X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=a235a2a162cc95753e75d0c17251079347cfc46d;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=b369b1f5ff3568292e6c3dba5b94ddd483ae9c99;hpb=b6d133ff2200a05764410900ed01b75760860fcf;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
old mode 100755
new mode 100644
index b369b1f..a235a2a
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,22 +1,23 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -24,173 +25,235 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+import jalview.api.AlignViewportI;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
 
-public class AlignViewport
+public class AlignViewport extends AlignmentViewport implements
+        AlignViewportI, SelectionSource, VamsasSource
 {
   int startRes;
+
   int endRes;
 
   int startSeq;
-  int endSeq;
 
+  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;
+  boolean showAnnotation = true;
 
-  SequenceGroup selectionGroup;
+  boolean upperCasebold = false;
 
   int charHeight;
+
   int charWidth;
+
   int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
-  boolean validCharWidth = true;
-  AlignmentI alignment;
 
-  ColumnSelection colSel = new ColumnSelection();
+  boolean validCharWidth = true;
 
   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
+  // currently visible, in the correct order or rendering
   public Hashtable featuresDisplayed;
 
-  boolean hasHiddenColumns = false;
-  boolean hasHiddenRows = false;
   boolean showHiddenMarkers = true;
 
+  public jalview.bin.JalviewLite applet;
 
-  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 MAC = false;
 
-  boolean ignoreGapsInConsensusCalculation = false;
+  Stack historyList = new Stack();
 
-  jalview.bin.JalviewLite applet;
+  Stack redoList = new Stack();
 
-  boolean MAC = false;
+  public void finalize()
+  {
+    applet = null;
+    quality = null;
+    alignment = null;
+    colSel = null;
+  }
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
+    calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     setAlignment(al);
+    // we always pad gaps
+    this.setPadGaps(true);
     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");
+      // get the width and height scaling factors if they were specified
+      String param = applet.getParameter("widthScale");
       if (param != null)
       {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
+        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 (applet.debug)
+        {
+          System.err
+                  .println("Alignment character width scaling factor is now "
+                          + widthScale);
+        }
       }
-
-      param = applet.getParameter("showAnnotation");
+      param = applet.getParameter("heightScale");
       if (param != null)
       {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
+        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 (applet.debug)
+        {
+          System.err
+                  .println("Alignment character height scaling factor is now "
+                          + heightScale);
+        }
       }
+    }
+    setFont(font);
 
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
+    MAC = new jalview.util.Platform().isAMac();
 
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
+    if (applet != null)
+    {
+      showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
 
-      param = applet.getParameter("showConsensus");
-      if (param != null)
-      {
-        showConsensus = Boolean.valueOf(param).booleanValue();
-      }
+      showAnnotation = applet.getDefaultParameter("showAnnotation",
+              showAnnotation);
+
+      showConservation = applet.getDefaultParameter("showConservation",
+              showConservation);
+
+      showQuality = applet.getDefaultParameter("showQuality", showQuality);
+
+      showConsensus = applet.getDefaultParameter("showConsensus",
+              showConsensus);
+
+      showUnconserved = applet.getDefaultParameter("showUnconserved",
+              showUnconserved);
 
-      param = applet.getParameter("upperCase");
+      String param = applet.getParameter("upperCase");
       if (param != null)
       {
-        if(param.equalsIgnoreCase("bold"))
+        if (param.equalsIgnoreCase("bold"))
+        {
           upperCasebold = true;
+        }
       }
+      sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
 
-    }
-    // We must set conservation and consensus before setting colour,
-    // as Blosum and Clustal require this to be done
-    updateConservation();
-    updateConsensus();
+      followHighlight = applet.getDefaultParameter("automaticScrolling",
+              followHighlight);
+      followSelection = followHighlight;
+
+      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 = applet.getParameter("defaultColour");
 
-      if(colour == null)
+      if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
+        if (colour != null)
+        {
           colour = "User Defined";
+        }
       }
 
-      if(colour != null)
+      if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        globalColourScheme = ColourSchemeProperty.getColour(alignment,
+                colour);
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);
         }
       }
 
-      if(applet.getParameter("userDefinedColour")!=null)
+      if (applet.getParameter("userDefinedColour") != null)
       {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
-            applet.getParameter("userDefinedColour"));
+        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+                .getParameter("userDefinedColour"));
       }
-
-
     }
+    initAutoAnnotation();
+
   }
 
   public void showSequenceFeatures(boolean b)
@@ -203,215 +266,42 @@ public class AlignViewport
     return showSequenceFeatures;
   }
 
-
-  public void updateConservation()
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
   {
-    if(alignment.isNucleotide())
-          return;
-
-    Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 3,
-        alignment.getSequences(), 0,
-        alignment.getWidth() - 1);
-    cons.calculate();
-    cons.verdict(false, ConsPercGaps);
-    cons.findQuality();
-    int alWidth = alignment.getWidth();
-    Annotation[] annotations = new Annotation[alWidth];
-    Annotation[] qannotations = new Annotation[alWidth];
-    String sequence = cons.getConsSequence().getSequence();
-    float minR, minG, minB, maxR, maxG, 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 = cons.qualityRange[0].floatValue();
-    float qmax = cons.qualityRange[1].floatValue();
-
-    for (int i = 0; i < alWidth; i++)
-    {
-      float value = 0;
-      try
-      {
-        value = Integer.parseInt(sequence.charAt(i) + "");
-      }
-      catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*')
-        {
-          value = 11;
-        }
-        if (sequence.charAt(i) == '+')
-        {
-          value = 10;
-        }
-      }
-      float vprop = value - min;
-      vprop /= max;
-
-      annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value,
-                                      new Color(minR + maxR * vprop,
-                                                minG + maxG * vprop,
-                                                minB + maxB * vprop));
-      // Quality calc
-      value = ( (Double) cons.quality.elementAt(i)).floatValue();
-      vprop = value - qmin;
-      vprop /= qmax;
-      qannotations[i] = new Annotation(" ",
-                                       String.valueOf(value), ' ', value,
-                                       new
-                                       Color(minR + maxR * vprop,
-                                             minG + maxG * vprop,
-                                             minB + maxB * vprop));
-    }
-
-    if (conservation == null)
-    {
-      conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than " +
-                                             ConsPercGaps + "% gaps",
-                                             annotations,
-                                             0f, // cons.qualityRange[0].floatValue(),
-                                             11f, // cons.qualityRange[1].floatValue()
-                                             AlignmentAnnotation.BAR_GRAPH);
-      if (showConservation)
-      {
-        alignment.addAnnotation(conservation);
-      }
-      quality = new AlignmentAnnotation("Quality",
-                                        "Alignment Quality based on Blosum62 scores",
-                                        qannotations,
-                                        cons.qualityRange[0].floatValue(),
-                                        cons.qualityRange[1].floatValue(),
-                                        AlignmentAnnotation.BAR_GRAPH);
-      if (showQuality)
-      {
-        alignment.addAnnotation(quality);
-      }
-    }
-    else
+    if (consensus == null)
     {
-      conservation.annotations = annotations;
-      quality.annotations = qannotations;
-      quality.graphMax = cons.qualityRange[1].floatValue();
+      updateConsensus(null);
     }
-
-  }
-
-  public void updateConsensus()
-  {
-    // this routine prevents vconsensus becoming a new object each time
-    // consenus is calculated. Important for speed of Blosum62
-    // and PID colouring of alignment
-    int aWidth = alignment.getWidth();
-
-    Annotation[] annotations = new Annotation[aWidth];
-
-    hconsensus = new Hashtable[aWidth];
-    AAFrequency.calculate(alignment.getSequencesArray(),
-                          0, aWidth,
-                          hconsensus);
-
-    for (int i = 0; i < aWidth; i++)
-    {
-      float value = 0;
-      if(ignoreGapsInConsensusCalculation)
-        value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();
-      else
-        value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();
-
-      String maxRes = hconsensus[i].get("maxResidue").toString();
-      String mouseOver = hconsensus[i].get("maxResidue") + " ";
-      if (maxRes.length() > 1)
-      {
-        mouseOver = "[" + maxRes + "] ";
-        maxRes = "+";
-      }
-
-
-      mouseOver += (int) value + "%";
-      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-
-    }
-
     if (consensus == null)
     {
-      consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      if (showConsensus)
-      {
-        alignment.addAnnotation(consensus);
-      }
+      return null;
     }
-    else
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
     {
-      consensus.annotations = annotations;
-    }
-
-    if(globalColourScheme!=null)
-          globalColourScheme.setConsensus(hconsensus);
-
-  }
-  /**
-   * 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)
-      updateConsensus();
-    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] != 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" : ""));
+    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()
   {
@@ -428,16 +318,6 @@ public class AlignViewport
     return startSeq;
   }
 
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
-
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
-
   public void setStartRes(int res)
   {
     this.startRes = res;
@@ -452,7 +332,8 @@ public class AlignViewport
   {
     if (res > alignment.getWidth() - 1)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+      // log.System.out.println(" Corrected res from " + res + " to maximum " +
+      // (alignment.getWidth()-1));
       res = alignment.getWidth() - 1;
     }
     if (res < 0)
@@ -481,24 +362,29 @@ public class AlignViewport
   }
 
   java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
   public void setFont(Font f)
   {
     font = f;
-    if(nullFrame == null)
+    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');
+    setCharHeight((int) (heightScale * fm.getHeight()));
+    charWidth = (int) (widthScale * fm.charWidth('M'));
 
-    if(upperCasebold)
+    if (upperCasebold)
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       fm = nullFrame.getGraphics().getFontMetrics(f2);
-      charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
+      charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
     }
   }
 
@@ -600,38 +486,6 @@ public class AlignViewport
     }
   }
 
-  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());
@@ -647,16 +501,6 @@ public class AlignViewport
     return currentTree;
   }
 
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
   public boolean getShowJVSuffix()
   {
     return showJVSuffix;
@@ -710,358 +554,114 @@ public class AlignViewport
   public void setIgnoreGapsConsensus(boolean b)
   {
     ignoreGapsInConsensusCalculation = b;
-    updateConsensus();
-    if (globalColourScheme!=null)
+    updateConsensus(null);
+    if (globalColourScheme != null)
     {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
+              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)
+  public boolean getShowHiddenMarkers()
   {
-      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+    return showHiddenMarkers;
   }
 
-
-
-  public boolean getIgnoreGapsConsensus()
+  public void setShowHiddenMarkers(boolean show)
   {
-    return ignoreGapsInConsensusCalculation;
+    showHiddenMarkers = show;
   }
-  public void hideSelectedColumns()
-  {
-    if (colSel.size() < 1)
-      return;
-
-    colSel.hideSelectedColumns();
-    setSelectionGroup(null);
 
-    hasHiddenColumns = true;
-  }
+  boolean centreColumnLabels;
 
-  public void invertColumnSelection()
+  public boolean getCentreColumnLabels()
   {
-    int column;
-    for (int i = 0; i < alignment.getWidth(); i++)
-    {
-      column = i;
-
-      if (colSel.contains(column))
-        colSel.removeElement(column);
-      else
-        colSel.addElement(column);
-
-    }
+    return centreColumnLabels;
   }
 
+  public boolean followHighlight = true;
 
-  public void hideColumns(int start, int end)
-  {
-    if(start==end)
-      colSel.hideColumns(start);
-    else
-      colSel.hideColumns(start, end);
-
-    hasHiddenColumns = true;
-  }
-
-  public void hideAllSelectedSeqs()
+  public boolean getFollowHighlight()
   {
-    if (selectionGroup == null)
-      return;
-
-    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-    hideSequence(seqs);
-
-    setSelectionGroup(null);
+    return followHighlight;
   }
 
-  public void hideSequence(SequenceI [] seq)
-  {
-    if(seq!=null)
-    {
-      for (int i = 0; i < seq.length; i++)
-        alignment.getHiddenSequences().hideSequence(seq[i]);
+  public boolean followSelection = true;
 
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
-  }
-
-  public void showColumn(int col)
+  /**
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
+   */
+  public boolean getFollowSelection()
   {
-    colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
-      hasHiddenColumns = false;
+    return followSelection;
   }
 
-  public void showAllHiddenColumns()
+  public void sendSelection()
   {
-    colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(applet).sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
   }
 
-  public void showAllHiddenSeqs()
-  {
-    if(alignment.getHiddenSequences().getSize()>0)
+  /**
+   * 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(selectionGroup==null)
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
       {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth()-1);
+        colSel = new ColumnSelection();
       }
-      Vector tmp = alignment.getHiddenSequences().showAll();
-      for(int t=0; t<tmp.size(); t++)
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
       {
-        selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
-            );
+        colSel.addElement(cspos);
       }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      hasHiddenRows = false;
     }
   }
 
-  public int adjustForHiddenSeqs(int alignmentIndex)
+  @Override
+  public boolean hasHiddenColumns()
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    return hasHiddenColumns;
   }
 
-  /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
-   * @return String[]
-   */
-  public SequenceI[] getSelectionAsNewSequence()
+  public boolean isNormaliseSequenceLogo()
   {
-    SequenceI[] sequences;
-
-    if (selectionGroup == null)
-      sequences = alignment.getSequencesArray();
-    else
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
-    return sequences;
+    return normaliseSequenceLogo;
   }
 
-  /**
-   * 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)
+  public void setNormaliseSequenceLogo(boolean state)
   {
-    CigarArray selection=null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize(false);
-      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;
+    normaliseSequenceLogo = state;
   }
+
   /**
-   * 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[]
+   * 
+   * @return true if alignment characters should be displayed
    */
-  public String [] getViewAsString(boolean selectedRegionOnly)
+  public boolean isValidCharWidth()
   {
-    String [] selection = null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize(false);
-      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].getSequence(start, end);
-      }
-    }
-
-    return selection;
+    return validCharWidth;
   }
 
-  public boolean getShowHiddenMarkers()
-  {
-    return showHiddenMarkers;
-  }
-
-  public void setShowHiddenMarkers(boolean show)
-  {
-    showHiddenMarkers = show;
-  }
-
-
 }