X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=729096bd70f9ff7d53f6a3e4f4375960185390c0;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=7fc240f4d84cd8d76114fdf2db961d68012ece14;hpb=141ad7e898f94594bacb1c77eabbcd837505409c;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
old mode 100755
new mode 100644
index 7fc240f..729096b
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,1354 +1,473 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class AlignViewport
-{
-  int startRes;
-  int endRes;
-
-  int startSeq;
-  int endSeq;
-
-
-  boolean cursorMode = false;
-
-  boolean showJVSuffix = true;
-  boolean showText = true;
-  boolean showColourText = false;
-  boolean showBoxes = true;
-  boolean wrapAlignment = false;
-  boolean renderGaps = true;
-  boolean showSequenceFeatures = false;
-  boolean showAnnotation = true;
-  boolean showConservation = true;
-  boolean showQuality = true;
-  boolean showConsensus = true;
-  boolean upperCasebold = false;
-
-  boolean colourAppliesToAllGroups = true;
-  ColourSchemeI globalColourScheme = null;
-  boolean conservationColourSelected = false;
-  boolean abovePIDThreshold = false;
-
-  SequenceGroup selectionGroup;
-
-  int charHeight;
-  int charWidth;
-  int wrappedWidth;
-
-  Font font = new Font("SansSerif", Font.PLAIN, 10);
-  boolean validCharWidth = true;
-  AlignmentI alignment;
-
-  ColumnSelection colSel = new ColumnSelection();
-
-  int threshold;
-  int increment;
-
-  NJTree currentTree = null;
-
-  boolean scaleAboveWrapped = true;
-  boolean scaleLeftWrapped = true;
-  boolean scaleRightWrapped = true;
-
-  // The following vector holds the features which are
- // currently visible, in the correct order or rendering
-  public Hashtable featuresDisplayed;
-
-  boolean hasHiddenColumns = false;
-  boolean hasHiddenRows = false;
-  boolean showHiddenMarkers = true;
-
-
-  public Hashtable [] hconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
-
-  boolean autocalculateConsensus = true;
-
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
-  boolean ignoreGapsInConsensusCalculation = false;
-
-  jalview.bin.JalviewLite applet;
-
-  Hashtable sequenceColours;
-
-  boolean MAC = false;
-
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-
-  String sequenceSetID;
-
-  Hashtable hiddenRepSequences;
-
-  public AlignViewport(AlignmentI al, JalviewLite applet)
-  {
-    this.applet = applet;
-    setAlignment(al);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
-    setFont(font);
-
-    if(System.getProperty("os.name").startsWith("Mac"))
-      MAC = true;
-
-    if (applet != null)
-    {
-      String param = applet.getParameter("showFullId");
-      if (param != null)
-      {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showAnnotation");
-      if (param != null)
-      {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("showConsensus");
-      if (param != null)
-      {
-        showConsensus = Boolean.valueOf(param).booleanValue();
-      }
-
-      param = applet.getParameter("upperCase");
-      if (param != null)
-      {
-        if(param.equalsIgnoreCase("bold"))
-          upperCasebold = true;
-      }
-
-    }
-
-    if (applet != null)
-    {
-      String colour = applet.getParameter("defaultColour");
-
-      if(colour == null)
-      {
-        colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
-          colour = "User Defined";
-      }
-
-      if(colour != null)
-      {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
-        if (globalColourScheme != null)
-        {
-          globalColourScheme.setConsensus(hconsensus);
-        }
-      }
-
-      if(applet.getParameter("userDefinedColour")!=null)
-      {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
-            applet.getParameter("userDefinedColour"));
-      }
-
-      if(hconsensus==null)
-      {
-        if(!alignment.isNucleotide())
-        {
-          conservation = new AlignmentAnnotation("Conservation",
-              "Conservation of total alignment less than " +
-              ConsPercGaps + "% gaps",
-              new Annotation[1], 0f,
-              11f,
-              AlignmentAnnotation.BAR_GRAPH);
-          conservation.hasText = true;
-          conservation.autoCalculated = true;
-
-
-
-          if (showConservation)
-          {
-            alignment.addAnnotation(conservation);
-          }
-
-          if (showQuality)
-          {
-            quality = new AlignmentAnnotation("Quality",
-                                              "Alignment Quality based on Blosum62 scores",
-                                              new Annotation[1],
-                                              0f,
-                                              11f,
-                                              AlignmentAnnotation.BAR_GRAPH);
-            quality.hasText = true;
-            quality.autoCalculated = true;
-
-            alignment.addAnnotation(quality);
-          }
-        }
-
-        consensus = new AlignmentAnnotation("Consensus", "PID",
-                                             new Annotation[1], 0f, 100f,
-                                             AlignmentAnnotation.BAR_GRAPH);
-        consensus.hasText = true;
-        consensus.autoCalculated = true;
-
-         if (showConsensus)
-         {
-           alignment.addAnnotation(consensus);
-         }
-      }
-    }
-  }
-
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
-
-  class ConservationThread extends Thread
-  {
-    AlignmentPanel ap;
-    public ConservationThread(AlignmentPanel ap)
-    {
-      this.ap = ap;
-    }
-
-    public void run()
-    {
-      try
-      {
-        updatingConservation = true;
-
-        while (UPDATING_CONSERVATION)
-        {
-          try
-          {
-            if (ap != null)
-            {
-              ap.repaint();
-            }
-            Thread.sleep(200);
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-        }
-
-        UPDATING_CONSERVATION = true;
-
-
-        int alWidth = alignment.getWidth();
-        if(alWidth<0)
-          return;
-
-        Conservation cons = new jalview.analysis.Conservation("All",
-            jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alWidth -1);
-
-        cons.calculate();
-        cons.verdict(false, ConsPercGaps);
-
-        if (quality!=null)
-        {
-          cons.findQuality();
-        }
-
-        char [] sequence = cons.getConsSequence().getSequence();
-        float minR;
-        float minG;
-        float minB;
-        float maxR;
-        float maxG;
-        float maxB;
-        minR = 0.3f;
-        minG = 0.0f;
-        minB = 0f;
-        maxR = 1.0f - minR;
-        maxG = 0.9f - minG;
-        maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
-        float min = 0f;
-        float max = 11f;
-        float qmin = 0f;
-        float qmax = 0f;
-
-        char c;
-
-        conservation.annotations = new Annotation[alWidth];
-
-        if (quality!=null)
-        {
-          quality.graphMax = cons.qualityRange[1].floatValue();
-          quality.annotations = new Annotation[alWidth];
-          qmin = cons.qualityRange[0].floatValue();
-          qmax = cons.qualityRange[1].floatValue();
-        }
-
-        for (int i = 0; i < alWidth; i++)
-        {
-          float value = 0;
-
-          c = sequence[i];
-
-          if (Character.isDigit(c))
-            value = (int) (c - '0');
-          else if (c == '*')
-            value = 11;
-          else if (c == '+')
-            value = 10;
-
-          float vprop = value - min;
-          vprop /= max;
-          conservation.annotations[i] =
-              new Annotation(String.valueOf(c),
-                             String.valueOf(value), ' ', value,
-                             new Color(minR + (maxR * vprop),
-                                       minG + (maxG * vprop),
-                                       minB + (maxB * vprop)));
-
-          // Quality calc
-          if (quality!=null)
-          {
-            value = ( (Double) cons.quality.elementAt(i)).floatValue();
-            vprop = value - qmin;
-            vprop /= qmax;
-            quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
-                                             value,
-                                             new Color(minR + (maxR * vprop),
-                minG + (maxG * vprop),
-                minB + (maxB * vprop)));
-          }
-        }
-      }
-      catch (OutOfMemoryError error)
-      {
-        System.out.println("Out of memory calculating conservation!!");
-        conservation = null;
-        quality = null;
-        System.gc();
-      }
-
-      UPDATING_CONSERVATION = false;
-      updatingConservation = false;
-
-      if(ap!=null)
-      {
-        ap.repaint();
-      }
-
-    }
-  }
-
-
-  ConservationThread conservationThread;
-
-  ConsensusThread consensusThread;
-
-  boolean consUpdateNeeded = false;
-
-  static boolean UPDATING_CONSENSUS = false;
-
-  static boolean UPDATING_CONSERVATION = false;
-
-  boolean updatingConsensus = false;
-
-  boolean updatingConservation = false;
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateConservation(final AlignmentPanel ap)
-  {
-    if (alignment.isNucleotide() || conservation==null)
-      return;
-
-    conservationThread = new ConservationThread(ap);
-    conservationThread.start();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateConsensus(final AlignmentPanel ap)
-  {
-    consensusThread = new ConsensusThread(ap);
-    consensusThread.start();
-  }
-
-
-  class ConsensusThread extends Thread
-  {
-    AlignmentPanel ap;
-    public ConsensusThread(AlignmentPanel ap)
-    {
-      this.ap = ap;
-    }
-    public void run()
-    {
-      updatingConsensus = true;
-      while (UPDATING_CONSENSUS)
-      {
-        try
-        {
-          if (ap != null)
-          {
-            ap.repaint();
-          }
-
-          Thread.sleep(200);
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-
-
-      UPDATING_CONSENSUS = true;
-
-      try
-      {
-        int aWidth = alignment.getWidth();
-        if(aWidth<0)
-          return;
-
-        consensus.annotations = null;
-        consensus.annotations = new Annotation[aWidth];
-
-
-        hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(),
-                              0,
-                              alignment.getWidth(),
-                              hconsensus);
-
-        for (int i = 0; i < aWidth; i++)
-        {
-          float value = 0;
-          if (ignoreGapsInConsensusCalculation)
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                floatValue();
-          else
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                floatValue();
-
-          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
-          if (maxRes.length() > 1)
-          {
-            mouseOver = "[" + maxRes + "] ";
-            maxRes = "+";
-          }
-
-          mouseOver += ( (int) value + "%");
-          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-        }
-
-
-        if (globalColourScheme != null)
-          globalColourScheme.setConsensus(hconsensus);
-
-      }
-      catch (OutOfMemoryError error)
-      {
-        alignment.deleteAnnotation(consensus);
-
-        consensus = null;
-        hconsensus = null;
-        System.out.println("Out of memory calculating consensus!!");
-        System.gc();
-      }
-      UPDATING_CONSENSUS = false;
-      updatingConsensus = false;
-
-      if (ap != null)
-      {
-        ap.repaint();
-      }
-    }
-  }
-
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
-   * @return consensus sequence as a new sequence object
-   */
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
-   * @return consensus sequence as a new sequence object
-   */
-  public SequenceI getConsensusSeq()
-  {
-    if (consensus==null)
-      return null;
-    StringBuffer seqs=new StringBuffer();
-    for (int i=0; i<consensus.annotations.length; i++) {
-      if (consensus.annotations[i]!=null) {
-        if (consensus.annotations[i].description.charAt(0) == '[')
-          seqs.append(consensus.annotations[i].description.charAt(1));
-        else
-          seqs.append(consensus.annotations[i].displayCharacter);
-      }
-    }
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-  public SequenceGroup getSelectionGroup()
-  {
-    return selectionGroup;
-  }
-
-  public void setSelectionGroup(SequenceGroup sg)
-  {
-    selectionGroup = sg;
-  }
-
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
-
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
-
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  public void setEndRes(int res)
-  {
-    if (res > alignment.getWidth() - 1)
-    {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
-    }
-    if (res < 0)
-    {
-      res = 0;
-    }
-    this.endRes = res;
-  }
-
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;
-  }
-
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
-
-  java.awt.Frame nullFrame;
-  public void setFont(Font f)
-  {
-    font = f;
-    if(nullFrame == null)
-    {
-      nullFrame = new java.awt.Frame();
-      nullFrame.addNotify();
-    }
-
-    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight(fm.getHeight());
-    charWidth = fm.charWidth('M');
-
-    if(upperCasebold)
-    {
-      Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
-      fm = nullFrame.getGraphics().getFontMetrics(f2);
-      charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
-    }
-  }
-
-  public Font getFont()
-  {
-    return font;
-  }
-
-  public int getCharWidth()
-  {
-    return charWidth;
-  }
-
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
-
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
-
-  public void setWrappedWidth(int w)
-  {
-    this.wrappedWidth = w;
-  }
-
-  public int getwrappedWidth()
-  {
-    return wrappedWidth;
-  }
-
-  public AlignmentI getAlignment()
-  {
-    return alignment;
-  }
-
-  public void setAlignment(AlignmentI align)
-  {
-    this.alignment = align;
-  }
-
-  public void setWrapAlignment(boolean state)
-  {
-    wrapAlignment = state;
-  }
-
-  public void setShowText(boolean state)
-  {
-    showText = state;
-  }
-
-  public void setRenderGaps(boolean state)
-  {
-    renderGaps = state;
-  }
-
-  public boolean getColourText()
-  {
-    return showColourText;
-  }
-
-  public void setColourText(boolean state)
-  {
-    showColourText = state;
-  }
-
-  public void setShowBoxes(boolean state)
-  {
-    showBoxes = state;
-  }
-
-  public boolean getWrapAlignment()
-  {
-    return wrapAlignment;
-  }
-
-  public boolean getShowText()
-  {
-    return showText;
-  }
-
-  public boolean getShowBoxes()
-  {
-    return showBoxes;
-  }
-
-  public char getGapCharacter()
-  {
-    return getAlignment().getGapCharacter();
-  }
-
-  public void setGapCharacter(char gap)
-  {
-    if (getAlignment() != null)
-    {
-      getAlignment().setGapCharacter(gap);
-    }
-  }
-
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  public int getIncrement()
-  {
-    return increment;
-  }
-
-  public void setHiddenColumns(ColumnSelection colsel)
-  {
-    this.colSel = colsel;
-    if(colSel.getHiddenColumns()!=null)
-      hasHiddenColumns = true;
-  }
-
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
-
-  public void resetSeqLimits(int height)
-  {
-    setEndSeq(height / getCharHeight());
-  }
-
-  public void setCurrentTree(NJTree tree)
-  {
-    currentTree = tree;
-  }
-
-  public NJTree getCurrentTree()
-  {
-    return currentTree;
-  }
-
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
-  public boolean getShowJVSuffix()
-  {
-    return showJVSuffix;
-  }
-
-  public void setShowJVSuffix(boolean b)
-  {
-    showJVSuffix = b;
-  }
-
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
-
-  public void setShowAnnotation(boolean b)
-  {
-    showAnnotation = b;
-  }
-
-  public boolean getScaleAboveWrapped()
-  {
-    return scaleAboveWrapped;
-  }
-
-  public boolean getScaleLeftWrapped()
-  {
-    return scaleLeftWrapped;
-  }
-
-  public boolean getScaleRightWrapped()
-  {
-    return scaleRightWrapped;
-  }
-
-  public void setScaleAboveWrapped(boolean b)
-  {
-    scaleAboveWrapped = b;
-  }
-
-  public void setScaleLeftWrapped(boolean b)
-  {
-    scaleLeftWrapped = b;
-  }
-
-  public void setScaleRightWrapped(boolean b)
-  {
-    scaleRightWrapped = b;
-  }
-
-  public void setIgnoreGapsConsensus(boolean b)
-  {
-    ignoreGapsInConsensusCalculation = b;
-    updateConsensus(null);
-    if (globalColourScheme!=null)
-    {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
-
-    }
-  }
-
-  /**
-   * Property change listener for changes in alignment
-   *
-   * @param listener DOCUMENT ME!
-   */
-  public void addPropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
-  {
-      changeSupport.addPropertyChangeListener(listener);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param listener DOCUMENT ME!
-   */
-  public void removePropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
-  {
-      changeSupport.removePropertyChangeListener(listener);
-  }
-
-  /**
-   * Property change listener for changes in alignment
-   *
-   * @param prop DOCUMENT ME!
-   * @param oldvalue DOCUMENT ME!
-   * @param newvalue DOCUMENT ME!
-   */
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
-  {
-      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-  }
-
-
-
-  public boolean getIgnoreGapsConsensus()
-  {
-    return ignoreGapsInConsensusCalculation;
-  }
-  public void hideSelectedColumns()
-  {
-    if (colSel.size() < 1)
-      return;
-
-    colSel.hideSelectedColumns();
-    setSelectionGroup(null);
-
-    hasHiddenColumns = true;
-  }
-
-  public void invertColumnSelection()
-  {
-    for (int i = 0; i < alignment.getWidth(); i++)
-    {
-      if (colSel.contains(i))
-        colSel.removeElement(i);
-      else
-      {
-        if (!hasHiddenColumns || colSel.isVisible(i))
-        {
-          colSel.addElement(i);
-        }
-      }
-    }
-  }
-
-
-  public void hideColumns(int start, int end)
-  {
-    if(start==end)
-      colSel.hideColumns(start);
-    else
-      colSel.hideColumns(start, end);
-
-    hasHiddenColumns = true;
-  }
-
-  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-  {
-    int sSize = sg.getSize();
-    if(sSize < 2)
-      return;
-
-    if(hiddenRepSequences==null)
-      hiddenRepSequences = new Hashtable();
-
-     hiddenRepSequences.put(repSequence, sg);
-
-    //Hide all sequences except the repSequence
-    SequenceI [] seqs = new SequenceI[sSize-1];
-    int index = 0;
-    for(int i=0; i<sSize; i++)
-      if(sg.getSequenceAt(i)!=repSequence)
-      {
-        if(index==sSize-1)
-          return;
-
-        seqs[index++] = sg.getSequenceAt(i);
-      }
-
-    hideSequence(seqs);
-
-    }
-
-  public void hideAllSelectedSeqs()
-  {
-    if (selectionGroup == null)
-      return;
-
-    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-    hideSequence(seqs);
-
-    setSelectionGroup(null);
-  }
-
-  public void hideSequence(SequenceI [] seq)
-  {
-    if(seq!=null)
-    {
-      for (int i = 0; i < seq.length; i++)
-        alignment.getHiddenSequences().hideSequence(seq[i]);
-
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
-  }
-
-  public void showColumn(int col)
-  {
-    colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
-      hasHiddenColumns = false;
-  }
-
-  public void showAllHiddenColumns()
-  {
-    colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
-  }
-
-  public void showAllHiddenSeqs()
-  {
-    if(alignment.getHiddenSequences().getSize()>0)
-    {
-      if(selectionGroup==null)
-      {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth()-1);
-      }
-      Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-      for(int t=0; t<tmp.size(); t++)
-      {
-        selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
-            );
-      }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      hasHiddenRows = false;
-      hiddenRepSequences = null;
-      }
-  }
-
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
-  }
-
-  /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
-   * @return String[]
-   */
-  public SequenceI[] getSelectionAsNewSequence()
-  {
-    SequenceI[] sequences;
-
-    if (selectionGroup == null)
-      sequences = alignment.getSequencesArray();
-    else
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
-    return sequences;
-  }
-
-  /**
-   * This method returns the visible alignment as text, as
-   * seen on the GUI, ie if columns are hidden they will not
-   * be returned in the result.
-   * Use this for calculating trees, PCA, redundancy etc on views
-   * which contain hidden columns.
-   * @return String[]
-   */
-  public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    CigarArray selection=null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
-    }
-    else
-    {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth()-1;
-    }
-    SeqCigar[] selseqs = new SeqCigar[iSize];
-    for(i=0; i<iSize; i++)
-    {
-      selseqs[i] = new SeqCigar(seqs[i], start, end);
-    }
-    selection=new CigarArray(selseqs);
-    // now construct the CigarArray operations
-    if (hasHiddenColumns) {
-      Vector regions = colSel.getHiddenColumns();
-      int [] region;
-      int hideStart, hideEnd;
-      int last=start;
-      for (int j = 0; last<end & j < regions.size(); j++)
-      {
-        region = (int[]) regions.elementAt(j);
-        hideStart = region[0];
-        hideEnd = region[1];
-        // edit hidden regions to selection range
-        if(hideStart<last) {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          } else
-            continue;
-        }
-
-        if (hideStart>end)
-          break;
-
-        if (hideEnd>end)
-          hideEnd=end;
-
-        if (hideStart>hideEnd)
-          break;
-        /**
-         * form operations...
-         */
-        if (last<hideStart)
-          selection.addOperation(CigarArray.M, hideStart-last);
-        selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-        last = hideEnd+1;
-      }
-      // Final match if necessary.
-      if (last<end)
-        selection.addOperation(CigarArray.M, end-last+1);
-    } else {
-      selection.addOperation(CigarArray.M, end-start+1);
-    }
-    return selection;
-  }
-  /**
-   * return a compact representation of the current alignment selection to
-   * pass to an analysis function
-   * @param selectedOnly boolean true to just return the selected view
-   * @return AlignmentView
-   */
-  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
-    // JBPNote:
-    // this is here because the AlignmentView constructor modifies the CigarArray
-    // object. Refactoring of Cigar and alignment view representation should
-    // be done to remove redundancy.
-    CigarArray aligview = getViewAsCigars(selectedOnly);
-    if (aligview!=null) {
-      return new AlignmentView(aligview,
-          (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
-    }
-    return null;
-  }
-  /**
-   * This method returns the visible alignment as text, as
-   * seen on the GUI, ie if columns are hidden they will not
-   * be returned in the result.
-   * Use this for calculating trees, PCA, redundancy etc on views
-   * which contain hidden columns.
-   * @return String[]
-   */
-  public String [] getViewAsString(boolean selectedRegionOnly)
-  {
-    String [] selection = null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes()+1;
-    }
-    else
-    {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth();
-    }
-
-    selection = new String[iSize];
-
-
-    for(i=0; i<iSize; i++)
-    {
-      if (hasHiddenColumns)
-      {
-           StringBuffer visibleSeq = new StringBuffer();
-           Vector regions = colSel.getHiddenColumns();
-
-           int blockStart = start, blockEnd=end;
-           int [] region;
-           int hideStart, hideEnd;
-
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
-
-             if(hideStart < start)
-             {
-               continue;
-             }
-
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
-
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
-
-
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
-
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
-           selection[i] = visibleSeq.toString();
-      }
-      else
-      {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
-      }
-    }
-
-    return selection;
-  }
-
-  public boolean getShowHiddenMarkers()
-  {
-    return showHiddenMarkers;
-  }
-
-  public void setShowHiddenMarkers(boolean show)
-  {
-    showHiddenMarkers = show;
-  }
-
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-      return Color.white;
-    else
-      return (Color) sequenceColours.get(seq);
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-      sequenceColours = new Hashtable();
-
-    if (col == null)
-      sequenceColours.remove(seq);
-    else
-      sequenceColours.put(seq, col);
-  }
-
-  public String getSequenceSetId()
-  {
-    if (sequenceSetID == null)
-      sequenceSetID = alignment.hashCode() + "";
-
-    return sequenceSetID;
-  }
-
-  public void alignmentChanged(AlignmentPanel ap)
-  {
-    alignment.padGaps();
-
-    if (hconsensus != null && autocalculateConsensus)
-    {
-      updateConsensus(ap);
-      updateConservation(ap);
-    }
-
-    //Reset endRes of groups if beyond alignment width
-    int alWidth = alignment.getWidth();
-    Vector groups = alignment.getGroups();
-    if(groups!=null)
-    {
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        if(sg.getEndRes()>alWidth)
-          sg.setEndRes(alWidth-1);
-      }
-    }
-
-    if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
-      selectionGroup.setEndRes(alWidth-1);
-
-    resetAllColourSchemes();
-
-  //AW  alignment.adjustSequenceAnnotations();
-  }
-
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = globalColourScheme;
-    if(cs!=null)
-    {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) cs).
-            resetClustalX(alignment.getSequences(),
-                          alignment.getWidth());
-      }
-
-      cs.setConsensus(hconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) alignment;
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, ConsPercGaps);
-
-        cs.setConservation(c);
-      }
-    }
-
-    int s, sSize = alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(
-            sg.getSequences(hiddenRepSequences), sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Font;
+
+public class AlignViewport extends AlignmentViewport implements
+        SelectionSource, VamsasSource, CommandListener
+{
+  boolean cursorMode = false;
+
+  Font font = new Font("SansSerif", Font.PLAIN, 10);
+
+  boolean validCharWidth = true;
+
+  NJTree currentTree = null;
+
+  public jalview.bin.JalviewLite applet;
+
+  boolean MAC = false;
+
+  private AnnotationColumnChooser annotationColumnSelectionState;
+
+  public void finalize()
+  {
+    applet = null;
+    quality = null;
+    alignment = null;
+    colSel = null;
+  }
+
+  public AlignViewport(AlignmentI al, JalviewLite applet)
+  {
+    super();
+    calculator = new jalview.workers.AlignCalcManager();
+    this.applet = applet;
+    alignment = al;
+    // we always pad gaps
+    this.setPadGaps(true);
+    this.startRes = 0;
+    this.endRes = al.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = al.getHeight() - 1;
+    if (applet != null)
+    {
+      // get the width and height scaling factors if they were specified
+      String param = applet.getParameter("widthScale");
+      if (param != null)
+      {
+        try
+        {
+          widthScale = new Float(param).floatValue();
+        } catch (Exception e)
+        {
+        }
+        if (widthScale <= 1.0)
+        {
+          System.err
+                  .println("Invalid alignment character width scaling factor ("
+                          + widthScale + "). Ignoring.");
+          widthScale = 1;
+        }
+        if (JalviewLite.debug)
+        {
+          System.err
+                  .println("Alignment character width scaling factor is now "
+                          + widthScale);
+        }
+      }
+      param = applet.getParameter("heightScale");
+      if (param != null)
+      {
+        try
+        {
+          heightScale = new Float(param).floatValue();
+        } catch (Exception e)
+        {
+        }
+        if (heightScale <= 1.0)
+        {
+          System.err
+                  .println("Invalid alignment character height scaling factor ("
+                          + heightScale + "). Ignoring.");
+          heightScale = 1;
+        }
+        if (JalviewLite.debug)
+        {
+          System.err
+                  .println("Alignment character height scaling factor is now "
+                          + heightScale);
+        }
+      }
+    }
+    setFont(font);
+
+    MAC = new jalview.util.Platform().isAMac();
+
+    if (applet != null)
+    {
+      setShowJVSuffix(applet.getDefaultParameter("showFullId",
+              getShowJVSuffix()));
+
+      setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+              isShowAnnotation()));
+
+      showConservation = applet.getDefaultParameter("showConservation",
+              showConservation);
+
+      showQuality = applet.getDefaultParameter("showQuality", showQuality);
+
+      showConsensus = applet.getDefaultParameter("showConsensus",
+              showConsensus);
+
+      setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+              getShowUnconserved()));
+
+      setScaleProteinAsCdna(applet.getDefaultParameter(
+              "scaleProteinAsCdna", isScaleProteinAsCdna()));
+
+      String param = applet.getParameter("upperCase");
+      if (param != null)
+      {
+        if (param.equalsIgnoreCase("bold"))
+        {
+          setUpperCasebold(true);
+        }
+      }
+      sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+      setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+              isFollowHighlight()));
+      followSelection = isFollowHighlight();
+
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+              showSequenceLogo);
+
+      normaliseSequenceLogo = applet.getDefaultParameter(
+              "normaliseSequenceLogo", applet.getDefaultParameter(
+                      "normaliseLogo", normaliseSequenceLogo));
+
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+              showGroupConsensus);
+
+      showGroupConservation = applet.getDefaultParameter(
+              "showGroupConservation", showGroupConservation);
+
+      showConsensusHistogram = applet.getDefaultParameter(
+              "showConsensusHistogram", showConsensusHistogram);
+
+    }
+
+    if (applet != null)
+    {
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
+      if (colour == null)
+      {
+        colour = applet.getParameter("userDefinedColour");
+        if (colour != null)
+        {
+          colour = "User Defined";
+        }
+      }
+
+      if (colour != null)
+      {
+        globalColourScheme = ColourSchemeProperty.getColour(alignment,
+                colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(hconsensus);
+        }
+      }
+
+      if (applet.getParameter("userDefinedColour") != null)
+      {
+        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+                .getParameter("userDefinedColour"));
+      }
+    }
+    initAutoAnnotation();
+
+  }
+
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
+  {
+    if (consensus == null)
+    {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
+      return null;
+    }
+    StringBuilder seqs = new StringBuilder(consensus.annotations.length);
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      if (consensus.annotations[i] != null)
+      {
+        if (consensus.annotations[i].description.charAt(0) == '[')
+        {
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        }
+        else
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
+      }
+    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
+
+  java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
+  public void setFont(Font f)
+  {
+    font = f;
+    if (nullFrame == null)
+    {
+      nullFrame = new java.awt.Frame();
+      nullFrame.addNotify();
+    }
+
+    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+    setCharHeight((int) (heightScale * fm.getHeight()));
+    setCharWidth((int) (widthScale * fm.charWidth('M')));
+
+    if (isUpperCasebold())
+    {
+      Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+      fm = nullFrame.getGraphics().getFontMetrics(f2);
+      setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
+    }
+  }
+
+  public Font getFont()
+  {
+    return font;
+  }
+
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
+  }
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
+
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
+
+  boolean centreColumnLabels;
+
+  public boolean getCentreColumnLabels()
+  {
+    return centreColumnLabels;
+  }
+
+  public boolean followSelection = true;
+
+  /**
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
+   */
+  public boolean getFollowSelection()
+  {
+    return followSelection;
+  }
+
+  public void sendSelection()
+  {
+    getStructureSelectionManager().sendSelection(
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
+  }
+
+  /**
+   * Returns an instance of the StructureSelectionManager scoped to this applet
+   * instance.
+   * 
+   * @return
+   */
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(applet);
+  }
+
+  /**
+   * synthesize a column selection if none exists so it covers the given
+   * selection group. if wholewidth is false, no column selection is made if the
+   * selection group covers the whole alignment width.
+   * 
+   * @param sg
+   * @param wholewidth
+   */
+  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+  {
+    int sgs, sge;
+    if (sg != null
+            && (sgs = sg.getStartRes()) >= 0
+            && sg.getStartRes() <= (sge = sg.getEndRes())
+            && (colSel == null || colSel.getSelected() == null || colSel
+                    .getSelected().size() == 0))
+    {
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
+        colSel.addElement(cspos);
+      }
+    }
+  }
+
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  /**
+   * 
+   * @return true if alignment characters should be displayed
+   */
+  public boolean isValidCharWidth()
+  {
+    return validCharWidth;
+  }
+
+  public AnnotationColumnChooser getAnnotationColumnSelectionState()
+  {
+    return annotationColumnSelectionState;
+  }
+
+  public void setAnnotationColumnSelectionState(
+          AnnotationColumnChooser annotationColumnSelectionState)
+  {
+    this.annotationColumnSelectionState = annotationColumnSelectionState;
+  }
+
+  @Override
+  public void mirrorCommand(CommandI command, boolean undo,
+          StructureSelectionManager ssm, VamsasSource source)
+  {
+    // TODO refactor so this can be pulled up to superclass or controller
+    /*
+     * Do nothing unless we are a 'complement' of the source. May replace this
+     * with direct calls not via SSM.
+     */
+    if (source instanceof AlignViewportI
+            && ((AlignViewportI) source).getCodingComplement() == this)
+    {
+      // ok to continue;
+    }
+    else
+    {
+      return;
+    }
+
+    CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+            getGapCharacter());
+    if (mappedCommand != null)
+    {
+      mappedCommand.doCommand(null);
+      firePropertyChange("alignment", null, getAlignment().getSequences());
+
+      // ap.scalePanelHolder.repaint();
+      // ap.repaint();
+    }
+  }
+
+  @Override
+  public VamsasSource getVamsasSource()
+  {
+    return this;
+  }
+
+  /**
+   * If this viewport has a (Protein/cDNA) complement, then scroll the
+   * complementary alignment to match this one.
+   */
+  public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+  {
+    if (complementPanel == null)
+    {
+      return;
+    }
+
+    /*
+     * Populate a SearchResults object with the mapped location to scroll to. If
+     * there is no complement, or it is not following highlights, or no mapping
+     * is found, the result will be empty.
+     */
+    SearchResults sr = new SearchResults();
+    int seqOffset = findComplementScrollTarget(sr);
+    if (!sr.isEmpty())
+    {
+      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.scrollToCentre(sr, seqOffset);
+    }
+  }
+
+}