel(null);
-      };
-    });
-
-    alignPanel.setOverviewPanel(overview);
-
-  }
-
-  void changeColour(ColourSchemeI cs)
-  {
-    int threshold = 0;
-
-    if (cs != null)
-    {
-      if (viewport.getAbovePIDThreshold())
-      {
-        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                "Background");
-
-        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-        viewport.setGlobalColourScheme(cs);
-      }
-      else
-      {
-        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-      }
-
-      if (viewport.getConservationSelected())
-      {
-
-        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);
-
-        cs.setConservation(c);
-
-        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
-                cs, "Background"));
-
-      }
-      else
-      {
-        cs.setConservation(null);
-      }
-
-      cs.setConsensus(viewport.hconsensus);
-
-    }
-    viewport.setGlobalColourScheme(cs);
-
-    if (viewport.getColourAppliesToAllGroups())
-    {
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-        if (cs == null)
-        {
-          sg.cs = null;
-          continue;
-        }
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(
-                  sg.getSequences(viewport.hiddenRepSequences),
-                  sg.getWidth());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
-        }
-
-        if (viewport.getAbovePIDThreshold()
-                || cs instanceof PIDColourScheme
-                || cs instanceof Blosum62ColourScheme)
-        {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(viewport.hiddenRepSequences), 0,
-                  sg.getWidth()));
-        }
-        else
-        {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-        }
-
-        if (viewport.getConservationSelected())
-        {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3,
-                  sg.getSequences(viewport.hiddenRepSequences), 0,
-                  viewport.alignment.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
-          sg.cs.setConservation(c);
-        }
-        else
-        {
-          sg.cs.setConservation(null);
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-        }
-
-      }
-    }
-
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().sequenceColoursChanged(
-                    alignPanel);
-
-    alignPanel.paintAlignment(true);
-  }
-
-  protected void modifyPID_actionPerformed()
-  {
-    if (viewport.getAbovePIDThreshold()
-            && viewport.globalColourScheme != null)
-    {
-      SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
-      SliderPanel.showPIDSlider();
-    }
-  }
-
-  protected void modifyConservation_actionPerformed()
-  {
-    if (viewport.getConservationSelected()
-            && viewport.globalColourScheme != null)
-    {
-      SliderPanel.setConservationSlider(alignPanel,
-              viewport.globalColourScheme, "Background");
-      SliderPanel.showConservationSlider();
-    }
-  }
-
-  protected void conservationMenuItem_actionPerformed()
-  {
-    viewport.setConservationSelected(conservationMenuItem.getState());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setState(false);
-
-    changeColour(viewport.getGlobalColourScheme());
-
-    modifyConservation_actionPerformed();
-  }
-
-  public void abovePIDThreshold_actionPerformed()
-  {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
-    conservationMenuItem.setState(false);
-    viewport.setConservationSelected(false);
-
-    changeColour(viewport.getGlobalColourScheme());
-
-    modifyPID_actionPerformed();
-  }
-
-  public void sortPairwiseMenuItem_actionPerformed()
-  {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
-            .getAlignment().getSequenceAt(0), null);
-
-    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
-            viewport.alignment));
-    alignPanel.paintAlignment(true);
-  }
-
-  public void sortIDMenuItem_actionPerformed()
-  {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByID(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
-    alignPanel.paintAlignment(true);
-  }
-
-  public void sortLengthMenuItem_actionPerformed()
-  {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByLength(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("Length Sort", oldOrder,
-            viewport.alignment));
-    alignPanel.paintAlignment(true);
-  }
-
-  public void sortGroupMenuItem_actionPerformed()
-  {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter.sortByGroup(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
-            viewport.alignment));
-    alignPanel.paintAlignment(true);
-
-  }
-
-  public void removeRedundancyMenuItem_actionPerformed()
-  {
-    new RedundancyPanel(alignPanel);
-  }
-
-  public void pairwiseAlignmentMenuItem_actionPerformed()
-  {
-    if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() > 1)
-    {
-      Frame frame = new Frame();
-      frame.add(new PairwiseAlignPanel(alignPanel));
-      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
-              500);
-    }
-  }
-
-  public void PCAMenuItem_actionPerformed()
-  {
-    // are the sequences aligned?
-    if (!viewport.alignment.isAligned(false))
-    {
-      SequenceI current;
-      int Width = viewport.getAlignment().getWidth();
-
-      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-      {
-        current = viewport.getAlignment().getSequenceAt(i);
-
-        if (current.getLength() < Width)
-        {
-          current.insertCharAt(Width - 1, viewport.getGapCharacter());
-        }
-      }
-      alignPanel.paintAlignment(true);
-    }
-
-    if ((viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() < 4 && viewport
-            .getSelectionGroup().getSize() > 0)
-            || viewport.getAlignment().getHeight() < 4)
-    {
-      return;
-    }
-
-    try
-    {
-      new PCAPanel(viewport);
-    } catch (java.lang.OutOfMemoryError ex)
-    {
-    }
-
-  }
-
-  public void averageDistanceTreeMenuItem_actionPerformed()
-  {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
-  }
-
-  public void neighbourTreeMenuItem_actionPerformed()
-  {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
-  }
-
-  protected void njTreeBlosumMenuItem_actionPerformed()
-  {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed()
-  {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
-  }
-
-  void NewTreePanel(String type, String pwType, String title)
-  {
-    // are the sequences aligned?
-    if (!viewport.alignment.isAligned(false))
-    {
-      SequenceI current;
-      int Width = viewport.getAlignment().getWidth();
-
-      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-      {
-        current = viewport.getAlignment().getSequenceAt(i);
-
-        if (current.getLength() < Width)
-        {
-          current.insertCharAt(Width - 1, viewport.getGapCharacter());
-        }
-      }
-      alignPanel.paintAlignment(true);
-
-    }
-
-    if ((viewport.getSelectionGroup() != null && viewport
-            .getSelectionGroup().getSize() > 1)
-            || (viewport.getSelectionGroup() == null && viewport.alignment
-                    .getHeight() > 1))
-    {
-      final TreePanel tp = new TreePanel(alignPanel, type, pwType);
-
-      addTreeMenuItem(tp, title);
-
-      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
-    }
-  }
-
-  void loadTree_actionPerformed()
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    cap.setText("Paste your Newick tree file here.");
-    cap.setTreeImport();
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
-  }
-
-  public void loadTree(jalview.io.NewickFile tree, String treeFile)
-  {
-    TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
-    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-    addTreeMenuItem(tp, treeFile);
-  }
-
-  /**
-   * sort the alignment using the given treePanel
-   * 
-   * @param treePanel
-   *          tree used to sort view
-   * @param title
-   *          string used for undo event name
-   */
-  public void sortByTree(TreePanel treePanel, String title)
-  {
-    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    AlignmentSorter
-            .sortByTree(viewport.getAlignment(), treePanel.getTree());
-    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-    // HistoryItem.SORT));
-    addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
-            viewport.alignment));
-    alignPanel.paintAlignment(true);
-  }
-
-  /**
-   * Do any automatic reordering of the alignment and add the necessary bits to
-   * the menu structure for the new tree
-   * 
-   * @param treePanel
-   * @param title
-   */
-  protected void addTreeMenuItem(final TreePanel treePanel,
-          final String title)
-  {
-    final MenuItem item = new MenuItem(title);
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent evt)
-      {
-        sortByTree(treePanel, title); // treePanel.getTitle());
-      }
-    });
-
-    treePanel.addWindowListener(new WindowAdapter()
-    {
-      public void windowOpened(WindowEvent e)
-      {
-        if (viewport.sortByTree)
-        {
-          sortByTree(treePanel, title);
-        }
-        super.windowOpened(e);
-      }
-
-      public void windowClosing(WindowEvent e)
-      {
-        sortByTreeMenu.remove(item);
-      };
-    });
-  }
-  public boolean sortBy(AlignmentOrder alorder, String undoname)
-  {
-    SequenceI[] oldOrder = viewport.getAlignment()
-    .getSequencesArray();
-    if (viewport.applet.debug)
-    {
-      System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
-    }
-    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
-    if (undoname!=null)
-    {
-      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
-    }
-    alignPanel.paintAlignment(true);
-    return true;
-  }
-  protected void documentation_actionPerformed()
-  {
-    showURL("http://www.jalview.org/help.html", "HELP");
-  }
-
-  protected void about_actionPerformed()
-  {
-
-    class AboutPanel extends Canvas
-    {
-      String version;
-
-      String builddate;
-
-      public AboutPanel(String version, String builddate)
-      {
-        this.version = version;
-        this.builddate = builddate;
-      }
-
-      public void paint(Graphics g)
-      {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getSize().width, getSize().height);
-        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        FontMetrics fm = g.getFontMetrics();
-        int fh = fm.getHeight();
-        int y = 5, x = 7;
-        g.setColor(Color.black);
-        // TODO: update this text for each release or centrally store it for
-        // lite and application
-        g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalviewLite - Release " + version, x, y += fh);
-        g.setFont(new Font("Helvetica", Font.BOLD, 12));
-        g.drawString("Build date: " + builddate, x, y += fh);
-        g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g.drawString(
-                "Authors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
-                x, y += fh * 1.5);
-        g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
-        g.drawString(
-                "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
-                x, y += fh);
-        g.drawString(
-                "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
-                x, y += fh);
-        g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);
-        g.drawString(
-                "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
-                x, y += fh);
-        g.drawString(
-                "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
-                x, y += fh);
-        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
-                x, y += fh);
-      }
-    }
-
-    Frame frame = new Frame();
-    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
-            .getBuildDate()));
-    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
-
-  }
-
-  public void showURL(String url, String target)
-  {
-    if (viewport.applet == null)
-    {
-      System.out.println("Not running as applet - no browser available.");
-    }
-    else
-    {
-      try
-      {
-        if (url.indexOf(":") == -1)
-        {
-          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
-          // form valid URL
-          if (url.indexOf("/") == 0)
-          {
-            String codebase = viewport.applet.getCodeBase().toString();
-            url = codebase.substring(0, codebase.length()
-                    - viewport.applet.getCodeBase().getFile().length())
-                    + url;
-          }
-          else
-          {
-            url = viewport.applet.getCodeBase() + url;
-          }
-          System.out.println("Show url (prepended codebase): " + url);
-        }
-        else
-        {
-          System.out.println("Show url: " + url);
-        }
-        if (url.indexOf("javascript:") == 0)
-        {
-          // no target for the javascript context
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url));
-        }
-        else
-        {
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url), target);
-        }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-    }
-  }
-
-  // ////////////////////////////////////////////////////////////////////////////////
-  // JBuilder Graphics here
-
-  MenuBar alignFrameMenuBar = new MenuBar();
-
-  Menu fileMenu = new Menu("File");
-
-  MenuItem loadApplication = new MenuItem("View in Full Application");
-
-  MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-
-  MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-
-  MenuItem outputFeatures = new MenuItem("Export Features ...");
-
-  MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
-  MenuItem closeMenuItem = new MenuItem("Close");
-
-  Menu editMenu = new Menu("Edit");
-
-  Menu viewMenu = new Menu("View");
-
-  Menu colourMenu = new Menu("Colour");
-
-  Menu calculateMenu = new Menu("Calculate");
-
-  MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-
-  MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-
-  MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-
-  MenuItem remove2LeftMenuItem = new MenuItem();
-
-  MenuItem remove2RightMenuItem = new MenuItem();
-
-  MenuItem removeGappedColumnMenuItem = new MenuItem();
-
-  MenuItem removeAllGapsMenuItem = new MenuItem();
-
-  CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-
-  CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-
-  MenuItem sortPairwiseMenuItem = new MenuItem();
-
-  MenuItem sortIDMenuItem = new MenuItem();
-
-  MenuItem sortLengthMenuItem = new MenuItem();
-
-  MenuItem sortGroupMenuItem = new MenuItem();
-
-  MenuItem removeRedundancyMenuItem = new MenuItem();
-
-  MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-
-  MenuItem PCAMenuItem = new MenuItem();
-
-  MenuItem averageDistanceTreeMenuItem = new MenuItem();
-
-  MenuItem neighbourTreeMenuItem = new MenuItem();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  public Label statusBar = new Label();
-
-  Menu outputTextboxMenu = new Menu();
-
-  MenuItem clustalColour = new MenuItem();
-
-  MenuItem zappoColour = new MenuItem();
-
-  MenuItem taylorColour = new MenuItem();
-
-  MenuItem hydrophobicityColour = new MenuItem();
-
-  MenuItem helixColour = new MenuItem();
-
-  MenuItem strandColour = new MenuItem();
-
-  MenuItem turnColour = new MenuItem();
-
-  MenuItem buriedColour = new MenuItem();
-
-  MenuItem userDefinedColour = new MenuItem();
-
-  MenuItem PIDColour = new MenuItem();
-
-  MenuItem BLOSUM62Colour = new MenuItem();
-
-  MenuItem njTreeBlosumMenuItem = new MenuItem();
-
-  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-
-  CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-
-  CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
-
-  CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
-
-  MenuItem alProperties = new MenuItem("Alignment Properties...");
-
-  MenuItem overviewMenuItem = new MenuItem();
-
-  MenuItem undoMenuItem = new MenuItem();
-
-  MenuItem redoMenuItem = new MenuItem();
-
-  CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-
-  MenuItem noColourmenuItem = new MenuItem();
-
-  CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-
-  CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-
-  MenuItem findMenuItem = new MenuItem();
-
-  CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-
-  MenuItem nucleotideColour = new MenuItem();
-
-  MenuItem deleteGroups = new MenuItem();
-
-  MenuItem grpsFromSelection = new MenuItem();
-
-  MenuItem delete = new MenuItem();
-
-  MenuItem copy = new MenuItem();
-
-  MenuItem cut = new MenuItem();
-
-  Menu pasteMenu = new Menu();
-
-  MenuItem pasteNew = new MenuItem();
-
-  MenuItem pasteThis = new MenuItem();
-
-  CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-
-  MenuItem font = new MenuItem();
-
-  CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-
-  CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-
-  CheckboxMenuItem scaleRight = new CheckboxMenuItem();
-
-  MenuItem modifyPID = new MenuItem();
-
-  MenuItem modifyConservation = new MenuItem();
-
-  CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
-          "Autocalculate Consensus", true);
-
-  Menu sortByTreeMenu = new Menu();
-
-  Menu sort = new Menu();
-
-  Menu calculate = new Menu();
-
-  MenuItem inputText = new MenuItem();
-
-  Menu helpMenu = new Menu();
-
-  MenuItem documentation = new MenuItem();
-
-  MenuItem about = new MenuItem();
-
-  CheckboxMenuItem seqLimits = new CheckboxMenuItem();
-
-  CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-  
-  CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
-  Menu autoAnnMenu=new Menu();
-  CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
-  CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
-  CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
-  CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
-  CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
-
-  private void jbInit() throws Exception
-  {
-
-    setMenuBar(alignFrameMenuBar);
-
-    MenuItem item;
-
-    // dynamically fill save as menu with available formats
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
-    {
-
-      item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
-
-      item.addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          outputText_actionPerformed(e);
-        }
-      });
-
-      outputTextboxMenu.add(item);
-    }
-    closeMenuItem.addActionListener(this);
-    loadApplication.addActionListener(this);
-
-    loadTree.addActionListener(this);
-    loadAnnotations.addActionListener(this);
-    outputFeatures.addActionListener(this);
-    outputAnnotations.addActionListener(this);
-    selectAllSequenceMenuItem.addActionListener(this);
-    deselectAllSequenceMenuItem.addActionListener(this);
-    invertSequenceMenuItem.addActionListener(this);
-    remove2LeftMenuItem.setLabel("Remove Left");
-    remove2LeftMenuItem.addActionListener(this);
-    remove2RightMenuItem.setLabel("Remove Right");
-    remove2RightMenuItem.addActionListener(this);
-    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
-    removeGappedColumnMenuItem.addActionListener(this);
-    removeAllGapsMenuItem.setLabel("Remove All Gaps");
-    removeAllGapsMenuItem.addActionListener(this);
-    viewBoxesMenuItem.setLabel("Boxes");
-    viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addItemListener(this);
-    viewTextMenuItem.setLabel("Text");
-    viewTextMenuItem.setState(true);
-    viewTextMenuItem.addItemListener(this);
-    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
-    sortPairwiseMenuItem.addActionListener(this);
-    sortIDMenuItem.setLabel("by ID");
-    sortIDMenuItem.addActionListener(this);
-    sortLengthMenuItem.setLabel("by Length");
-    sortLengthMenuItem.addActionListener(this);
-    sortGroupMenuItem.setLabel("by Group");
-    sortGroupMenuItem.addActionListener(this);
-    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
-    removeRedundancyMenuItem.addActionListener(this);
-    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(this);
-    PCAMenuItem.setLabel("Principal Component Analysis");
-    PCAMenuItem.addActionListener(this);
-    averageDistanceTreeMenuItem
-            .setLabel("Average Distance Using % Identity");
-    averageDistanceTreeMenuItem.addActionListener(this);
-    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
-    neighbourTreeMenuItem.addActionListener(this);
-    statusBar.setBackground(Color.white);
-    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setText("Status bar");
-    outputTextboxMenu.setLabel("Output to Textbox");
-    clustalColour.setLabel("Clustalx");
-
-    clustalColour.addActionListener(this);
-    zappoColour.setLabel("Zappo");
-    zappoColour.addActionListener(this);
-    taylorColour.setLabel("Taylor");
-    taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel("Hydrophobicity");
-    hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel("Helix Propensity");
-    helixColour.addActionListener(this);
-    strandColour.setLabel("Strand Propensity");
-    strandColour.addActionListener(this);
-    turnColour.setLabel("Turn Propensity");
-    turnColour.addActionListener(this);
-    buriedColour.setLabel("Buried Index");
-    buriedColour.addActionListener(this);
-    userDefinedColour.setLabel("User Defined...");
-    userDefinedColour.addActionListener(this);
-    PIDColour.setLabel("Percentage Identity");
-    PIDColour.addActionListener(this);
-    BLOSUM62Colour.setLabel("BLOSUM62 Score");
-    BLOSUM62Colour.addActionListener(this);
-    avDistanceTreeBlosumMenuItem
-            .setLabel("Average Distance Using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(this);
-    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(this);
-    annotationPanelMenuItem.setLabel("Show Annotations");
-    annotationPanelMenuItem.addItemListener(this);
-    colourTextMenuItem.setLabel("Colour Text");
-    colourTextMenuItem.addItemListener(this);
-    displayNonconservedMenuItem.setLabel("Show nonconserved");
-    displayNonconservedMenuItem.addItemListener(this);
-    alProperties.addActionListener(this);
-    overviewMenuItem.setLabel("Overview Window");
-    overviewMenuItem.addActionListener(this);
-    undoMenuItem.setEnabled(false);
-    undoMenuItem.setLabel("Undo");
-    undoMenuItem.addActionListener(this);
-    redoMenuItem.setEnabled(false);
-    redoMenuItem.setLabel("Redo");
-    redoMenuItem.addActionListener(this);
-    conservationMenuItem.setLabel("by Conservation");
-    conservationMenuItem.addItemListener(this);
-    noColourmenuItem.setLabel("None");
-    noColourmenuItem.addActionListener(this);
-    wrapMenuItem.setLabel("Wrap");
-    wrapMenuItem.addItemListener(this);
-    renderGapsMenuItem.setLabel("Show Gaps");
-    renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addItemListener(this);
-    findMenuItem.setLabel("Find...");
-    findMenuItem.addActionListener(this);
-    abovePIDThreshold.setLabel("Above Identity Threshold");
-    abovePIDThreshold.addItemListener(this);
-    nucleotideColour.setLabel("Nucleotide");
-    nucleotideColour.addActionListener(this);
-    deleteGroups.setLabel("Undefine Groups");
-    deleteGroups.addActionListener(this);
-    grpsFromSelection.setLabel("Make Groups for selection");
-    grpsFromSelection.addActionListener(this);
-    copy.setLabel("Copy");
-    copy.addActionListener(this);
-    cut.setLabel("Cut");
-    cut.addActionListener(this);
-    delete.setLabel("Delete");
-    delete.addActionListener(this);
-    pasteMenu.setLabel("Paste");
-    pasteNew.setLabel("To New Alignment");
-    pasteNew.addActionListener(this);
-    pasteThis.setLabel("Add To This Alignment");
-    pasteThis.addActionListener(this);
-    applyToAllGroups.setLabel("Apply Colour To All Groups");
-    applyToAllGroups.setState(true);
-    applyToAllGroups.addItemListener(this);
-    font.setLabel("Font...");
-    font.addActionListener(this);
-    scaleAbove.setLabel("Scale Above");
-    scaleAbove.setState(true);
-    scaleAbove.setEnabled(false);
-    scaleAbove.addItemListener(this);
-    scaleLeft.setEnabled(false);
-    scaleLeft.setState(true);
-    scaleLeft.setLabel("Scale Left");
-    scaleLeft.addItemListener(this);
-    scaleRight.setEnabled(false);
-    scaleRight.setState(true);
-    scaleRight.setLabel("Scale Right");
-    scaleRight.addItemListener(this);
-    modifyPID.setLabel("Modify Identity Threshold...");
-    modifyPID.addActionListener(this);
-    modifyConservation.setLabel("Modify Conservation Threshold...");
-    modifyConservation.addActionListener(this);
-    sortByTreeMenu.setLabel("By Tree Order");
-    sort.setLabel("Sort");
-    calculate.setLabel("Calculate Tree");
-    autoCalculate.addItemListener(this);
-    inputText.setLabel("Input from textbox");
-    inputText.addActionListener(this);
-    centreColumnLabelFlag.setLabel("Centre column labels");
-    centreColumnLabelFlag.addItemListener(this);
-    followMouseOverFlag.setLabel("Automatic Scrolling");
-    followMouseOverFlag.addItemListener(this);
-    helpMenu.setLabel("Help");
-    documentation.setLabel("Documentation");
-    documentation.addActionListener(this);
-
-    about.setLabel("About...");
-    about.addActionListener(this);
-    seqLimits.setState(true);
-    seqLimits.setLabel("Show Sequence Limits");
-    seqLimits.addItemListener(this);
-    featureSettings.setLabel("Feature Settings...");
-    featureSettings.addActionListener(this);
-    sequenceFeatures.setLabel("Sequence Features");
-    sequenceFeatures.addItemListener(this);
-    sequenceFeatures.setState(false);
-    annotationColour.setLabel("by Annotation...");
-    annotationColour.addActionListener(this);
-    invertSequenceMenuItem.setLabel("Invert Sequence Selection");
-    invertColSel.setLabel("Invert Column Selection");
-    menu1.setLabel("Show");
-    showColumns.setLabel("All Columns ");
-    showSeqs.setLabel("All Sequences");
-    menu2.setLabel("Hide");
-    hideColumns.setLabel("Selected Columns");
-    hideSequences.setLabel("Selected Sequences");
-    hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
-    hideAllSelection.setLabel("Selected Region");
-    showAllHidden.setLabel("All Sequences and Columns");
-    showGroupConsensus.setLabel("Group Consensus");
-    showGroupConservation.setLabel("Group Conservation");
-    showConsensusHistogram.setLabel("Show Consensus Histogram");
-    showSequenceLogo.setLabel("Show Consensus Logo");
-    applyAutoAnnotationSettings.setLabel("Apply to all groups");
-    applyAutoAnnotationSettings.setState(true);
-    autoAnnMenu.setLabel("Autocalculated Annotation");
-    
-    invertColSel.addActionListener(this);
-    showColumns.addActionListener(this);
-    showSeqs.addActionListener(this);
-    hideColumns.addActionListener(this);
-    hideSequences.addActionListener(this);
-    hideAllButSelection.addActionListener(this);
-    hideAllSelection.addActionListener(this);
-    showAllHidden.addActionListener(this);
-    showGroupConsensus.addItemListener(this);
-    showGroupConservation.addItemListener(this);
-    showConsensusHistogram.addItemListener(this);
-    showSequenceLogo.addItemListener(this);
-    applyAutoAnnotationSettings.addItemListener(this);
-    formatMenu.setLabel("Format");
-    selectMenu.setLabel("Select");
-    newView.setLabel("New View");
-    newView.addActionListener(this);
-    alignFrameMenuBar.add(fileMenu);
-    alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(selectMenu);
-    alignFrameMenuBar.add(viewMenu);
-    alignFrameMenuBar.add(formatMenu);
-    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(closeMenuItem);
-
-    editMenu.add(undoMenuItem);
-    editMenu.add(redoMenuItem);
-    editMenu.add(cut);
-    editMenu.add(copy);
-    editMenu.add(pasteMenu);
-    editMenu.add(delete);
-    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();
-    viewMenu.add(followMouseOverFlag);
-    viewMenu.add(annotationPanelMenuItem);
-    autoAnnMenu.add(applyAutoAnnotationSettings);
-    autoAnnMenu.add(showConsensusHistogram);
-    autoAnnMenu.add(showSequenceLogo);
-    autoAnnMenu.addSeparator();
-    autoAnnMenu.add(showGroupConservation);
-    autoAnnMenu.add(showGroupConsensus);
-    viewMenu.add(autoAnnMenu);
-    viewMenu.addSeparator();
-    viewMenu.add(sequenceFeatures);
-    viewMenu.add(featureSettings);
-    viewMenu.addSeparator();
-    viewMenu.add(alProperties);
-    viewMenu.addSeparator();
-    viewMenu.add(overviewMenuItem);
-    colourMenu.add(applyToAllGroups);
-    colourMenu.addSeparator();
-    colourMenu.add(noColourmenuItem);
-    colourMenu.add(clustalColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydrophobicityColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(nucleotideColour);
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(conservationMenuItem);
-    colourMenu.add(modifyConservation);
-    colourMenu.add(abovePIDThreshold);
-    colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
-    calculateMenu.add(sort);
-    calculateMenu.add(calculate);
-    calculateMenu.addSeparator();
-    calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
-    calculateMenu.add(autoCalculate);
-    this.add(statusBar, BorderLayout.SOUTH);
-    pasteMenu.add(pasteNew);
-    pasteMenu.add(pasteThis);
-    sort.add(sortIDMenuItem);
-    sort.add(sortLengthMenuItem);
-    sort.add(sortByTreeMenu);
-    sort.add(sortGroupMenuItem);
-    sort.add(sortPairwiseMenuItem);
-    calculate.add(averageDistanceTreeMenuItem);
-    calculate.add(neighbourTreeMenuItem);
-    calculate.add(avDistanceTreeBlosumMenuItem);
-    calculate.add(njTreeBlosumMenuItem);
-    helpMenu.add(documentation);
-    helpMenu.add(about);
-    menu1.add(showColumns);
-    menu1.add(showSeqs);
-    menu1.add(showAllHidden);
-    menu2.add(hideColumns);
-    menu2.add(hideSequences);
-    menu2.add(hideAllSelection);
-    menu2.add(hideAllButSelection);
-    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(displayNonconservedMenuItem);
-    formatMenu.add(renderGapsMenuItem);
-    formatMenu.add(centreColumnLabelFlag);
-    selectMenu.add(findMenuItem);
-    selectMenu.addSeparator();
-    selectMenu.add(selectAllSequenceMenuItem);
-    selectMenu.add(deselectAllSequenceMenuItem);
-    selectMenu.add(invertSequenceMenuItem);
-    selectMenu.add(invertColSel);
-    selectMenu.add(grpsFromSelection);
-    selectMenu.add(deleteGroups);
-
-  }
-
-  MenuItem featureSettings = new MenuItem();
-
-  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
-
-  MenuItem annotationColour = new MenuItem();
-
-  MenuItem invertColSel = new MenuItem();
-
-  Menu menu1 = new Menu();
-
-  MenuItem showColumns = new MenuItem();
-
-  MenuItem showSeqs = new MenuItem();
-
-  Menu menu2 = new Menu();
-
-  MenuItem hideColumns = new MenuItem();
-
-  MenuItem hideSequences = new MenuItem();
-
-  MenuItem hideAllButSelection = new MenuItem();
-
-  MenuItem hideAllSelection = new MenuItem();
-
-  MenuItem showAllHidden = new MenuItem();
-
-  Menu formatMenu = new Menu();
-
-  Menu selectMenu = new Menu();
-
-  MenuItem newView = new MenuItem();
-
-  /**
-   * Attach the alignFrame panels after embedding menus, if necessary. This used
-   * to be called setEmbedded, but is now creates the dropdown menus in a
-   * platform independent manner to avoid OSX/Mac menu appendage daftness.
-   * 
-   * @param reallyEmbedded
-   *          true to attach the view to the applet area on the page rather than
-   *          in a new window
-   */
-  public void createAlignFrameWindow(boolean reallyEmbedded, String title)
-  {
-    if (reallyEmbedded)
-    {
-      // ////
-      // Explicly build the embedded menu panel for the on-page applet
-      //
-      // view cannot be closed if its actually on the page
-      fileMenu.remove(closeMenuItem);
-      fileMenu.remove(3); // Remove Seperator
-      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
-              Font.PLAIN, 10, false); // use our own fonts.
-      // and actually add the components to the applet area
-      viewport.applet.setLayout(new BorderLayout());
-      viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
-      viewport.applet.add(statusBar, BorderLayout.SOUTH);
-      alignPanel.setSize(viewport.applet.getSize().width,
-              viewport.applet.getSize().height - embeddedMenu.HEIGHT
-                      - statusBar.HEIGHT);
-      viewport.applet.add(alignPanel, BorderLayout.CENTER);
-      final AlignFrame me = this;
-      viewport.applet.addFocusListener(new FocusListener()
-      {
-        
-        @Override
-        public void focusLost(FocusEvent e)
-        {
-          if (me.viewport.applet.currentAlignFrame==me) {
-                  me.viewport.applet.currentAlignFrame = null;
-        }}
-        
-        @Override
-        public void focusGained(FocusEvent e)
-        {
-          me.viewport.applet.currentAlignFrame = me;
-        }
-      });
-      viewport.applet.validate();
-    }
-    else
-    {
-      // //////
-      // test and embed menu bar if necessary.
-      //
-      if (embedMenuIfNeeded(alignPanel))
-      {
-        // adjust for status bar height too
-        alignPanel.setSize(getSize().width, getSize().height
-                - statusBar.HEIGHT);
-      }
-      add(statusBar, BorderLayout.SOUTH);
-      add(alignPanel, BorderLayout.CENTER);
-      // and register with the applet so it can pass external API calls to us
-      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
-              DEFAULT_HEIGHT);
-    }
-  }
-
-  /**
-   * create a new binding between structures in an existing jmol viewer instance
-   * and an alignpanel with sequences that have existing PDBFile entries. Note,
-   * this does not open a new Jmol window, or modify the display of the
-   * structures in the original jmol window. Note This method doesn't work
-   * without an additional javascript library to exchange messages between the
-   * distinct applets. See http://issues.jalview.org/browse/JAL-621
-   * 
-   * @param viewer
-   *          JmolViewer instance
-   * @param sequenceIds
-   *          - sequence Ids to search for associations
-   */
-  public SequenceStructureBinding addStructureViewInstance(
-          Object jmolviewer, String[] sequenceIds)
-  {
-    org.jmol.api.JmolViewer viewer = null;
-    try
-    {
-      viewer = (org.jmol.api.JmolViewer) jmolviewer;
-    } catch (ClassCastException ex)
-    {
-      System.err.println("Unsupported viewer object :"
-              + jmolviewer.getClass());
-    }
-    if (viewer == null)
-    {
-      System.err.println("Can't use this object as a structure viewer:"
-              + jmolviewer.getClass());
-      return null;
-    }
-    SequenceI[] seqs = null;
-    if (sequenceIds == null || sequenceIds.length == 0)
-    {
-      seqs = viewport.getAlignment().getSequencesArray();
-    }
-    else
-    {
-      Vector sqi = new Vector();
-      AlignmentI al = viewport.getAlignment();
-      for (int sid = 0; sid < sequenceIds.length; sid++)
-      {
-        SequenceI sq = al.findName(sequenceIds[sid]);
-        if (sq != null)
-        {
-          sqi.addElement(sq);
-        }
-      }
-      if (sqi.size() > 0)
-      {
-        seqs = new SequenceI[sqi.size()];
-        for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
-        {
-          seqs[sid] = (SequenceI) sqi.elementAt(sid);
-        }
-      }
-      else
-      {
-        return null;
-      }
-    }
-    ExtJmol jmv = null;
-    // TODO: search for a jmv that involves viewer
-    if (jmv == null)
-    { // create a new viewer/jalview binding.
-      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
-    }
-    return jmv;
-
-  }
-
-  public boolean addPdbFile(String sequenceId, String pdbEntryString,
-          String pdbFile)
-  {
-    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
-    boolean needtoadd = false;
-    if (toaddpdb != null)
-    {
-      Vector pdbe = toaddpdb.getPDBId();
-      PDBEntry pdbentry = null;
-      if (pdbe != null && pdbe.size() > 0)
-      {
-        for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
-        {
-          pdbentry = (PDBEntry) pdbe.elementAt(pe);
-          if (!pdbentry.getId().equals(pdbEntryString)
-                  && !pdbentry.getFile().equals(pdbFile))
-          {
-            pdbentry = null;
-          }
-          else
-          {
-            continue;
-          }
-        }
-      }
-      if (pdbentry == null)
-      {
-        pdbentry = new PDBEntry();
-        pdbentry.setId(pdbEntryString);
-        pdbentry.setFile(pdbFile);
-        needtoadd = true; // add this new entry to sequence.
-      }
-      // resolve data source
-      // TODO: this code should be a refactored to an io package
-      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
-      if (protocol == null)
-      {
-        return false;
-      }
-      if (needtoadd)
-      {
-        // make a note of the access mode and add
-        if (pdbentry.getProperty() == null)
-        {
-          pdbentry.setProperty(new Hashtable());
-        }
-        pdbentry.getProperty().put("protocol", protocol);
-        toaddpdb.addPDBId(pdbentry);
-      }
-    }
-    return true;
-  }
-
-  private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
-  {
-    if (seqs != null)
-    {
-      Vector sequences = new Vector();
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i] != null)
-        {
-          sequences.addElement(new Object[]
-          { seqs[i], (chains != null) ? chains[i] : null });
-        }
-      }
-      seqs = new SequenceI[sequences.size()];
-      chains = new String[sequences.size()];
-      for (int i = 0, isize = sequences.size(); i < isize; i++)
-      {
-        Object[] oj = (Object[]) sequences.elementAt(i);
-
-        seqs[i] = (SequenceI) oj[0];
-        chains[i] = (String) oj[1];
-      }
-    }
-    return new Object[]
-    { seqs, chains };
-
-  }
-
-  public void newStructureView(JalviewLite applet, PDBEntry pdb,
-          SequenceI[] seqs, String[] chains, String protocol)
-  {
-    // Scrub any null sequences from the array
-    Object[] sqch = cleanSeqChainArrays(seqs, chains);
-    seqs = (SequenceI[]) sqch[0];
-    chains = (String[]) sqch[1];
-    if (seqs == null || seqs.length == 0)
-    {
-      System.err
-              .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
-    }
-    if (protocol == null || protocol.trim().length() == 0
-            || protocol.equals("null"))
-    {
-      protocol = (String) pdb.getProperty().get("protocol");
-      if (protocol == null)
-      {
-        System.err.println("Couldn't work out protocol to open structure: "
-                + pdb.getId());
-        return;
-      }
-    }
-    if (applet.useXtrnalSviewer)
-    {
-      // register the association(s) and quit, don't create any windows.
-      StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
-      return;
-    }
-    if (applet.isAlignPdbStructures() && applet.jmolAvailable)
-    {
-      // can only do alignments with Jmol
-      // find the last jmol window assigned to this alignment
-      jalview.appletgui.AppletJmol ajm = null, tajm;
-      Vector jmols = applet
-              .getAppletWindow(jalview.appletgui.AppletJmol.class);
-      for (int i = 0, iSize = jmols.size(); i < iSize; i++)
-      {
-        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
-        if (tajm.ap.alignFrame == this)
-        {
-          ajm = tajm;
-          break;
-        }
-      }
-      if (ajm != null)
-      {
-        System.err
-                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
-        // try and add the pdb structure
-        // ajm.addS
-        ajm = null;
-      }
-    }
-    // otherwise, create a new window
-    if (applet.jmolAvailable)
-    {
-      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
-              protocol);
-      applet.lastFrameX += 40;
-      applet.lastFrameY += 40;
-    }
-    else
-    {
-      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
-    }
-
-  }
-
-  public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
-          SequenceI[][] seqs, String[][] chains, String[] protocols)
-  {
-    // TODO Auto-generated method stub
-    System.err.println("Aligned Structure View: Not yet implemented.");
-  }
-
-  /**
-   * modify the current selection, providing the user has not made a selection already.
-   * @param sel - sequences from this alignment 
-   * @param csel - columns to be selected on the alignment
-   */
-  public void select(SequenceGroup sel, ColumnSelection csel)
-  {
-    alignPanel.seqPanel.selection(sel, csel, null);
-  }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import java.net.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
+        ItemListener, KeyListener\r
+{\r
+  public AlignmentPanel alignPanel;\r
+\r
+  public AlignViewport viewport;\r
+\r
+  int DEFAULT_WIDTH = 700;\r
+\r
+  int DEFAULT_HEIGHT = 500;\r
+\r
+  String jalviewServletURL;\r
+\r
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
+          String title, boolean embedded)\r
+  {\r
+\r
+    if (applet != null)\r
+    {\r
+      jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+    }\r
+\r
+    try\r
+    {\r
+      jbInit();\r
+    } catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+\r
+    viewport = new AlignViewport(al, applet);\r
+    alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+    viewport.updateConservation(alignPanel);\r
+    viewport.updateConsensus(alignPanel);\r
+\r
+    annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+    displayNonconservedMenuItem.setState(viewport.getShowunconserved());\r
+    followMouseOverFlag.setState(viewport.getFollowHighlight());\r
+    showGroupConsensus.setState(viewport.showGroupConsensus);\r
+    showGroupConservation.setState(viewport.showGroupConservation);\r
+    showConsensusHistogram.setState(viewport.showConsensusHistogram);\r
+    showSequenceLogo.setState(viewport.showSequenceLogo);\r
+\r
+    seqLimits.setState(viewport.showJVSuffix);\r
+\r
+    if (applet != null)\r
+    {\r
+      String param = applet.getParameter("sortBy");\r
+      if (param != null)\r
+      {\r
+        if (param.equalsIgnoreCase("Id"))\r
+        {\r
+          sortIDMenuItem_actionPerformed();\r
+        }\r
+        else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+        {\r
+          sortPairwiseMenuItem_actionPerformed();\r
+        }\r
+        else if (param.equalsIgnoreCase("Length"))\r
+        {\r
+          sortLengthMenuItem_actionPerformed();\r
+        }\r
+      }\r
+\r
+      param = applet.getParameter("wrap");\r
+      if (param != null)\r
+      {\r
+        if (param.equalsIgnoreCase("true"))\r
+        {\r
+          wrapMenuItem.setState(true);\r
+          wrapMenuItem_actionPerformed();\r
+        }\r
+      }\r
+      param = applet.getParameter("centrecolumnlabels");\r
+      if (param != null)\r
+      {\r
+        centreColumnLabelFlag.setState(true);\r
+        centreColumnLabelFlag_stateChanged();\r
+      }\r
+      try\r
+      {\r
+        param = applet.getParameter("windowWidth");\r
+        if (param != null)\r
+        {\r
+          int width = Integer.parseInt(param);\r
+          DEFAULT_WIDTH = width;\r
+        }\r
+        param = applet.getParameter("windowHeight");\r
+        if (param != null)\r
+        {\r
+          int height = Integer.parseInt(param);\r
+          DEFAULT_HEIGHT = height;\r
+        }\r
+      } catch (Exception ex)\r
+      {\r
+      }\r
+\r
+    }\r
+\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\r
+    // now\r
+    this.addKeyListener(this);\r
+    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+    alignPanel.scalePanel.addKeyListener(this);\r
+    alignPanel.annotationPanel.addKeyListener(this);\r
+    alignPanel.annotationPanelHolder.addKeyListener(this);\r
+    alignPanel.annotationSpaceFillerHolder.addKeyListener(this);\r
+    alignPanel.alabels.addKeyListener(this);\r
+    createAlignFrameWindow(embedded, title);\r
+    alignPanel.validate();\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public AlignViewport getAlignViewport()\r
+  {\r
+    return viewport;\r
+  }\r
+\r
+  public SeqCanvas getSeqcanvas()\r
+  {\r
+    return alignPanel.seqPanel.seqCanvas;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param String\r
+   *          DOCUMENT ME!\r
+   */\r
+\r
+  public void parseFeaturesFile(String file, String type)\r
+  {\r
+    Hashtable featureLinks = new Hashtable();\r
+    boolean featuresFile = false;\r
+    try\r
+    {\r
+      featuresFile = new jalview.io.FeaturesFile(file, type)\r
+              .parse(viewport.alignment,\r
+                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
+                      featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
+    } catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+\r
+    if (featuresFile)\r
+    {\r
+      if (featureLinks.size() > 0)\r
+      {\r
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
+      }\r
+      viewport.showSequenceFeatures = true;\r
+      sequenceFeatures.setState(true);\r
+      if (viewport.featureSettings != null)\r
+      {\r
+        viewport.featureSettings.refreshTable();\r
+      }\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+\r
+  }\r
+\r
+  public void keyPressed(KeyEvent evt)\r
+  {\r
+    if (viewport.cursorMode\r
+            && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
+                    .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
+                    .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
+            && Character.isDigit(evt.getKeyChar()))\r
+      alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+\r
+    switch (evt.getKeyCode())\r
+    {\r
+    case 27: // escape key\r
+      deselectAllSequenceMenuItem_actionPerformed();\r
+      \r
+      alignPanel.alabels.cancelDrag(); \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 (viewport.cursorMode && !evt.isControlDown())\r
+      {\r
+        alignPanel.seqPanel.setCursorColumn();\r
+      }\r
+      if (evt.isControlDown() || evt.isMetaDown())\r
+      {\r
+        copy_actionPerformed();\r
+      }\r
+      break;\r
+    case KeyEvent.VK_V:\r
+      if (evt.isControlDown())\r
+      {\r
+        paste(evt.isShiftDown());\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
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.moveCursor(0, 1);\r
+      }\r
+      else\r
+      {\r
+        moveSelectedSequences(false);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_UP:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.moveCursor(0, -1);\r
+      }\r
+      else\r
+      {\r
+        moveSelectedSequences(true);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_LEFT:\r
+      if (evt.isAltDown() || !viewport.cursorMode)\r
+        slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
+      else\r
+        alignPanel.seqPanel.moveCursor(-1, 0);\r
+      break;\r
+\r
+    case KeyEvent.VK_RIGHT:\r
+      if (evt.isAltDown() || !viewport.cursorMode)\r
+        slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
+      else\r
+        alignPanel.seqPanel.moveCursor(1, 0);\r
+      break;\r
+\r
+    case KeyEvent.VK_SPACE:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+                || evt.isShiftDown() || evt.isAltDown());\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_DELETE:\r
+    case KeyEvent.VK_BACK_SPACE:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+                || evt.isShiftDown() || evt.isAltDown());\r
+      }\r
+      else\r
+      {\r
+        cut_actionPerformed();\r
+        alignPanel.seqPanel.seqCanvas.repaint();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_S:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.setCursorRow();\r
+      }\r
+      break;\r
+    case KeyEvent.VK_P:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.setCursorPosition();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_ENTER:\r
+    case KeyEvent.VK_COMMA:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.setCursorRowAndColumn();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_Q:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+      }\r
+      break;\r
+    case KeyEvent.VK_M:\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_F2:\r
+      viewport.cursorMode = !viewport.cursorMode;\r
+      statusBar.setText("Keyboard editing mode is "\r
+              + (viewport.cursorMode ? "on" : "off"));\r
+      if (viewport.cursorMode)\r
+      {\r
+        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_F:\r
+      if (evt.isControlDown())\r
+      {\r
+        findMenuItem_actionPerformed();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_H:\r
+    {\r
+      boolean toggleSeqs = !evt.isControlDown();\r
+      boolean toggleCols = !evt.isShiftDown();\r
+      toggleHiddenRegions(toggleSeqs, toggleCols);\r
+      break;\r
+    }\r
+\r
+    case KeyEvent.VK_PAGE_UP:\r
+      if (viewport.wrapAlignment)\r
+      {\r
+        alignPanel.scrollUp(true);\r
+      }\r
+      else\r
+      {\r
+        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+                - viewport.endSeq + viewport.startSeq);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_PAGE_DOWN:\r
+      if (viewport.wrapAlignment)\r
+      {\r
+        alignPanel.scrollUp(false);\r
+      }\r
+      else\r
+      {\r
+        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+                + viewport.endSeq - viewport.startSeq);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_Z:\r
+      if (evt.isControlDown())\r
+      {\r
+        undoMenuItem_actionPerformed();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_Y:\r
+      if (evt.isControlDown())\r
+      {\r
+        redoMenuItem_actionPerformed();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_L:\r
+      if (evt.isControlDown())\r
+      {\r
+        trimAlignment(true);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_R:\r
+      if (evt.isControlDown())\r
+      {\r
+        trimAlignment(false);\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_E:\r
+      if (evt.isControlDown())\r
+      {\r
+        if (evt.isShiftDown())\r
+        {\r
+          this.removeAllGapsMenuItem_actionPerformed();\r
+        }\r
+        else\r
+        {\r
+          removeGappedColumnMenuItem_actionPerformed();\r
+        }\r
+      }\r
+      break;\r
+    case KeyEvent.VK_I:\r
+      if (evt.isControlDown())\r
+      {\r
+        if (evt.isAltDown())\r
+        {\r
+          invertColSel_actionPerformed();\r
+        }\r
+        else\r
+        {\r
+          invertSequenceMenuItem_actionPerformed();\r
+        }\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_U:\r
+      if (evt.isControlDown())\r
+      {\r
+        this.deleteGroups_actionPerformed();\r
+      }\r
+      break;\r
+\r
+    case KeyEvent.VK_T:\r
+      if (evt.isControlDown())\r
+      {\r
+        newView(null);\r
+      }\r
+      break;\r
+\r
+    }\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  /**\r
+   * called by key handler and the hide all/show all menu items\r
+   * \r
+   * @param toggleSeqs\r
+   * @param toggleCols\r
+   */\r
+  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
+  {\r
+    boolean hide = false;\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
+    if (!toggleSeqs && !toggleCols)\r
+    {\r
+      // Hide everything by the current selection - this is a hack - we do the\r
+      // invert and then hide\r
+      // first check that there will be visible columns after the invert.\r
+      if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel\r
+              .getSelected().size() > 0)\r
+              || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
+                      .getEndRes()))\r
+      {\r
+        // now invert the sequence set, if required - empty selection implies\r
+        // that no hiding is required.\r
+        if (sg != null)\r
+        {\r
+          invertSequenceMenuItem_actionPerformed();\r
+          sg = viewport.getSelectionGroup();\r
+          toggleSeqs = true;\r
+\r
+        }\r
+        viewport.expandColSelection(sg, true);\r
+        // finally invert the column selection and get the new sequence\r
+        // selection and indicate it should be hidden.\r
+        invertColSel_actionPerformed();\r
+        toggleCols = true;\r
+      }\r
+    }\r
+\r
+    if (toggleSeqs)\r
+    {\r
+      if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+      {\r
+        hide = true;\r
+        viewport.hideAllSelectedSeqs();\r
+      }\r
+      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+      {\r
+        viewport.showAllHiddenSeqs();\r
+      }\r
+    }\r
+\r
+    if (toggleCols)\r
+    {\r
+      if (viewport.colSel.getSelected().size() > 0)\r
+      {\r
+        viewport.hideSelectedColumns();\r
+        if (!toggleSeqs)\r
+        {\r
+          viewport.selectionGroup = sg;\r
+        }\r
+      }\r
+      else if (!hide)\r
+      {\r
+        viewport.showAllHiddenColumns();\r
+      }\r
+    }\r
+  }\r
+\r
+  public void keyReleased(KeyEvent evt)\r
+  {\r
+  }\r
+\r
+  public void keyTyped(KeyEvent evt)\r
+  {\r
+  }\r
+\r
+  public void itemStateChanged(ItemEvent evt)\r
+  {\r
+    if (evt.getSource() == displayNonconservedMenuItem)\r
+    {\r
+      displayNonconservedMenuItem_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == colourTextMenuItem)\r
+    {\r
+      colourTextMenuItem_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == wrapMenuItem)\r
+    {\r
+      wrapMenuItem_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == scaleAbove)\r
+    {\r
+      viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+    }\r
+    else if (evt.getSource() == scaleLeft)\r
+    {\r
+      viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+    }\r
+    else if (evt.getSource() == scaleRight)\r
+    {\r
+      viewport.setScaleRightWrapped(scaleRight.getState());\r
+    }\r
+    else if (evt.getSource() == seqLimits)\r
+    {\r
+      seqLimits_itemStateChanged();\r
+    }\r
+    else if (evt.getSource() == viewBoxesMenuItem)\r
+    {\r
+      viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+    }\r
+    else if (evt.getSource() == viewTextMenuItem)\r
+    {\r
+      viewport.setShowText(viewTextMenuItem.getState());\r
+    }\r
+    else if (evt.getSource() == renderGapsMenuItem)\r
+    {\r
+      viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+    }\r
+    else if (evt.getSource() == annotationPanelMenuItem)\r
+    {\r
+      viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+    }\r
+    else if (evt.getSource() == sequenceFeatures)\r
+    {\r
+      viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+      alignPanel.seqPanel.seqCanvas.repaint();\r
+    }\r
+    else if (evt.getSource() == conservationMenuItem)\r
+    {\r
+      conservationMenuItem_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == abovePIDThreshold)\r
+    {\r
+      abovePIDThreshold_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == applyToAllGroups)\r
+    {\r
+      viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+    }\r
+    else if (evt.getSource() == autoCalculate)\r
+    {\r
+      viewport.autocalculateConsensus = autoCalculate.getState();\r
+    }\r
+    else if (evt.getSource() == this.centreColumnLabelFlag)\r
+    {\r
+      centreColumnLabelFlag_stateChanged();\r
+    }\r
+    else if (evt.getSource() == this.followMouseOverFlag)\r
+    {\r
+      mouseOverFlag_stateChanged();\r
+    }\r
+    else if (evt.getSource() == showGroupConsensus)\r
+    {\r
+      showGroupConsensus_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == showGroupConservation)\r
+    {\r
+      showGroupConservation_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == showSequenceLogo)\r
+    {\r
+      showSequenceLogo_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == showConsensusHistogram)\r
+    {\r
+      showConsensusHistogram_actionPerformed();\r
+    }\r
+    else if (evt.getSource() == applyAutoAnnotationSettings)\r
+    {\r
+      applyAutoAnnotationSettings_actionPerformed();\r
+    }\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  private void mouseOverFlag_stateChanged()\r
+  {\r
+    viewport.followHighlight = followMouseOverFlag.getState();\r
+    // TODO: could kick the scrollTo mechanism to reset view for current\r
+    // searchresults.\r
+  }\r
+\r
+  private void centreColumnLabelFlag_stateChanged()\r
+  {\r
+    viewport.centreColumnLabels = centreColumnLabelFlag.getState();\r
+    this.alignPanel.annotationPanel.repaint();\r
+  }\r
+\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    Object source = evt.getSource();\r
+\r
+    if (source == inputText)\r
+    {\r
+      inputText_actionPerformed();\r
+    }\r
+    else if (source == loadTree)\r
+    {\r
+      loadTree_actionPerformed();\r
+    }\r
+    else if (source == loadApplication)\r
+    {\r
+      launchFullApplication();\r
+    }\r
+    else if (source == loadAnnotations)\r
+    {\r
+      loadAnnotations();\r
+    }\r
+    else if (source == outputAnnotations)\r
+    {\r
+      outputAnnotations(true);\r
+    }\r
+    else if (source == outputFeatures)\r
+    {\r
+      outputFeatures(true, "Jalview");\r
+    }\r
+    else if (source == closeMenuItem)\r
+    {\r
+      closeMenuItem_actionPerformed();\r
+    }\r
+    else if (source == copy)\r
+    {\r
+      copy_actionPerformed();\r
+    }\r
+    else if (source == undoMenuItem)\r
+    {\r
+      undoMenuItem_actionPerformed();\r
+    }\r
+    else if (source == redoMenuItem)\r
+    {\r
+      redoMenuItem_actionPerformed();\r
+    }\r
+    else if (source == inputText)\r
+    {\r
+      inputText_actionPerformed();\r
+    }\r
+    else if (source == closeMenuItem)\r
+    {\r
+      closeMenuItem_actionPerformed();\r
+    }\r
+    else if (source == undoMenuItem)\r
+    {\r
+      undoMenuItem_actionPerformed();\r
+    }\r
+    else if (source == redoMenuItem)\r
+    {\r
+      redoMenuItem_actionPerformed();\r
+    }\r
+    else if (source == copy)\r
+    {\r
+      copy_actionPerformed();\r
+    }\r
+    else if (source == pasteNew)\r
+    {\r
+      pasteNew_actionPerformed();\r
+    }\r
+    else if (source == pasteThis)\r
+    {\r
+      pasteThis_actionPerformed();\r
+    }\r
+    else if (source == cut)\r
+    {\r
+      cut_actionPerformed();\r
+    }\r
+    else if (source == delete)\r
+    {\r
+      delete_actionPerformed();\r
+    }\r
+    else if (source == grpsFromSelection)\r
+    {\r
+      makeGrpsFromSelection_actionPerformed();\r
+    }\r
+    else if (source == deleteGroups)\r
+    {\r
+      deleteGroups_actionPerformed();\r
+    }\r
+    else if (source == selectAllSequenceMenuItem)\r
+    {\r
+      selectAllSequenceMenuItem_actionPerformed();\r
+    }\r
+    else if (source == deselectAllSequenceMenuItem)\r
+    {\r
+      deselectAllSequenceMenuItem_actionPerformed();\r
+    }\r
+    else if (source == invertSequenceMenuItem)\r
+    {\r
+      invertSequenceMenuItem_actionPerformed();\r
+    }\r
+    else if (source == invertColSel)\r
+    {\r
+      viewport.invertColumnSelection();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == remove2LeftMenuItem)\r
+    {\r
+      trimAlignment(true);\r
+    }\r
+    else if (source == remove2RightMenuItem)\r
+    {\r
+      trimAlignment(false);\r
+    }\r
+    else if (source == removeGappedColumnMenuItem)\r
+    {\r
+      removeGappedColumnMenuItem_actionPerformed();\r
+    }\r
+    else if (source == removeAllGapsMenuItem)\r
+    {\r
+      removeAllGapsMenuItem_actionPerformed();\r
+    }\r
+    else if (source == findMenuItem)\r
+    {\r
+      findMenuItem_actionPerformed();\r
+    }\r
+    else if (source == font)\r
+    {\r
+      new FontChooser(alignPanel);\r
+    }\r
+    else if (source == newView)\r
+    {\r
+      newView(null);\r
+    }\r
+    else if (source == showColumns)\r
+    {\r
+      viewport.showAllHiddenColumns();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == showSeqs)\r
+    {\r
+      viewport.showAllHiddenSeqs();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == hideColumns)\r
+    {\r
+      viewport.hideSelectedColumns();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == hideSequences\r
+            && viewport.getSelectionGroup() != null)\r
+    {\r
+      viewport.hideAllSelectedSeqs();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == hideAllButSelection)\r
+    {\r
+      toggleHiddenRegions(false, false);\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == hideAllSelection)\r
+    {\r
+      SequenceGroup sg = viewport.getSelectionGroup();\r
+      viewport.expandColSelection(sg, false);\r
+      viewport.hideAllSelectedSeqs();\r
+      viewport.hideSelectedColumns();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == showAllHidden)\r
+    {\r
+      viewport.showAllHiddenColumns();\r
+      viewport.showAllHiddenSeqs();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+    else if (source == showGroupConsensus)\r
+    {\r
+      showGroupConsensus_actionPerformed();\r
+    }\r
+    else if (source == showGroupConservation)\r
+    {\r
+      showGroupConservation_actionPerformed();\r
+    }\r
+    else if (source == showSequenceLogo)\r
+    {\r
+      showSequenceLogo_actionPerformed();\r
+    }\r
+    else if (source == showConsensusHistogram)\r
+    {\r
+      showConsensusHistogram_actionPerformed();\r
+    }\r
+    else if (source == applyAutoAnnotationSettings)\r
+    {\r
+      applyAutoAnnotationSettings_actionPerformed();\r
+    }\r
+    else if (source == featureSettings)\r
+    {\r
+      new FeatureSettings(alignPanel);\r
+    }\r
+    else if (source == alProperties)\r
+    {\r
+      StringBuffer contents = new jalview.io.AlignmentProperties(\r
+              viewport.alignment).formatAsString();\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+      cap.setText(contents.toString());\r
+      Frame frame = new Frame();\r
+      frame.add(cap);\r
+      jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "\r
+              + getTitle(), 400, 250);\r
+    }\r
+    else if (source == overviewMenuItem)\r
+    {\r
+      overviewMenuItem_actionPerformed();\r
+    }\r
+    else if (source == noColourmenuItem)\r
+    {\r
+      changeColour(null);\r
+    }\r
+    else if (source == clustalColour)\r
+    {\r
+      abovePIDThreshold.setState(false);\r
+      changeColour(new ClustalxColourScheme(\r
+              viewport.alignment.getSequences(),\r
+              viewport.alignment.getWidth()));\r
+    }\r
+    else if (source == zappoColour)\r
+    {\r
+      changeColour(new ZappoColourScheme());\r
+    }\r
+    else if (source == taylorColour)\r
+    {\r
+      changeColour(new TaylorColourScheme());\r
+    }\r
+    else if (source == hydrophobicityColour)\r
+    {\r
+      changeColour(new HydrophobicColourScheme());\r
+    }\r
+    else if (source == helixColour)\r
+    {\r
+      changeColour(new HelixColourScheme());\r
+    }\r
+    else if (source == strandColour)\r
+    {\r
+      changeColour(new StrandColourScheme());\r
+    }\r
+    else if (source == turnColour)\r
+    {\r
+      changeColour(new TurnColourScheme());\r
+    }\r
+    else if (source == buriedColour)\r
+    {\r
+      changeColour(new BuriedColourScheme());\r
+    }\r
+    else if (source == nucleotideColour)\r
+    {\r
+      changeColour(new NucleotideColourScheme());\r
+    }\r
+    else if (source == modifyPID)\r
+    {\r
+      modifyPID_actionPerformed();\r
+    }\r
+    else if (source == modifyConservation)\r
+    {\r
+      modifyConservation_actionPerformed();\r
+    }\r
+    else if (source == userDefinedColour)\r
+    {\r
+      new UserDefinedColours(alignPanel, null);\r
+    }\r
+    else if (source == PIDColour)\r
+    {\r
+      changeColour(new PIDColourScheme());\r
+    }\r
+    else if (source == BLOSUM62Colour)\r
+    {\r
+      changeColour(new Blosum62ColourScheme());\r
+    }\r
+    else if (source == annotationColour)\r
+    {\r
+      new AnnotationColourChooser(viewport, alignPanel);\r
+    }\r
+    else if (source == sortPairwiseMenuItem)\r
+    {\r
+      sortPairwiseMenuItem_actionPerformed();\r
+    }\r
+    else if (source == sortIDMenuItem)\r
+    {\r
+      sortIDMenuItem_actionPerformed();\r
+    }\r
+    else if (source == sortLengthMenuItem)\r
+    {\r
+      sortLengthMenuItem_actionPerformed();\r
+    }\r
+    else if (source == sortGroupMenuItem)\r
+    {\r
+      sortGroupMenuItem_actionPerformed();\r
+    }\r
+    else if (source == removeRedundancyMenuItem)\r
+    {\r
+      removeRedundancyMenuItem_actionPerformed();\r
+    }\r
+    else if (source == pairwiseAlignmentMenuItem)\r
+    {\r
+      pairwiseAlignmentMenuItem_actionPerformed();\r
+    }\r
+    else if (source == PCAMenuItem)\r
+    {\r
+      PCAMenuItem_actionPerformed();\r
+    }\r
+    else if (source == averageDistanceTreeMenuItem)\r
+    {\r
+      averageDistanceTreeMenuItem_actionPerformed();\r
+    }\r
+    else if (source == neighbourTreeMenuItem)\r
+    {\r
+      neighbourTreeMenuItem_actionPerformed();\r
+    }\r
+    else if (source == njTreeBlosumMenuItem)\r
+    {\r
+      njTreeBlosumMenuItem_actionPerformed();\r
+    }\r
+    else if (source == avDistanceTreeBlosumMenuItem)\r
+    {\r
+      avTreeBlosumMenuItem_actionPerformed();\r
+    }\r
+    else if (source == documentation)\r
+    {\r
+      documentation_actionPerformed();\r
+    }\r
+    else if (source == about)\r
+    {\r
+      about_actionPerformed();\r
+    }\r
+\r
+  }\r
+\r
+  public void inputText_actionPerformed()\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+  }\r
+\r
+  protected void outputText_actionPerformed(ActionEvent e)\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame,\r
+            "Alignment output - " + e.getActionCommand(), 600, 500);\r
+    cap.setText(new AppletFormatAdapter().formatSequences(\r
+            e.getActionCommand(), viewport.getAlignment(),\r
+            viewport.showJVSuffix));\r
+  }\r
+\r
+  public void loadAnnotations()\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+    cap.setText("Paste your features / annotations file here.");\r
+    cap.setAnnotationImport();\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+  }\r
+\r
+  public String outputAnnotations(boolean displayTextbox)\r
+  {\r
+    String annotation = new AnnotationFile().printAnnotations(\r
+            viewport.showAnnotation ? viewport.alignment\r
+                    .getAlignmentAnnotation() : null, viewport.alignment\r
+                    .getGroups(),\r
+            ((Alignment) viewport.alignment).alignmentProperties);\r
+\r
+    if (displayTextbox)\r
+    {\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+      Frame frame = new Frame();\r
+      frame.add(cap);\r
+      jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);\r
+      cap.setText(annotation);\r
+    }\r
+\r
+    return annotation;\r
+  }\r
+\r
+  private Hashtable getDisplayedFeatureCols()\r
+  {\r
+    if (alignPanel.getFeatureRenderer() != null)\r
+    {\r
+      FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
+      Hashtable fcols = new Hashtable();\r
+      Enumeration en = viewport.featuresDisplayed.keys();\r
+      while (en.hasMoreElements())\r
+      {\r
+        Object col = en.nextElement();\r
+        fcols.put(col, fr.featureColours.get(col));\r
+      }\r
+      return fcols;\r
+    }\r
+    return null;\r
+  }\r
+\r
+  public String outputFeatures(boolean displayTextbox, String format)\r
+  {\r
+    String features;\r
+    if (format.equalsIgnoreCase("Jalview"))\r
+    {\r
+      features = new FeaturesFile().printJalviewFormat(\r
+              viewport.alignment.getSequencesArray(),\r
+              getDisplayedFeatureCols());\r
+    }\r
+    else\r
+    {\r
+      features = new FeaturesFile().printGFFFormat(\r
+              viewport.alignment.getSequencesArray(),\r
+              getDisplayedFeatureCols());\r
+    }\r
+\r
+    if (displayTextbox)\r
+    {\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+      Frame frame = new Frame();\r
+      frame.add(cap);\r
+      jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
+\r
+      cap.setText(features);\r
+    }\r
+\r
+    return features;\r
+  }\r
+\r
+  void launchFullApplication()\r
+  {\r
+    StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+    url.append("?open="\r
+            + appendProtocol(viewport.applet.getParameter("file")));\r
+\r
+    if (viewport.applet.getParameter("features") != null)\r
+    {\r
+      url.append("&features=");\r
+      url.append(appendProtocol(viewport.applet.getParameter("features")));\r
+    }\r
+\r
+    if (viewport.applet.getParameter("annotations") != null)\r
+    {\r
+      url.append("&annotations=");\r
+      url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
+    }\r
+\r
+    if (viewport.applet.getParameter("jnetfile") != null)\r
+    {\r
+      url.append("&annotations=");\r
+      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
+    }\r
+\r
+    if (viewport.applet.getParameter("defaultColour") != null)\r
+    {\r
+      url.append("&colour="\r
+              + removeWhiteSpace(viewport.applet\r
+                      .getParameter("defaultColour")));\r
+    }\r
+\r
+    if (viewport.applet.getParameter("userDefinedColour") != null)\r
+    {\r
+      url.append("&colour="\r
+              + removeWhiteSpace(viewport.applet\r
+                      .getParameter("userDefinedColour")));\r
+    }\r
+    if (viewport.applet.getParameter("tree") != null)\r
+    {\r
+      url.append("&tree="\r
+              + appendProtocol(viewport.applet.getParameter("tree")));\r
+    }\r
+    if (viewport.applet.getParameter("treeFile") != null)\r
+    {\r
+      url.append("&tree="\r
+              + appendProtocol(viewport.applet.getParameter("treeFile")));\r
+    }\r
+\r
+    showURL(url.toString(), "FULL_APP");\r
+  }\r
+\r
+  String removeWhiteSpace(String colour)\r
+  {\r
+    StringBuffer sb = new StringBuffer();\r
+    for (int i = 0; i < colour.length(); i++)\r
+    {\r
+      if (Character.isWhitespace(colour.charAt(i)))\r
+      {\r
+        sb.append("%20");\r
+      }\r
+      else\r
+      {\r
+        sb.append(colour.charAt(i));\r
+      }\r
+    }\r
+\r
+    return sb.toString();\r
+  }\r
+\r
+  String appendProtocol(String url)\r
+  {\r
+    try\r
+    {\r
+      new URL(url);\r
+      url = URLEncoder.encode(url);\r
+    }\r
+    /*\r
+     * When we finally deprecate 1.1 compatibility, we can start to use\r
+     * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch\r
+     * (UnsupportedEncodingException ex) { System.err.println("WARNING -\r
+     * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);\r
+     * ex.printStackTrace(); }\r
+     */\r
+    catch (java.net.MalformedURLException ex)\r
+    {\r
+      url = viewport.applet.getCodeBase() + url;\r
+    }\r
+    return url;\r
+  }\r
+\r
+  public void closeMenuItem_actionPerformed()\r
+  {\r
+    PaintRefresher.RemoveComponent(alignPanel);\r
+    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
+    if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
+    {\r
+      System.exit(0);\r
+    }\r
+\r
+    this.dispose();\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
+  void updateEditMenuBar()\r
+  {\r
+\r
+    if (viewport.historyList.size() > 0)\r
+    {\r
+      undoMenuItem.setEnabled(true);\r
+      CommandI command = (CommandI) viewport.historyList.peek();\r
+      undoMenuItem.setLabel("Undo " + command.getDescription());\r
+    }\r
+    else\r
+    {\r
+      undoMenuItem.setEnabled(false);\r
+      undoMenuItem.setLabel("Undo");\r
+    }\r
+\r
+    if (viewport.redoList.size() > 0)\r
+    {\r
+      redoMenuItem.setEnabled(true);\r
+\r
+      CommandI command = (CommandI) viewport.redoList.peek();\r
+      redoMenuItem.setLabel("Redo " + command.getDescription());\r
+    }\r
+    else\r
+    {\r
+      redoMenuItem.setEnabled(false);\r
+      redoMenuItem.setLabel("Redo");\r
+    }\r
+  }\r
+\r
+  public void addHistoryItem(CommandI command)\r
+  {\r
+    if (command.getSize() > 0)\r
+    {\r
+      viewport.historyList.push(command);\r
+      viewport.redoList.removeAllElements();\r
+      updateEditMenuBar();\r
+      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+    }\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param e\r
+   *          DOCUMENT ME!\r
+   */\r
+  protected void undoMenuItem_actionPerformed()\r
+  {\r
+    if (viewport.historyList.size() < 1)\r
+    {\r
+      return;\r
+    }\r
+\r
+    CommandI command = (CommandI) viewport.historyList.pop();\r
+    viewport.redoList.push(command);\r
+    command.undoCommand(null);\r
+\r
+    AlignViewport originalSource = getOriginatingSource(command);\r
+\r
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+    updateEditMenuBar();\r
+    originalSource.firePropertyChange("alignment", null,\r
+            originalSource.alignment.getSequences());\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param e\r
+   *          DOCUMENT ME!\r
+   */\r
+  protected void redoMenuItem_actionPerformed()\r
+  {\r
+    if (viewport.redoList.size() < 1)\r
+    {\r
+      return;\r
+    }\r
+\r
+    CommandI command = (CommandI) viewport.redoList.pop();\r
+    viewport.historyList.push(command);\r
+    command.doCommand(null);\r
+\r
+    AlignViewport originalSource = getOriginatingSource(command);\r
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+\r
+    updateEditMenuBar();\r
+    originalSource.firePropertyChange("alignment", null,\r
+            originalSource.alignment.getSequences());\r
+  }\r
+\r
+  AlignViewport getOriginatingSource(CommandI command)\r
+  {\r
+    AlignViewport originalSource = null;\r
+    // For sequence removal and addition, we need to fire\r
+    // the property change event FROM the viewport where the\r
+    // original alignment was altered\r
+    AlignmentI al = null;\r
+    if (command instanceof EditCommand)\r
+    {\r
+      EditCommand editCommand = (EditCommand) command;\r
+      al = editCommand.getAlignment();\r
+      Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+              .getSequenceSetId());\r
+      for (int i = 0; i < comps.size(); i++)\r
+      {\r
+        if (comps.elementAt(i) instanceof AlignmentPanel)\r
+        {\r
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+          {\r
+            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
+            break;\r
+          }\r
+        }\r
+      }\r
+    }\r
+\r
+    if (originalSource == null)\r
+    {\r
+      // The original view is closed, we must validate\r
+      // the current view against the closed view first\r
+      if (al != null)\r
+      {\r
+        PaintRefresher.validateSequences(al, viewport.alignment);\r
+      }\r
+\r
+      originalSource = viewport;\r
+    }\r
+\r
+    return originalSource;\r
+  }\r
+\r
+  public void moveSelectedSequences(boolean up)\r
+  {\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
+    if (sg == null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    if (up)\r
+    {\r
+      for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+      {\r
+        SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+        if (!sg.getSequences(null).contains(seq))\r
+        {\r
+          continue;\r
+        }\r
+\r
+        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+        if (sg.getSequences(null).contains(temp))\r
+        {\r
+          continue;\r
+        }\r
+\r
+        viewport.alignment.getSequences().setElementAt(temp, i);\r
+        viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+      }\r
+    }\r
+    else\r
+    {\r
+      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+      {\r
+        SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
+        {\r
+          continue;\r
+        }\r
+\r
+        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
+        {\r
+          continue;\r
+        }\r
+\r
+        viewport.alignment.getSequences().setElementAt(temp, i);\r
+        viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+      }\r
+    }\r
+\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  synchronized void slideSequences(boolean right, int size)\r
+  {\r
+    Vector sg = new Vector();\r
+    if (viewport.cursorMode)\r
+    {\r
+      sg.addElement(viewport.alignment\r
+              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
+    }\r
+    else if (viewport.getSelectionGroup() != null\r
+            && viewport.getSelectionGroup().getSize() != viewport.alignment\r
+                    .getHeight())\r
+    {\r
+      sg = viewport.getSelectionGroup().getSequences(\r
+              viewport.hiddenRepSequences);\r
+    }\r
+\r
+    if (sg.size() < 1)\r
+    {\r
+      return;\r
+    }\r
+\r
+    Vector invertGroup = new Vector();\r
+\r
+    for (int i = 0; i < viewport.alignment.getHeight(); i++)\r
+    {\r
+      if (!sg.contains(viewport.alignment.getSequenceAt(i)))\r
+        invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
+    }\r
+\r
+    SequenceI[] seqs1 = new SequenceI[sg.size()];\r
+    for (int i = 0; i < sg.size(); i++)\r
+      seqs1[i] = (SequenceI) sg.elementAt(i);\r
+\r
+    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+    for (int i = 0; i < invertGroup.size(); i++)\r
+      seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
+\r
+    SlideSequencesCommand ssc;\r
+    if (right)\r
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
+              size, viewport.getGapCharacter());\r
+    else\r
+      ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
+              size, viewport.getGapCharacter());\r
+\r
+    int groupAdjustment = 0;\r
+    if (ssc.getGapsInsertedBegin() && right)\r
+    {\r
+      if (viewport.cursorMode)\r
+        alignPanel.seqPanel.moveCursor(size, 0);\r
+      else\r
+        groupAdjustment = size;\r
+    }\r
+    else if (!ssc.getGapsInsertedBegin() && !right)\r
+    {\r
+      if (viewport.cursorMode)\r
+        alignPanel.seqPanel.moveCursor(-size, 0);\r
+      else\r
+        groupAdjustment = -size;\r
+    }\r
+\r
+    if (groupAdjustment != 0)\r
+    {\r
+      viewport.getSelectionGroup().setStartRes(\r
+              viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+      viewport.getSelectionGroup().setEndRes(\r
+              viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+    }\r
+\r
+    boolean appendHistoryItem = false;\r
+    if (viewport.historyList != null && viewport.historyList.size() > 0\r
+            && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+    {\r
+      appendHistoryItem = ssc\r
+              .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
+                      .peek());\r
+    }\r
+\r
+    if (!appendHistoryItem)\r
+      addHistoryItem(ssc);\r
+\r
+    repaint();\r
+  }\r
+\r
+  static StringBuffer copiedSequences;\r
+\r
+  static Vector copiedHiddenColumns;\r
+\r
+  protected void copy_actionPerformed()\r
+  {\r
+    if (viewport.getSelectionGroup() == null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
+    copiedSequences = new StringBuffer();\r
+    Hashtable orderedSeqs = new Hashtable();\r
+    for (int i = 0; i < sg.getSize(); i++)\r
+    {\r
+      SequenceI seq = sg.getSequenceAt(i);\r
+      int index = viewport.alignment.findIndex(seq);\r
+      orderedSeqs.put(index + "", seq);\r
+    }\r
+\r
+    int index = 0, startRes, endRes;\r
+    char ch;\r
+\r
+    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+    {\r
+      copiedHiddenColumns = new Vector();\r
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
+              .size(); i++)\r
+      {\r
+        int[] region = (int[]) viewport.getColumnSelection()\r
+                .getHiddenColumns().elementAt(i);\r
+\r
+        copiedHiddenColumns.addElement(new int[]\r
+        { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
+      }\r
+    }\r
+    else\r
+    {\r
+      copiedHiddenColumns = null;\r
+    }\r
+\r
+    for (int i = 0; i < sg.getSize(); i++)\r
+    {\r
+      SequenceI seq = null;\r
+\r
+      while (seq == null)\r
+      {\r
+        if (orderedSeqs.containsKey(index + ""))\r
+        {\r
+          seq = (SequenceI) orderedSeqs.get(index + "");\r
+          index++;\r
+\r
+          break;\r
+        }\r
+        else\r
+        {\r
+          index++;\r
+        }\r
+      }\r
+\r
+      // FIND START RES\r
+      // Returns residue following index if gap\r
+      startRes = seq.findPosition(sg.getStartRes());\r
+\r
+      // FIND END RES\r
+      // Need to find the residue preceeding index if gap\r
+      endRes = 0;\r
+\r
+      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+      {\r
+        ch = seq.getCharAt(j);\r
+        if (!jalview.util.Comparison.isGap((ch)))\r
+        {\r
+          endRes++;\r
+        }\r
+      }\r
+\r
+      if (endRes > 0)\r
+      {\r
+        endRes += seq.getStart() - 1;\r
+      }\r
+\r
+      copiedSequences.append(seq.getName()\r
+              + "\t"\r
+              + startRes\r
+              + "\t"\r
+              + endRes\r
+              + "\t"\r
+              + seq.getSequenceAsString(sg.getStartRes(),\r
+                      sg.getEndRes() + 1) + "\n");\r
+    }\r
+\r
+  }\r
+\r
+  protected void pasteNew_actionPerformed()\r
+  {\r
+    paste(true);\r
+  }\r
+\r
+  protected void pasteThis_actionPerformed()\r
+  {\r
+    paste(false);\r
+  }\r
+\r
+  void paste(boolean newAlignment)\r
+  {\r
+    try\r
+    {\r
+\r
+      if (copiedSequences == null)\r
+      {\r
+        return;\r
+      }\r
+\r
+      StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
+      Vector seqs = new Vector();\r
+      while (st.hasMoreElements())\r
+      {\r
+        String name = st.nextToken();\r
+        int start = Integer.parseInt(st.nextToken());\r
+        int end = Integer.parseInt(st.nextToken());\r
+        seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
+      }\r
+      SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+      for (int i = 0; i < seqs.size(); i++)\r
+      {\r
+        newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+      }\r
+\r
+      if (newAlignment)\r
+      {\r
+        String newtitle = new String("Copied sequences");\r
+        if (getTitle().startsWith("Copied sequences"))\r
+        {\r
+          newtitle = getTitle();\r
+        }\r
+        else\r
+        {\r
+          newtitle = newtitle.concat("- from " + getTitle());\r
+        }\r
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+                viewport.applet, newtitle, false);\r
+        if (copiedHiddenColumns != null)\r
+        {\r
+          for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+          {\r
+            int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+            af.viewport.hideColumns(region[0], region[1]);\r
+          }\r
+        }\r
+\r
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+                DEFAULT_HEIGHT);\r
+      }\r
+      else\r
+      {\r
+        addSequences(newSeqs);\r
+      }\r
+\r
+    } catch (Exception ex)\r
+    {\r
+    } // could be anything being pasted in here\r
+\r
+  }\r
+\r
+  void addSequences(SequenceI[] seqs)\r
+  {\r
+    for (int i = 0; i < seqs.length; i++)\r
+    {\r
+      viewport.alignment.addSequence(seqs[i]);\r
+    }\r
+\r
+    // !newAlignment\r
+    addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
+            seqs, 0, viewport.alignment.getWidth(), viewport.alignment));\r
+\r
+    viewport.setEndSeq(viewport.alignment.getHeight());\r
+    viewport.alignment.getWidth();\r
+    viewport.firePropertyChange("alignment", null,\r
+            viewport.alignment.getSequences());\r
+\r
+  }\r
+\r
+  protected void cut_actionPerformed()\r
+  {\r
+    copy_actionPerformed();\r
+    delete_actionPerformed();\r
+  }\r
+\r
+  protected void delete_actionPerformed()\r
+  {\r
+\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
+    if (sg == null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    Vector seqs = new Vector();\r
+    SequenceI seq;\r
+    for (int i = 0; i < sg.getSize(); i++)\r
+    {\r
+      seq = sg.getSequenceAt(i);\r
+      seqs.addElement(seq);\r
+    }\r
+\r
+    // If the cut affects all sequences, remove highlighted columns\r
+    if (sg.getSize() == viewport.alignment.getHeight())\r
+    {\r
+      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+              sg.getEndRes() + 1);\r
+    }\r
+\r
+    SequenceI[] cut = new SequenceI[seqs.size()];\r
+    for (int i = 0; i < seqs.size(); i++)\r
+    {\r
+      cut[i] = (SequenceI) seqs.elementAt(i);\r
+    }\r
+\r
+    /*\r
+     * //ADD HISTORY ITEM\r
+     */\r
+    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
+            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
+            viewport.alignment));\r
+\r
+    viewport.setSelectionGroup(null);\r
+    viewport.alignment.deleteGroup(sg);\r
+\r
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+            .getSequences());\r
+\r
+    if (viewport.getAlignment().getHeight() < 1)\r
+    {\r
+      this.setVisible(false);\r
+    }\r
+    viewport.sendSelection();\r
+  }\r
+\r
+  /**\r
+   * group consensus toggled\r
+   * \r
+   */\r
+  protected void showGroupConsensus_actionPerformed()\r
+  {\r
+    viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+\r
+  }\r
+\r
+  /**\r
+   * group conservation toggled.\r
+   */\r
+  protected void showGroupConservation_actionPerformed()\r
+  {\r
+    viewport.setShowGroupConservation(showGroupConservation.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
+   * @see\r
+   * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
+   * .event.ActionEvent)\r
+   */\r
+  protected void showConsensusHistogram_actionPerformed()\r
+  {\r
+    viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
+   * @see\r
+   * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
+   * .event.ActionEvent)\r
+   */\r
+  protected void showSequenceLogo_actionPerformed()\r
+  {\r
+    viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
+\r
+  protected void applyAutoAnnotationSettings_actionPerformed()\r
+  {\r
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+  }\r
+\r
+  protected void makeGrpsFromSelection_actionPerformed()\r
+  {\r
+    if (viewport.getSelectionGroup() != null)\r
+    {\r
+      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
+              viewport.getSequenceSelection(),\r
+              viewport.getAlignmentView(true).getSequenceStrings(\r
+                      viewport.getGapCharacter()),\r
+              viewport.alignment.getGroups());\r
+      viewport.alignment.deleteAllGroups();\r
+      viewport.sequenceColours = null;\r
+      viewport.setSelectionGroup(null);\r
+      // set view properties for each group\r
+      for (int g = 0; g < gps.length; g++)\r
+      {\r
+        // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
+        viewport.alignment.addGroup(gps[g]);\r
+        Color col = new Color((int) (Math.random() * 255),\r
+                (int) (Math.random() * 255), (int) (Math.random() * 255));\r
+        col = col.brighter();\r
+        for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
+                .hasMoreElements(); viewport.setSequenceColour(\r
+                (SequenceI) sq.nextElement(), col))\r
+          ;\r
+      }\r
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+      alignPanel.updateAnnotation();\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+  }\r
+\r
+  protected void deleteGroups_actionPerformed()\r
+  {\r
+    viewport.alignment.deleteAllGroups();\r
+    viewport.sequenceColours = null;\r
+    viewport.setSelectionGroup(null);\r
+\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public void selectAllSequenceMenuItem_actionPerformed()\r
+  {\r
+    SequenceGroup sg = new SequenceGroup();\r
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+    {\r
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+    }\r
+    sg.setEndRes(viewport.alignment.getWidth() - 1);\r
+    viewport.setSelectionGroup(sg);\r
+    alignPanel.paintAlignment(true);\r
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+    viewport.sendSelection();\r
+  }\r
+\r
+  public void deselectAllSequenceMenuItem_actionPerformed()\r
+  {\r
+    if (viewport.cursorMode)\r
+    {\r
+      alignPanel.seqPanel.keyboardNo1 = null;\r
+      alignPanel.seqPanel.keyboardNo2 = null;\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.paintAlignment(true);\r
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+    viewport.sendSelection();\r
+  }\r
+\r
+  public void invertSequenceMenuItem_actionPerformed()\r
+  {\r
+    SequenceGroup sg = viewport.getSelectionGroup();\r
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+    {\r
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+    }\r
+\r
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+    viewport.sendSelection();\r
+  }\r
+\r
+  public void invertColSel_actionPerformed()\r
+  {\r
+    viewport.invertColumnSelection();\r
+    alignPanel.paintAlignment(true);\r
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+    viewport.sendSelection();\r
+  }\r
+\r
+  void trimAlignment(boolean trimLeft)\r
+  {\r
+    ColumnSelection colSel = viewport.getColumnSelection();\r
+    int column;\r
+\r
+    if (colSel.size() > 0)\r
+    {\r
+      if (trimLeft)\r
+      {\r
+        column = colSel.getMin();\r
+      }\r
+      else\r
+      {\r
+        column = colSel.getMax();\r
+      }\r
+\r
+      SequenceI[] seqs;\r
+      if (viewport.getSelectionGroup() != null)\r
+      {\r
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+                viewport.hiddenRepSequences);\r
+      }\r
+      else\r
+      {\r
+        seqs = viewport.alignment.getSequencesArray();\r
+      }\r
+\r
+      TrimRegionCommand trimRegion;\r
+      if (trimLeft)\r
+      {\r
+        trimRegion = new TrimRegionCommand("Remove Left",\r
+                TrimRegionCommand.TRIM_LEFT, seqs, column,\r
+                viewport.alignment, viewport.colSel,\r
+                viewport.selectionGroup);\r
+        viewport.setStartRes(0);\r
+      }\r
+      else\r
+      {\r
+        trimRegion = new TrimRegionCommand("Remove Right",\r
+                TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
+                viewport.alignment, viewport.colSel,\r
+                viewport.selectionGroup);\r
+      }\r
+\r
+      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
+\r
+      addHistoryItem(trimRegion);\r
+\r
+      Vector groups = viewport.alignment.getGroups();\r
+\r
+      for (int i = 0; i < groups.size(); i++)\r
+      {\r
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+        if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
+                || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+        {\r
+          viewport.alignment.deleteGroup(sg);\r
+        }\r
+      }\r
+\r
+      viewport.firePropertyChange("alignment", null, viewport\r
+              .getAlignment().getSequences());\r
+    }\r
+  }\r
+\r
+  public void removeGappedColumnMenuItem_actionPerformed()\r
+  {\r
+    int start = 0, end = viewport.alignment.getWidth() - 1;\r
+\r
+    SequenceI[] seqs;\r
+    if (viewport.getSelectionGroup() != null)\r
+    {\r
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+              viewport.hiddenRepSequences);\r
+      start = viewport.getSelectionGroup().getStartRes();\r
+      end = viewport.getSelectionGroup().getEndRes();\r
+    }\r
+    else\r
+    {\r
+      seqs = viewport.alignment.getSequencesArray();\r
+    }\r
+\r
+    RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
+            "Remove Gapped Columns", seqs, start, end, viewport.alignment);\r
+\r
+    addHistoryItem(removeGapCols);\r
+\r
+    statusBar.setText("Removed " + removeGapCols.getSize()\r
+            + " empty columns.");\r
+\r
+    // This is to maintain viewport position on first residue\r
+    // of first sequence\r
+    SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+    int startRes = seq.findPosition(viewport.startRes);\r
+    // ShiftList shifts;\r
+    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+    // edit.alColumnChanges=shifts.getInverse();\r
+    // if (viewport.hasHiddenColumns)\r
+    // viewport.getColumnSelection().compensateForEdits(shifts);\r
+    viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+            .getSequences());\r
+\r
+  }\r
+\r
+  public void removeAllGapsMenuItem_actionPerformed()\r
+  {\r
+    int start = 0, end = viewport.alignment.getWidth() - 1;\r
+\r
+    SequenceI[] seqs;\r
+    if (viewport.getSelectionGroup() != null)\r
+    {\r
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+              viewport.hiddenRepSequences);\r
+      start = viewport.getSelectionGroup().getStartRes();\r
+      end = viewport.getSelectionGroup().getEndRes();\r
+    }\r
+    else\r
+    {\r
+      seqs = viewport.alignment.getSequencesArray();\r
+    }\r
+\r
+    // This is to maintain viewport position on first residue\r
+    // of first sequence\r
+    SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+    int startRes = seq.findPosition(viewport.startRes);\r
+\r
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
+            viewport.alignment));\r
+\r
+    viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+\r
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+            .getSequences());\r
+\r
+  }\r
+\r
+  public void findMenuItem_actionPerformed()\r
+  {\r
+    new Finder(alignPanel);\r
+  }\r
+\r
+  /**\r
+   * create a new view derived from the current view\r
+   * \r
+   * @param viewtitle\r
+   * @return frame for the new view\r
+   */\r
+  public AlignFrame newView(String viewtitle)\r
+  {\r
+    AlignmentI newal;\r
+    if (viewport.hasHiddenRows)\r
+    {\r
+      newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
+              .getFullAlignment().getSequencesArray());\r
+    }\r
+    else\r
+    {\r
+      newal = new Alignment(viewport.alignment.getSequencesArray());\r
+    }\r
+\r
+    if (viewport.alignment.getAlignmentAnnotation() != null)\r
+    {\r
+      for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)\r
+      {\r
+        if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+        {\r
+          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+        }\r
+      }\r
+    }\r
+\r
+    AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
+\r
+    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+    PaintRefresher.Register(newaf.alignPanel,\r
+            newaf.alignPanel.av.getSequenceSetId());\r
+\r
+    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+            newaf.alignPanel.av.getSequenceSetId());\r
+    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+            newaf.alignPanel.av.getSequenceSetId());\r
+\r
+    Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+            .getSequenceSetId());\r
+    int viewSize = -1;\r
+    for (int i = 0; i < comps.size(); i++)\r
+    {\r
+      if (comps.elementAt(i) instanceof AlignmentPanel)\r
+      {\r
+        viewSize++;\r
+      }\r
+    }\r
+\r
+    String title = new String(this.getTitle());\r
+    if (viewtitle != null)\r
+    {\r
+      title = viewtitle + " ( " + title + ")";\r
+    }\r
+    else\r
+    {\r
+      if (title.indexOf("(View") > -1)\r
+      {\r
+        title = title.substring(0, title.indexOf("(View"));\r
+      }\r
+      title += "(View " + viewSize + ")";\r
+    }\r
+\r
+    newaf.setTitle(title.toString());\r
+\r
+    newaf.viewport.historyList = viewport.historyList;\r
+    newaf.viewport.redoList = viewport.redoList;\r
+    return newaf;\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @return list of feature groups on the view\r
+   */\r
+  public String[] getFeatureGroups()\r
+  {\r
+    FeatureRenderer fr = null;\r
+    if (alignPanel != null\r
+            && (fr = alignPanel.getFeatureRenderer()) != null)\r
+    {\r
+      return fr.getGroups();\r
+    }\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * get sequence feature groups that are hidden or shown\r
+   * \r
+   * @param visible\r
+   *          true is visible\r
+   * @return list\r
+   */\r
+  public String[] getFeatureGroupsOfState(boolean visible)\r
+  {\r
+    FeatureRenderer fr = null;\r
+    if (alignPanel != null\r
+            && (fr = alignPanel.getFeatureRenderer()) != null)\r
+    {\r
+      return fr.getGroups(visible);\r
+    }\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * Change the display state for the given feature groups\r
+   * \r
+   * @param groups\r
+   *          list of group strings\r
+   * @param state\r
+   *          visible or invisible\r
+   */\r
+  public void setFeatureGroupState(String[] groups, boolean state)\r
+  {\r
+    FeatureRenderer fr = null;\r
+    this.sequenceFeatures.setState(true);\r
+    viewport.showSequenceFeatures(true);\r
+    if (alignPanel != null\r
+            && (fr = alignPanel.getFeatureRenderer()) != null)\r
+    {\r
+      fr.setGroupState(groups, state);\r
+      alignPanel.seqPanel.seqCanvas.repaint();\r
+      if (alignPanel.overviewPanel != null)\r
+      {\r
+        alignPanel.overviewPanel.updateOverviewImage();\r
+      }\r
+    }\r
+  }\r
+\r
+  public void seqLimits_itemStateChanged()\r
+  {\r
+    viewport.setShowJVSuffix(seqLimits.getState());\r
+    alignPanel.fontChanged();\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  protected void colourTextMenuItem_actionPerformed()\r
+  {\r
+    viewport.setColourText(colourTextMenuItem.getState());\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  protected void displayNonconservedMenuItem_actionPerformed()\r
+  {\r
+    viewport.setShowunconserved(displayNonconservedMenuItem.getState());\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  protected void wrapMenuItem_actionPerformed()\r
+  {\r
+    viewport.setWrapAlignment(wrapMenuItem.getState());\r
+    alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+    scaleAbove.setEnabled(wrapMenuItem.getState());\r
+    scaleLeft.setEnabled(wrapMenuItem.getState());\r
+    scaleRight.setEnabled(wrapMenuItem.getState());\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public void overviewMenuItem_actionPerformed()\r
+  {\r
+    if (alignPanel.overviewPanel != null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    Frame frame = new Frame();\r
+    OverviewPanel overview = new OverviewPanel(alignPanel);\r
+    frame.add(overview);\r
+    // +50 must allow for applet frame window\r
+    jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
+            overview.getPreferredSize().width,\r
+            overview.getPreferredSize().height + 50);\r
+\r
+    frame.pack();\r
+    frame.addWindowListener(new WindowAdapter()\r
+    {\r
+      public void windowClosing(WindowEvent e)\r
+      {\r
+        alignPanel.setOverviewPanel(null);\r
+      };\r
+    });\r
+\r
+    alignPanel.setOverviewPanel(overview);\r
+\r
+  }\r
+\r
+  void changeColour(ColourSchemeI cs)\r
+  {\r
+    int threshold = 0;\r
+\r
+    if (cs != null)\r
+    {\r
+      if (viewport.getAbovePIDThreshold())\r
+      {\r
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+                "Background");\r
+\r
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+\r
+        viewport.setGlobalColourScheme(cs);\r
+      }\r
+      else\r
+      {\r
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+      }\r
+\r
+      if (viewport.getConservationSelected())\r
+      {\r
+\r
+        Alignment al = (Alignment) viewport.alignment;\r
+        Conservation c = new Conservation("All",\r
+                ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+                al.getWidth() - 1);\r
+\r
+        c.calculate();\r
+        c.verdict(false, viewport.ConsPercGaps);\r
+\r
+        cs.setConservation(c);\r
+\r
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
+                cs, "Background"));\r
+\r
+      }\r
+      else\r
+      {\r
+        cs.setConservation(null);\r
+      }\r
+\r
+      cs.setConsensus(viewport.hconsensus);\r
+\r
+    }\r
+    viewport.setGlobalColourScheme(cs);\r
+\r
+    if (viewport.getColourAppliesToAllGroups())\r
+    {\r
+      Vector groups = viewport.alignment.getGroups();\r
+      for (int i = 0; i < groups.size(); i++)\r
+      {\r
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+        if (cs == null)\r
+        {\r
+          sg.cs = null;\r
+          continue;\r
+        }\r
+        if (cs instanceof ClustalxColourScheme)\r
+        {\r
+          sg.cs = new ClustalxColourScheme(\r
+                  sg.getSequences(viewport.hiddenRepSequences),\r
+                  sg.getWidth());\r
+        }\r
+        else\r
+        {\r
+          try\r
+          {\r
+            sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+          } catch (Exception ex)\r
+          {\r
+            ex.printStackTrace();\r
+            sg.cs = cs;\r
+          }\r
+        }\r
+\r
+        if (viewport.getAbovePIDThreshold()\r
+                || cs instanceof PIDColourScheme\r
+                || cs instanceof Blosum62ColourScheme)\r
+        {\r
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+          sg.cs.setConsensus(AAFrequency.calculate(\r
+                  sg.getSequences(viewport.hiddenRepSequences), 0,\r
+                  sg.getWidth()));\r
+        }\r
+        else\r
+        {\r
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+        }\r
+\r
+        if (viewport.getConservationSelected())\r
+        {\r
+          Conservation c = new Conservation("Group",\r
+                  ResidueProperties.propHash, 3,\r
+                  sg.getSequences(viewport.hiddenRepSequences), 0,\r
+                  viewport.alignment.getWidth() - 1);\r
+          c.calculate();\r
+          c.verdict(false, viewport.ConsPercGaps);\r
+          sg.cs.setConservation(c);\r
+        }\r
+        else\r
+        {\r
+          sg.cs.setConservation(null);\r
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+        }\r
+\r
+      }\r
+    }\r
+\r
+    if (alignPanel.getOverviewPanel() != null)\r
+    {\r
+      alignPanel.getOverviewPanel().updateOverviewImage();\r
+    }\r
+\r
+    jalview.structure.StructureSelectionManager\r
+            .getStructureSelectionManager().sequenceColoursChanged(\r
+                    alignPanel);\r
+\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  protected void modifyPID_actionPerformed()\r
+  {\r
+    if (viewport.getAbovePIDThreshold()\r
+            && viewport.globalColourScheme != null)\r
+    {\r
+      SliderPanel.setPIDSliderSource(alignPanel,\r
+              viewport.getGlobalColourScheme(), "Background");\r
+      SliderPanel.showPIDSlider();\r
+    }\r
+  }\r
+\r
+  protected void modifyConservation_actionPerformed()\r
+  {\r
+    if (viewport.getConservationSelected()\r
+            && viewport.globalColourScheme != null)\r
+    {\r
+      SliderPanel.setConservationSlider(alignPanel,\r
+              viewport.globalColourScheme, "Background");\r
+      SliderPanel.showConservationSlider();\r
+    }\r
+  }\r
+\r
+  protected void conservationMenuItem_actionPerformed()\r
+  {\r
+    viewport.setConservationSelected(conservationMenuItem.getState());\r
+\r
+    viewport.setAbovePIDThreshold(false);\r
+    abovePIDThreshold.setState(false);\r
+\r
+    changeColour(viewport.getGlobalColourScheme());\r
+\r
+    modifyConservation_actionPerformed();\r
+  }\r
+\r
+  public void abovePIDThreshold_actionPerformed()\r
+  {\r
+    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
+\r
+    conservationMenuItem.setState(false);\r
+    viewport.setConservationSelected(false);\r
+\r
+    changeColour(viewport.getGlobalColourScheme());\r
+\r
+    modifyPID_actionPerformed();\r
+  }\r
+\r
+  public void sortPairwiseMenuItem_actionPerformed()\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
+            .getAlignment().getSequenceAt(0), null);\r
+\r
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+            viewport.alignment));\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public void sortIDMenuItem_actionPerformed()\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+    AlignmentSorter.sortByID(viewport.getAlignment());\r
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public void sortLengthMenuItem_actionPerformed()\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+    AlignmentSorter.sortByLength(viewport.getAlignment());\r
+    addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
+            viewport.alignment));\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  public void sortGroupMenuItem_actionPerformed()\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+    AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
+            viewport.alignment));\r
+    alignPanel.paintAlignment(true);\r
+\r
+  }\r
+\r
+  public void removeRedundancyMenuItem_actionPerformed()\r
+  {\r
+    new RedundancyPanel(alignPanel);\r
+  }\r
+\r
+  public void pairwiseAlignmentMenuItem_actionPerformed()\r
+  {\r
+    if (viewport.getSelectionGroup() != null\r
+            && viewport.getSelectionGroup().getSize() > 1)\r
+    {\r
+      Frame frame = new Frame();\r
+      frame.add(new PairwiseAlignPanel(alignPanel));\r
+      jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,\r
+              500);\r
+    }\r
+  }\r
+\r
+  public void PCAMenuItem_actionPerformed()\r
+  {\r
+    // are the sequences aligned?\r
+    if (!viewport.alignment.isAligned(false))\r
+    {\r
+      SequenceI current;\r
+      int Width = viewport.getAlignment().getWidth();\r
+\r
+      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+      {\r
+        current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+        if (current.getLength() < Width)\r
+        {\r
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+        }\r
+      }\r
+      alignPanel.paintAlignment(true);\r
+    }\r
+\r
+    if ((viewport.getSelectionGroup() != null\r
+            && viewport.getSelectionGroup().getSize() < 4 && viewport\r
+            .getSelectionGroup().getSize() > 0)\r
+            || viewport.getAlignment().getHeight() < 4)\r
+    {\r
+      return;\r
+    }\r
+\r
+    try\r
+    {\r
+      new PCAPanel(viewport);\r
+    } catch (java.lang.OutOfMemoryError ex)\r
+    {\r
+    }\r
+\r
+  }\r
+\r
+  public void averageDistanceTreeMenuItem_actionPerformed()\r
+  {\r
+    NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+  }\r
+\r
+  public void neighbourTreeMenuItem_actionPerformed()\r
+  {\r
+    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+  }\r
+\r
+  protected void njTreeBlosumMenuItem_actionPerformed()\r
+  {\r
+    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+  }\r
+\r
+  protected void avTreeBlosumMenuItem_actionPerformed()\r
+  {\r
+    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+  }\r
+\r
+  void NewTreePanel(String type, String pwType, String title)\r
+  {\r
+    // are the sequences aligned?\r
+    if (!viewport.alignment.isAligned(false))\r
+    {\r
+      SequenceI current;\r
+      int Width = viewport.getAlignment().getWidth();\r
+\r
+      for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+      {\r
+        current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+        if (current.getLength() < Width)\r
+        {\r
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+        }\r
+      }\r
+      alignPanel.paintAlignment(true);\r
+\r
+    }\r
+\r
+    if ((viewport.getSelectionGroup() != null && viewport\r
+            .getSelectionGroup().getSize() > 1)\r
+            || (viewport.getSelectionGroup() == null && viewport.alignment\r
+                    .getHeight() > 1))\r
+    {\r
+      final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
+\r
+      addTreeMenuItem(tp, title);\r
+\r
+      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+    }\r
+  }\r
+\r
+  void loadTree_actionPerformed()\r
+  {\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+    cap.setText("Paste your Newick tree file here.");\r
+    cap.setTreeImport();\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+  }\r
+\r
+  public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+  {\r
+    TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);\r
+    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+    addTreeMenuItem(tp, treeFile);\r
+  }\r
+\r
+  /**\r
+   * sort the alignment using the given treePanel\r
+   * \r
+   * @param treePanel\r
+   *          tree used to sort view\r
+   * @param title\r
+   *          string used for undo event name\r
+   */\r
+  public void sortByTree(TreePanel treePanel, String title)\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+    AlignmentSorter\r
+            .sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+    // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+    // HistoryItem.SORT));\r
+    addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
+            viewport.alignment));\r
+    alignPanel.paintAlignment(true);\r
+  }\r
+\r
+  /**\r
+   * Do any automatic reordering of the alignment and add the necessary bits to\r
+   * the menu structure for the new tree\r
+   * \r
+   * @param treePanel\r
+   * @param title\r
+   */\r
+  protected void addTreeMenuItem(final TreePanel treePanel,\r
+          final String title)\r
+  {\r
+    final MenuItem item = new MenuItem(title);\r
+    sortByTreeMenu.add(item);\r
+    item.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent evt)\r
+      {\r
+        sortByTree(treePanel, title); // treePanel.getTitle());\r
+      }\r
+    });\r
+\r
+    treePanel.addWindowListener(new WindowAdapter()\r
+    {\r
+      public void windowOpened(WindowEvent e)\r
+      {\r
+        if (viewport.sortByTree)\r
+        {\r
+          sortByTree(treePanel, title);\r
+        }\r
+        super.windowOpened(e);\r
+      }\r
+\r
+      public void windowClosing(WindowEvent e)\r
+      {\r
+        sortByTreeMenu.remove(item);\r
+      };\r
+    });\r
+  }\r
+  public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+  {\r
+    SequenceI[] oldOrder = viewport.getAlignment()\r
+    .getSequencesArray();\r
+    if (viewport.applet.debug)\r
+    {\r
+      System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
+    }\r
+    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+    if (undoname!=null)\r
+    {\r
+      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));\r
+    }\r
+    alignPanel.paintAlignment(true);\r
+    return true;\r
+  }\r
+  protected void documentation_actionPerformed()\r
+  {\r
+    showURL("http://www.jalview.org/help.html", "HELP");\r
+  }\r
+\r
+  protected void about_actionPerformed()\r
+  {\r
+\r
+    class AboutPanel extends Canvas\r
+    {\r
+      String version;\r
+\r
+      String builddate;\r
+\r
+      public AboutPanel(String version, String builddate)\r
+      {\r
+        this.version = version;\r
+        this.builddate = builddate;\r
+      }\r
+\r
+      public void paint(Graphics g)\r
+      {\r
+        g.setColor(Color.white);\r
+        g.fillRect(0, 0, getSize().width, getSize().height);\r
+        g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+        FontMetrics fm = g.getFontMetrics();\r
+        int fh = fm.getHeight();\r
+        int y = 5, x = 7;\r
+        g.setColor(Color.black);\r
+        // TODO: update this text for each release or centrally store it for\r
+        // lite and application\r
+        g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
+        g.drawString("JalviewLite - Release " + version, x, y += fh);\r
+        g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
+        g.drawString("Build date: " + builddate, x, y += fh);\r
+        g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+        g.drawString(\r
+                "Authors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+                x, y += fh * 1.5);\r
+        g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+        g.drawString(\r
+                "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
+                x, y += fh);\r
+        g.drawString(\r
+                "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
+                x, y += fh);\r
+        g.drawString("If  you use Jalview, please cite:", x, y += fh + 8);\r
+        g.drawString(\r
+                "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
+                x, y += fh);\r
+        g.drawString(\r
+                "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
+                x, y += fh);\r
+        g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
+                x, y += fh);\r
+      }\r
+    }\r
+\r
+    Frame frame = new Frame();\r
+    frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
+            .getBuildDate()));\r
+    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
+\r
+  }\r
+\r
+  public void showURL(String url, String target)\r
+  {\r
+    if (viewport.applet == null)\r
+    {\r
+      System.out.println("Not running as applet - no browser available.");\r
+    }\r
+    else\r
+    {\r
+      try\r
+      {\r
+        if (url.indexOf(":") == -1)\r
+        {\r
+          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to\r
+          // form valid URL\r
+          // Should really use docbase, not codebase.\r
+          if (url.indexOf("/") == 0)\r
+          {\r
+            String codebase = viewport.applet.getCodeBase().toString();\r
+            url = codebase.substring(0, codebase.length()\r
+                    - viewport.applet.getCodeBase().getFile().length())\r
+                    + url;\r
+          }\r
+          else\r
+          {\r
+            url = viewport.applet.getCodeBase() + url;\r
+          }\r
+          System.out.println("Show url (prepended codebase): " + url);\r
+        }\r
+        else\r
+        {\r
+          System.out.println("Show url: " + url);\r
+        }\r
+        if (url.indexOf("javascript:") == 0)\r
+        {\r
+          // no target for the javascript context\r
+          viewport.applet.getAppletContext().showDocument(\r
+                  new java.net.URL(url));\r
+        }\r
+        else\r
+        {\r
+          viewport.applet.getAppletContext().showDocument(\r
+                  new java.net.URL(url), target);\r
+        }\r
+      } catch (Exception ex)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
+  }\r
+\r
+  // ////////////////////////////////////////////////////////////////////////////////\r
+  // JBuilder Graphics here\r
+\r
+  MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+  Menu fileMenu = new Menu("File");\r
+\r
+  MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+  MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+  MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+\r
+  MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+  MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+  MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+  Menu editMenu = new Menu("Edit");\r
+\r
+  Menu viewMenu = new Menu("View");\r
+\r
+  Menu colourMenu = new Menu("Colour");\r
+\r
+  Menu calculateMenu = new Menu("Calculate");\r
+\r
+  MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+  MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+  MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+  MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+  MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+  MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+  MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+  CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+  MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+  MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+  MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+  MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+  MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+  MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+  MenuItem PCAMenuItem = new MenuItem();\r
+\r
+  MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+  MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+  public Label statusBar = new Label();\r
+\r
+  Menu outputTextboxMenu = new Menu();\r
+\r
+  MenuItem clustalColour = new MenuItem();\r
+\r
+  MenuItem zappoColour = new MenuItem();\r
+\r
+  MenuItem taylorColour = new MenuItem();\r
+\r
+  MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+  MenuItem helixColour = new MenuItem();\r
+\r
+  MenuItem strandColour = new MenuItem();\r
+\r
+  MenuItem turnColour = new MenuItem();\r
+\r
+  MenuItem buriedColour = new MenuItem();\r
+\r
+  MenuItem userDefinedColour = new MenuItem();\r
+\r
+  MenuItem PIDColour = new MenuItem();\r
+\r
+  MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
+  MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
+  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+\r
+  CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+  MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+  MenuItem overviewMenuItem = new MenuItem();\r
+\r
+  MenuItem undoMenuItem = new MenuItem();\r
+\r
+  MenuItem redoMenuItem = new MenuItem();\r
+\r
+  CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+  MenuItem noColourmenuItem = new MenuItem();\r
+\r
+  CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+  MenuItem findMenuItem = new MenuItem();\r
+\r
+  CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+  MenuItem nucleotideColour = new MenuItem();\r
+\r
+  MenuItem deleteGroups = new MenuItem();\r
+\r
+  MenuItem grpsFromSelection = new MenuItem();\r
+\r
+  MenuItem delete = new MenuItem();\r
+\r
+  MenuItem copy = new MenuItem();\r
+\r
+  MenuItem cut = new MenuItem();\r
+\r
+  Menu pasteMenu = new Menu();\r
+\r
+  MenuItem pasteNew = new MenuItem();\r
+\r
+  MenuItem pasteThis = new MenuItem();\r
+\r
+  CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+\r
+  MenuItem font = new MenuItem();\r
+\r
+  CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
+  MenuItem modifyPID = new MenuItem();\r
+\r
+  MenuItem modifyConservation = new MenuItem();\r
+\r
+  CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
+          "Autocalculate Consensus", true);\r
+\r
+  Menu sortByTreeMenu = new Menu();\r
+\r
+  Menu sort = new Menu();\r
+\r
+  Menu calculate = new Menu();\r
+\r
+  MenuItem inputText = new MenuItem();\r
+\r
+  Menu helpMenu = new Menu();\r
+\r
+  MenuItem documentation = new MenuItem();\r
+\r
+  MenuItem about = new MenuItem();\r
+\r
+  CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+  CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
+  \r
+  CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
+  Menu autoAnnMenu=new Menu();\r
+  CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+  CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+  CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+  CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+  CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\r
+  private void jbInit() throws Exception\r
+  {\r
+\r
+    setMenuBar(alignFrameMenuBar);\r
+\r
+    MenuItem item;\r
+\r
+    // dynamically fill save as menu with available formats\r
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+    {\r
+\r
+      item = new MenuItem(\r
+              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+      item.addActionListener(new java.awt.event.ActionListener()\r
+      {\r
+        public void actionPerformed(ActionEvent e)\r
+        {\r
+          outputText_actionPerformed(e);\r
+        }\r
+      });\r
+\r
+      outputTextboxMenu.add(item);\r
+    }\r
+    closeMenuItem.addActionListener(this);\r
+    loadApplication.addActionListener(this);\r
+\r
+    loadTree.addActionListener(this);\r
+    loadAnnotations.addActionListener(this);\r
+    outputFeatures.addActionListener(this);\r
+    outputAnnotations.addActionListener(this);\r
+    selectAllSequenceMenuItem.addActionListener(this);\r
+    deselectAllSequenceMenuItem.addActionListener(this);\r
+    invertSequenceMenuItem.addActionListener(this);\r
+    remove2LeftMenuItem.setLabel("Remove Left");\r
+    remove2LeftMenuItem.addActionListener(this);\r
+    remove2RightMenuItem.setLabel("Remove Right");\r
+    remove2RightMenuItem.addActionListener(this);\r
+    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+    removeGappedColumnMenuItem.addActionListener(this);\r
+    removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+    removeAllGapsMenuItem.addActionListener(this);\r
+    viewBoxesMenuItem.setLabel("Boxes");\r
+    viewBoxesMenuItem.setState(true);\r
+    viewBoxesMenuItem.addItemListener(this);\r
+    viewTextMenuItem.setLabel("Text");\r
+    viewTextMenuItem.setState(true);\r
+    viewTextMenuItem.addItemListener(this);\r
+    sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+    sortPairwiseMenuItem.addActionListener(this);\r
+    sortIDMenuItem.setLabel("by ID");\r
+    sortIDMenuItem.addActionListener(this);\r
+    sortLengthMenuItem.setLabel("by Length");\r
+    sortLengthMenuItem.addActionListener(this);\r
+    sortGroupMenuItem.setLabel("by Group");\r
+    sortGroupMenuItem.addActionListener(this);\r
+    removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+    removeRedundancyMenuItem.addActionListener(this);\r
+    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+    pairwiseAlignmentMenuItem.addActionListener(this);\r
+    PCAMenuItem.setLabel("Principal Component Analysis");\r
+    PCAMenuItem.addActionListener(this);\r
+    averageDistanceTreeMenuItem\r
+            .setLabel("Average Distance Using % Identity");\r
+    averageDistanceTreeMenuItem.addActionListener(this);\r
+    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+    neighbourTreeMenuItem.addActionListener(this);\r
+    statusBar.setBackground(Color.white);\r
+    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+    statusBar.setText("Status bar");\r
+    outputTextboxMenu.setLabel("Output to Textbox");\r
+    clustalColour.setLabel("Clustalx");\r
+\r
+    clustalColour.addActionListener(this);\r
+    zappoColour.setLabel("Zappo");\r
+    zappoColour.addActionListener(this);\r
+    taylorColour.setLabel("Taylor");\r
+    taylorColour.addActionListener(this);\r
+    hydrophobicityColour.setLabel("Hydrophobicity");\r
+    hydrophobicityColour.addActionListener(this);\r
+    helixColour.setLabel("Helix Propensity");\r
+    helixColour.addActionListener(this);\r
+    strandColour.setLabel("Strand Propensity");\r
+    strandColour.addActionListener(this);\r
+    turnColour.setLabel("Turn Propensity");\r
+    turnColour.addActionListener(this);\r
+    buriedColour.setLabel("Buried Index");\r
+    buriedColour.addActionListener(this);\r
+    userDefinedColour.setLabel("User Defined...");\r
+    userDefinedColour.addActionListener(this);\r
+    PIDColour.setLabel("Percentage Identity");\r
+    PIDColour.addActionListener(this);\r
+    BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+    BLOSUM62Colour.addActionListener(this);\r
+    avDistanceTreeBlosumMenuItem\r
+            .setLabel("Average Distance Using BLOSUM62");\r
+    avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+    njTreeBlosumMenuItem.addActionListener(this);\r
+    annotationPanelMenuItem.setLabel("Show Annotations");\r
+    annotationPanelMenuItem.addItemListener(this);\r
+    colourTextMenuItem.setLabel("Colour Text");\r
+    colourTextMenuItem.addItemListener(this);\r
+    displayNonconservedMenuItem.setLabel("Show nonconserved");\r
+    displayNonconservedMenuItem.addItemListener(this);\r
+    alProperties.addActionListener(this);\r
+    overviewMenuItem.setLabel("Overview Window");\r
+    overviewMenuItem.addActionListener(this);\r
+    undoMenuItem.setEnabled(false);\r
+    undoMenuItem.setLabel("Undo");\r
+    undoMenuItem.addActionListener(this);\r
+    redoMenuItem.setEnabled(false);\r
+    redoMenuItem.setLabel("Redo");\r
+    redoMenuItem.addActionListener(this);\r
+    conservationMenuItem.setLabel("by Conservation");\r
+    conservationMenuItem.addItemListener(this);\r
+    noColourmenuItem.setLabel("None");\r
+    noColourmenuItem.addActionListener(this);\r
+    wrapMenuItem.setLabel("Wrap");\r
+    wrapMenuItem.addItemListener(this);\r
+    renderGapsMenuItem.setLabel("Show Gaps");\r
+    renderGapsMenuItem.setState(true);\r
+    renderGapsMenuItem.addItemListener(this);\r
+    findMenuItem.setLabel("Find...");\r
+    findMenuItem.addActionListener(this);\r
+    abovePIDThreshold.setLabel("Above Identity Threshold");\r
+    abovePIDThreshold.addItemListener(this);\r
+    nucleotideColour.setLabel("Nucleotide");\r
+    nucleotideColour.addActionListener(this);\r
+    deleteGroups.setLabel("Undefine Groups");\r
+    deleteGroups.addActionListener(this);\r
+    grpsFromSelection.setLabel("Make Groups for selection");\r
+    grpsFromSelection.addActionListener(this);\r
+    copy.setLabel("Copy");\r
+    copy.addActionListener(this);\r
+    cut.setLabel("Cut");\r
+    cut.addActionListener(this);\r
+    delete.setLabel("Delete");\r
+    delete.addActionListener(this);\r
+    pasteMenu.setLabel("Paste");\r
+    pasteNew.setLabel("To New Alignment");\r
+    pasteNew.addActionListener(this);\r
+    pasteThis.setLabel("Add To This Alignment");\r
+    pasteThis.addActionListener(this);\r
+    applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+    applyToAllGroups.setState(true);\r
+    applyToAllGroups.addItemListener(this);\r
+    font.setLabel("Font...");\r
+    font.addActionListener(this);\r
+    scaleAbove.setLabel("Scale Above");\r
+    scaleAbove.setState(true);\r
+    scaleAbove.setEnabled(false);\r
+    scaleAbove.addItemListener(this);\r
+    scaleLeft.setEnabled(false);\r
+    scaleLeft.setState(true);\r
+    scaleLeft.setLabel("Scale Left");\r
+    scaleLeft.addItemListener(this);\r
+    scaleRight.setEnabled(false);\r
+    scaleRight.setState(true);\r
+    scaleRight.setLabel("Scale Right");\r
+    scaleRight.addItemListener(this);\r
+    modifyPID.setLabel("Modify Identity Threshold...");\r
+    modifyPID.addActionListener(this);\r
+    modifyConservation.setLabel("Modify Conservation Threshold...");\r
+    modifyConservation.addActionListener(this);\r
+    sortByTreeMenu.setLabel("By Tree Order");\r
+    sort.setLabel("Sort");\r
+    calculate.setLabel("Calculate Tree");\r
+    autoCalculate.addItemListener(this);\r
+    inputText.setLabel("Input from textbox");\r
+    inputText.addActionListener(this);\r
+    centreColumnLabelFlag.setLabel("Centre column labels");\r
+    centreColumnLabelFlag.addItemListener(this);\r
+    followMouseOverFlag.setLabel("Automatic Scrolling");\r
+    followMouseOverFlag.addItemListener(this);\r
+    helpMenu.setLabel("Help");\r
+    documentation.setLabel("Documentation");\r
+    documentation.addActionListener(this);\r
+\r
+    about.setLabel("About...");\r
+    about.addActionListener(this);\r
+    seqLimits.setState(true);\r
+    seqLimits.setLabel("Show Sequence Limits");\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(false);\r
+    annotationColour.setLabel("by Annotation...");\r
+    annotationColour.addActionListener(this);\r
+    invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+    invertColSel.setLabel("Invert Column Selection");\r
+    menu1.setLabel("Show");\r
+    showColumns.setLabel("All Columns ");\r
+    showSeqs.setLabel("All Sequences");\r
+    menu2.setLabel("Hide");\r
+    hideColumns.setLabel("Selected Columns");\r
+    hideSequences.setLabel("Selected Sequences");\r
+    hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");\r
+    hideAllSelection.setLabel("Selected Region");\r
+    showAllHidden.setLabel("All Sequences and Columns");\r
+    showGroupConsensus.setLabel("Group Consensus");\r
+    showGroupConservation.setLabel("Group Conservation");\r
+    showConsensusHistogram.setLabel("Show Consensus Histogram");\r
+    showSequenceLogo.setLabel("Show Consensus Logo");\r
+    applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
+    applyAutoAnnotationSettings.setState(true);\r
+    autoAnnMenu.setLabel("Autocalculated Annotation");\r
+    \r
+    invertColSel.addActionListener(this);\r
+    showColumns.addActionListener(this);\r
+    showSeqs.addActionListener(this);\r
+    hideColumns.addActionListener(this);\r
+    hideSequences.addActionListener(this);\r
+    hideAllButSelection.addActionListener(this);\r
+    hideAllSelection.addActionListener(this);\r
+    showAllHidden.addActionListener(this);\r
+    showGroupConsensus.addItemListener(this);\r
+    showGroupConservation.addItemListener(this);\r
+    showConsensusHistogram.addItemListener(this);\r
+    showSequenceLogo.addItemListener(this);\r
+    applyAutoAnnotationSettings.addItemListener(this);\r
+    formatMenu.setLabel("Format");\r
+    selectMenu.setLabel("Select");\r
+    newView.setLabel("New View");\r
+    newView.addActionListener(this);\r
+    alignFrameMenuBar.add(fileMenu);\r
+    alignFrameMenuBar.add(editMenu);\r
+    alignFrameMenuBar.add(selectMenu);\r
+    alignFrameMenuBar.add(viewMenu);\r
+    alignFrameMenuBar.add(formatMenu);\r
+    alignFrameMenuBar.add(colourMenu);\r
+    alignFrameMenuBar.add(calculateMenu);\r
+    alignFrameMenuBar.add(helpMenu);\r
+\r
+    fileMenu.add(inputText);\r
+    fileMenu.add(loadTree);\r
+    fileMenu.add(loadAnnotations);\r
+\r
+    fileMenu.addSeparator();\r
+    fileMenu.add(outputTextboxMenu);\r
+    fileMenu.add(outputFeatures);\r
+    fileMenu.add(outputAnnotations);\r
+\r
+    if (jalviewServletURL != null)\r
+    {\r
+      fileMenu.add(loadApplication);\r
+    }\r
+\r
+    fileMenu.addSeparator();\r
+    fileMenu.add(closeMenuItem);\r
+\r
+    editMenu.add(undoMenuItem);\r
+    editMenu.add(redoMenuItem);\r
+    editMenu.add(cut);\r
+    editMenu.add(copy);\r
+    editMenu.add(pasteMenu);\r
+    editMenu.add(delete);\r
+    editMenu.addSeparator();\r
+    editMenu.add(remove2LeftMenuItem);\r
+    editMenu.add(remove2RightMenuItem);\r
+    editMenu.add(removeGappedColumnMenuItem);\r
+    editMenu.add(removeAllGapsMenuItem);\r
+    editMenu.add(removeRedundancyMenuItem);\r
+    viewMenu.add(newView);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(menu1);\r
+    viewMenu.add(menu2);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(followMouseOverFlag);\r
+    viewMenu.add(annotationPanelMenuItem);\r
+    autoAnnMenu.add(applyAutoAnnotationSettings);\r
+    autoAnnMenu.add(showConsensusHistogram);\r
+    autoAnnMenu.add(showSequenceLogo);\r
+    autoAnnMenu.addSeparator();\r
+    autoAnnMenu.add(showGroupConservation);\r
+    autoAnnMenu.add(showGroupConsensus);\r
+    viewMenu.add(autoAnnMenu);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(sequenceFeatures);\r
+    viewMenu.add(featureSettings);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(alProperties);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(overviewMenuItem);\r
+    colourMenu.add(applyToAllGroups);\r
+    colourMenu.addSeparator();\r
+    colourMenu.add(noColourmenuItem);\r
+    colourMenu.add(clustalColour);\r
+    colourMenu.add(BLOSUM62Colour);\r
+    colourMenu.add(PIDColour);\r
+    colourMenu.add(zappoColour);\r
+    colourMenu.add(taylorColour);\r
+    colourMenu.add(hydrophobicityColour);\r
+    colourMenu.add(helixColour);\r
+    colourMenu.add(strandColour);\r
+    colourMenu.add(turnColour);\r
+    colourMenu.add(buriedColour);\r
+    colourMenu.add(nucleotideColour);\r
+    colourMenu.add(userDefinedColour);\r
+    colourMenu.addSeparator();\r
+    colourMenu.add(conservationMenuItem);\r
+    colourMenu.add(modifyConservation);\r
+    colourMenu.add(abovePIDThreshold);\r
+    colourMenu.add(modifyPID);\r
+    colourMenu.add(annotationColour);\r
+    calculateMenu.add(sort);\r
+    calculateMenu.add(calculate);\r
+    calculateMenu.addSeparator();\r
+    calculateMenu.add(pairwiseAlignmentMenuItem);\r
+    calculateMenu.add(PCAMenuItem);\r
+    calculateMenu.add(autoCalculate);\r
+    this.add(statusBar, BorderLayout.SOUTH);\r
+    pasteMenu.add(pasteNew);\r
+    pasteMenu.add(pasteThis);\r
+    sort.add(sortIDMenuItem);\r
+    sort.add(sortLengthMenuItem);\r
+    sort.add(sortByTreeMenu);\r
+    sort.add(sortGroupMenuItem);\r
+    sort.add(sortPairwiseMenuItem);\r
+    calculate.add(averageDistanceTreeMenuItem);\r
+    calculate.add(neighbourTreeMenuItem);\r
+    calculate.add(avDistanceTreeBlosumMenuItem);\r
+    calculate.add(njTreeBlosumMenuItem);\r
+    helpMenu.add(documentation);\r
+    helpMenu.add(about);\r
+    menu1.add(showColumns);\r
+    menu1.add(showSeqs);\r
+    menu1.add(showAllHidden);\r
+    menu2.add(hideColumns);\r
+    menu2.add(hideSequences);\r
+    menu2.add(hideAllSelection);\r
+    menu2.add(hideAllButSelection);\r
+    formatMenu.add(font);\r
+    formatMenu.add(seqLimits);\r
+    formatMenu.add(wrapMenuItem);\r
+    formatMenu.add(scaleAbove);\r
+    formatMenu.add(scaleLeft);\r
+    formatMenu.add(scaleRight);\r
+    formatMenu.add(viewBoxesMenuItem);\r
+    formatMenu.add(viewTextMenuItem);\r
+    formatMenu.add(colourTextMenuItem);\r
+    formatMenu.add(displayNonconservedMenuItem);\r
+    formatMenu.add(renderGapsMenuItem);\r
+    formatMenu.add(centreColumnLabelFlag);\r
+    selectMenu.add(findMenuItem);\r
+    selectMenu.addSeparator();\r
+    selectMenu.add(selectAllSequenceMenuItem);\r
+    selectMenu.add(deselectAllSequenceMenuItem);\r
+    selectMenu.add(invertSequenceMenuItem);\r
+    selectMenu.add(invertColSel);\r
+    selectMenu.add(grpsFromSelection);\r
+    selectMenu.add(deleteGroups);\r
+\r
+  }\r
+\r
+  MenuItem featureSettings = new MenuItem();\r
+\r
+  CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+\r
+  MenuItem annotationColour = new MenuItem();\r
+\r
+  MenuItem invertColSel = new MenuItem();\r
+\r
+  Menu menu1 = new Menu();\r
+\r
+  MenuItem showColumns = new MenuItem();\r
+\r
+  MenuItem showSeqs = new MenuItem();\r
+\r
+  Menu menu2 = new Menu();\r
+\r
+  MenuItem hideColumns = new MenuItem();\r
+\r
+  MenuItem hideSequences = new MenuItem();\r
+\r
+  MenuItem hideAllButSelection = new MenuItem();\r
+\r
+  MenuItem hideAllSelection = new MenuItem();\r
+\r
+  MenuItem showAllHidden = new MenuItem();\r
+\r
+  Menu formatMenu = new Menu();\r
+\r
+  Menu selectMenu = new Menu();\r
+\r
+  MenuItem newView = new MenuItem();\r
+\r
+  /**\r
+   * Attach the alignFrame panels after embedding menus, if necessary. This used\r
+   * to be called setEmbedded, but is now creates the dropdown menus in a\r
+   * platform independent manner to avoid OSX/Mac menu appendage daftness.\r
+   * \r
+   * @param reallyEmbedded\r
+   *          true to attach the view to the applet area on the page rather than\r
+   *          in a new window\r
+   */\r
+  public void createAlignFrameWindow(boolean reallyEmbedded, String title)\r
+  {\r
+    if (reallyEmbedded)\r
+    {\r
+      // ////\r
+      // Explicly build the embedded menu panel for the on-page applet\r
+      //\r
+      // view cannot be closed if its actually on the page\r
+      fileMenu.remove(closeMenuItem);\r
+      fileMenu.remove(3); // Remove Seperator\r
+      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",\r
+              Font.PLAIN, 10, false); // use our own fonts.\r
+      // and actually add the components to the applet area\r
+      viewport.applet.setLayout(new BorderLayout());\r
+      viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+      viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+      alignPanel.setSize(viewport.applet.getSize().width,\r
+              viewport.applet.getSize().height - embeddedMenu.HEIGHT\r
+                      - statusBar.HEIGHT);\r
+      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+      final AlignFrame me = this;\r
+      viewport.applet.addFocusListener(new FocusListener()\r
+      {\r
+        \r
+        @Override\r
+        public void focusLost(FocusEvent e)\r
+        {\r
+          if (me.viewport.applet.currentAlignFrame==me) {\r
+                  me.viewport.applet.currentAlignFrame = null;\r
+        }}\r
+        \r
+        @Override\r
+        public void focusGained(FocusEvent e)\r
+        {\r
+          me.viewport.applet.currentAlignFrame = me;\r
+        }\r
+      });\r
+      viewport.applet.validate();\r
+    }\r
+    else\r
+    {\r
+      // //////\r
+      // test and embed menu bar if necessary.\r
+      //\r
+      if (embedMenuIfNeeded(alignPanel))\r
+      {\r
+        // adjust for status bar height too\r
+        alignPanel.setSize(getSize().width, getSize().height\r
+                - statusBar.HEIGHT);\r
+      }\r
+      add(statusBar, BorderLayout.SOUTH);\r
+      add(alignPanel, BorderLayout.CENTER);\r
+      // and register with the applet so it can pass external API calls to us\r
+      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+              DEFAULT_HEIGHT);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * create a new binding between structures in an existing jmol viewer instance\r
+   * and an alignpanel with sequences that have existing PDBFile entries. Note,\r
+   * this does not open a new Jmol window, or modify the display of the\r
+   * structures in the original jmol window. Note This method doesn't work\r
+   * without an additional javascript library to exchange messages between the\r
+   * distinct applets. See http://issues.jalview.org/browse/JAL-621\r
+   * \r
+   * @param viewer\r
+   *          JmolViewer instance\r
+   * @param sequenceIds\r
+   *          - sequence Ids to search for associations\r
+   */\r
+  public SequenceStructureBinding addStructureViewInstance(\r
+          Object jmolviewer, String[] sequenceIds)\r
+  {\r
+    org.jmol.api.JmolViewer viewer = null;\r
+    try\r
+    {\r
+      viewer = (org.jmol.api.JmolViewer) jmolviewer;\r
+    } catch (ClassCastException ex)\r
+    {\r
+      System.err.println("Unsupported viewer object :"\r
+              + jmolviewer.getClass());\r
+    }\r
+    if (viewer == null)\r
+    {\r
+      System.err.println("Can't use this object as a structure viewer:"\r
+              + jmolviewer.getClass());\r
+      return null;\r
+    }\r
+    SequenceI[] seqs = null;\r
+    if (sequenceIds == null || sequenceIds.length == 0)\r
+    {\r
+      seqs = viewport.getAlignment().getSequencesArray();\r
+    }\r
+    else\r
+    {\r
+      Vector sqi = new Vector();\r
+      AlignmentI al = viewport.getAlignment();\r
+      for (int sid = 0; sid < sequenceIds.length; sid++)\r
+      {\r
+        SequenceI sq = al.findName(sequenceIds[sid]);\r
+        if (sq != null)\r
+        {\r
+          sqi.addElement(sq);\r
+        }\r
+      }\r
+      if (sqi.size() > 0)\r
+      {\r
+        seqs = new SequenceI[sqi.size()];\r
+        for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)\r
+        {\r
+          seqs[sid] = (SequenceI) sqi.elementAt(sid);\r
+        }\r
+      }\r
+      else\r
+      {\r
+        return null;\r
+      }\r
+    }\r
+    ExtJmol jmv = null;\r
+    // TODO: search for a jmv that involves viewer\r
+    if (jmv == null)\r
+    { // create a new viewer/jalview binding.\r
+      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
+    }\r
+    return jmv;\r
+\r
+  }\r
+  /**\r
+   * bind a pdb file to a sequence in the current view\r
+   * \r
+   * @param sequenceId\r
+   *          - sequenceId within the dataset.\r
+   * @param pdbEntryString\r
+   *          - the short name for the PDB file\r
+   * @param pdbFile\r
+   *          - pdb file - either a URL or a valid PDB file.\r
+   * @return true if binding was as success TODO: consider making an exception\r
+   *         structure for indicating when PDB parsing or sequenceId location\r
+   *         fails.\r
+   */\r
+  public boolean addPdbFile(String sequenceId, String pdbEntryString,\r
+          String pdbFile)\r
+  {\r
+    SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);\r
+    boolean needtoadd = false;\r
+    if (toaddpdb != null)\r
+    {\r
+      Vector pdbe = toaddpdb.getPDBId();\r
+      PDBEntry pdbentry = null;\r
+      if (pdbe != null && pdbe.size() > 0)\r
+      {\r
+        for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)\r
+        {\r
+          pdbentry = (PDBEntry) pdbe.elementAt(pe);\r
+          if (!pdbentry.getId().equals(pdbEntryString)\r
+                  && !pdbentry.getFile().equals(pdbFile))\r
+          {\r
+            pdbentry = null;\r
+          }\r
+          else\r
+          {\r
+            continue;\r
+          }\r
+        }\r
+      }\r
+      if (pdbentry == null)\r
+      {\r
+        pdbentry = new PDBEntry();\r
+        pdbentry.setId(pdbEntryString);\r
+        pdbentry.setFile(pdbFile);\r
+        needtoadd = true; // add this new entry to sequence.\r
+      }\r
+      // resolve data source\r
+      // TODO: this code should be a refactored to an io package\r
+      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");\r
+      if (protocol == null)\r
+      {\r
+        return false;\r
+      }\r
+      if (needtoadd)\r
+      {\r
+        // make a note of the access mode and add\r
+        if (pdbentry.getProperty() == null)\r
+        {\r
+          pdbentry.setProperty(new Hashtable());\r
+        }\r
+        pdbentry.getProperty().put("protocol", protocol);\r
+        toaddpdb.addPDBId(pdbentry);\r
+      }\r
+    }\r
+    return true;\r
+  }\r
+\r
+  private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)\r
+  {\r
+    if (seqs != null)\r
+    {\r
+      Vector sequences = new Vector();\r
+      for (int i = 0; i < seqs.length; i++)\r
+      {\r
+        if (seqs[i] != null)\r
+        {\r
+          sequences.addElement(new Object[]\r
+          { seqs[i], (chains != null) ? chains[i] : null });\r
+        }\r
+      }\r
+      seqs = new SequenceI[sequences.size()];\r
+      chains = new String[sequences.size()];\r
+      for (int i = 0, isize = sequences.size(); i < isize; i++)\r
+      {\r
+        Object[] oj = (Object[]) sequences.elementAt(i);\r
+\r
+        seqs[i] = (SequenceI) oj[0];\r
+        chains[i] = (String) oj[1];\r
+      }\r
+    }\r
+    return new Object[]\r
+    { seqs, chains };\r
+\r
+  }\r
+\r
+  public void newStructureView(JalviewLite applet, PDBEntry pdb,\r
+          SequenceI[] seqs, String[] chains, String protocol)\r
+  {\r
+    // Scrub any null sequences from the array\r
+    Object[] sqch = cleanSeqChainArrays(seqs, chains);\r
+    seqs = (SequenceI[]) sqch[0];\r
+    chains = (String[]) sqch[1];\r
+    if (seqs == null || seqs.length == 0)\r
+    {\r
+      System.err\r
+              .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");\r
+    }\r
+    if (protocol == null || protocol.trim().length() == 0\r
+            || protocol.equals("null"))\r
+    {\r
+      protocol = (String) pdb.getProperty().get("protocol");\r
+      if (protocol == null)\r
+      {\r
+        System.err.println("Couldn't work out protocol to open structure: "\r
+                + pdb.getId());\r
+        return;\r
+      }\r
+    }\r
+    if (applet.useXtrnalSviewer)\r
+    {\r
+      // register the association(s) and quit, don't create any windows.\r
+      if (StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
+        System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
+      }\r
+      return;\r
+    }\r
+    if (applet.isAlignPdbStructures() && applet.jmolAvailable)\r
+    {\r
+      // can only do alignments with Jmol\r
+      // find the last jmol window assigned to this alignment\r
+      jalview.appletgui.AppletJmol ajm = null, tajm;\r
+      Vector jmols = applet\r
+              .getAppletWindow(jalview.appletgui.AppletJmol.class);\r
+      for (int i = 0, iSize = jmols.size(); i < iSize; i++)\r
+      {\r
+        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);\r
+        if (tajm.ap.alignFrame == this)\r
+        {\r
+          ajm = tajm;\r
+          break;\r
+        }\r
+      }\r
+      if (ajm != null)\r
+      {\r
+        System.err\r
+                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");\r
+        // try and add the pdb structure\r
+        // ajm.addS\r
+        ajm = null;\r
+      }\r
+    }\r
+    // otherwise, create a new window\r
+    if (applet.jmolAvailable)\r
+    {\r
+      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,\r
+              protocol);\r
+      applet.lastFrameX += 40;\r
+      applet.lastFrameY += 40;\r
+    }\r
+    else\r
+    {\r
+      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);\r
+    }\r
+\r
+  }\r
+\r
+  public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,\r
+          SequenceI[][] seqs, String[][] chains, String[] protocols)\r
+  {\r
+    // TODO Auto-generated method stub\r
+    System.err.println("Aligned Structure View: Not yet implemented.");\r
+  }\r
+\r
+  /**\r
+   * modify the current selection, providing the user has not made a selection already.\r
+   * @param sel - sequences from this alignment \r
+   * @param csel - columns to be selected on the alignment\r
+   */\r
+  public void select(SequenceGroup sel, ColumnSelection csel)\r
+  {\r
+    alignPanel.seqPanel.selection(sel, csel, null);\r
+  }\r
+}\r