X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=01668a5bb5dc8eaf8af5cc900a77ce79d1ff91bd;hb=f2b03e9fecf41886ebf5f747fd4be02edf042bee;hp=d6aa400e9daa425449fc1d360734bf40d164edbd;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d6aa400..01668a5 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,22 +20,12 @@
  */
 package jalview.viewmodel;
 
-import java.awt.Color;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.ColorI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
 import jalview.commands.CommandI;
@@ -53,6 +43,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.Colour;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
@@ -60,6 +51,7 @@ import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
@@ -67,6 +59,15 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -75,7 +76,7 @@ import jalview.workers.StrucConsensusThread;
  * 
  */
 public abstract class AlignmentViewport implements AlignViewportI,
-        ViewStyleI, CommandListener, VamsasSource
+        CommandListener, VamsasSource
 {
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -95,6 +96,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
    */
+  @Override
   public void setFontName(String name)
   {
     viewStyle.setFontName(name);
@@ -104,6 +106,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param style
    * @see jalview.api.ViewStyleI#setFontStyle(int)
    */
+  @Override
   public void setFontStyle(int style)
   {
     viewStyle.setFontStyle(style);
@@ -113,6 +116,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param size
    * @see jalview.api.ViewStyleI#setFontSize(int)
    */
+  @Override
   public void setFontSize(int size)
   {
     viewStyle.setFontSize(size);
@@ -122,6 +126,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontStyle()
    */
+  @Override
   public int getFontStyle()
   {
     return viewStyle.getFontStyle();
@@ -131,6 +136,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontName()
    */
+  @Override
   public String getFontName()
   {
     return viewStyle.getFontName();
@@ -140,6 +146,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontSize()
    */
+  @Override
   public int getFontSize()
   {
     return viewStyle.getFontSize();
@@ -149,6 +156,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param upperCasebold
    * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
    */
+  @Override
   public void setUpperCasebold(boolean upperCasebold)
   {
     viewStyle.setUpperCasebold(upperCasebold);
@@ -158,6 +166,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isUpperCasebold()
    */
+  @Override
   public boolean isUpperCasebold()
   {
     return viewStyle.isUpperCasebold();
@@ -167,6 +176,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isSeqNameItalics()
    */
+  @Override
   public boolean isSeqNameItalics()
   {
     return viewStyle.isSeqNameItalics();
@@ -176,6 +186,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param colourByReferenceSeq
    * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
    */
+  @Override
   public void setColourByReferenceSeq(boolean colourByReferenceSeq)
   {
     viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
@@ -185,6 +196,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
    */
+  @Override
   public void setColourAppliesToAllGroups(boolean b)
   {
     viewStyle.setColourAppliesToAllGroups(b);
@@ -194,6 +206,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
    */
+  @Override
   public boolean getColourAppliesToAllGroups()
   {
     return viewStyle.getColourAppliesToAllGroups();
@@ -203,6 +216,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
    */
+  @Override
   public boolean getAbovePIDThreshold()
   {
     return viewStyle.getAbovePIDThreshold();
@@ -212,6 +226,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param inc
    * @see jalview.api.ViewStyleI#setIncrement(int)
    */
+  @Override
   public void setIncrement(int inc)
   {
     viewStyle.setIncrement(inc);
@@ -221,6 +236,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIncrement()
    */
+  @Override
   public int getIncrement()
   {
     return viewStyle.getIncrement();
@@ -230,6 +246,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
    */
+  @Override
   public void setConservationSelected(boolean b)
   {
     viewStyle.setConservationSelected(b);
@@ -239,6 +256,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param show
    * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
    */
+  @Override
   public void setShowHiddenMarkers(boolean show)
   {
     viewStyle.setShowHiddenMarkers(show);
@@ -248,6 +266,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
    */
+  @Override
   public boolean getShowHiddenMarkers()
   {
     return viewStyle.getShowHiddenMarkers();
@@ -257,6 +276,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
    */
+  @Override
   public void setScaleRightWrapped(boolean b)
   {
     viewStyle.setScaleRightWrapped(b);
@@ -266,6 +286,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
    */
+  @Override
   public void setScaleLeftWrapped(boolean b)
   {
     viewStyle.setScaleLeftWrapped(b);
@@ -275,6 +296,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
    */
+  @Override
   public void setScaleAboveWrapped(boolean b)
   {
     viewStyle.setScaleAboveWrapped(b);
@@ -284,6 +306,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
    */
+  @Override
   public boolean getScaleLeftWrapped()
   {
     return viewStyle.getScaleLeftWrapped();
@@ -293,6 +316,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
    */
+  @Override
   public boolean getScaleAboveWrapped()
   {
     return viewStyle.getScaleAboveWrapped();
@@ -302,6 +326,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleRightWrapped()
    */
+  @Override
   public boolean getScaleRightWrapped()
   {
     return viewStyle.getScaleRightWrapped();
@@ -311,6 +336,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
    */
+  @Override
   public void setAbovePIDThreshold(boolean b)
   {
     viewStyle.setAbovePIDThreshold(b);
@@ -320,6 +346,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresh
    * @see jalview.api.ViewStyleI#setThreshold(int)
    */
+  @Override
   public void setThreshold(int thresh)
   {
     viewStyle.setThreshold(thresh);
@@ -329,6 +356,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThreshold()
    */
+  @Override
   public int getThreshold()
   {
     return viewStyle.getThreshold();
@@ -338,6 +366,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowJVSuffix()
    */
+  @Override
   public boolean getShowJVSuffix()
   {
     return viewStyle.getShowJVSuffix();
@@ -347,6 +376,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param b
    * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
    */
+  @Override
   public void setShowJVSuffix(boolean b)
   {
     viewStyle.setShowJVSuffix(b);
@@ -356,6 +386,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
    */
+  @Override
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
@@ -365,6 +396,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setShowText(boolean)
    */
+  @Override
   public void setShowText(boolean state)
   {
     viewStyle.setShowText(state);
@@ -374,6 +406,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
    */
+  @Override
   public void setRenderGaps(boolean state)
   {
     viewStyle.setRenderGaps(state);
@@ -383,6 +416,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourText()
    */
+  @Override
   public boolean getColourText()
   {
     return viewStyle.getColourText();
@@ -392,6 +426,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param state
    * @see jalview.api.ViewStyleI#setColourText(boolean)
    */
+  @Override
   public void setColourText(boolean state)
   {
     viewStyle.setColourText(state);
@@ -401,6 +436,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrapAlignment()
    */
+  @Override
   public boolean getWrapAlignment()
   {
     return viewStyle.getWrapAlignment();
@@ -410,6 +446,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowText()
    */
+  @Override
   public boolean getShowText()
   {
     return viewStyle.getShowText();
@@ -419,6 +456,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrappedWidth()
    */
+  @Override
   public int getWrappedWidth()
   {
     return viewStyle.getWrappedWidth();
@@ -428,6 +466,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setWrappedWidth(int)
    */
+  @Override
   public void setWrappedWidth(int w)
   {
     viewStyle.setWrappedWidth(w);
@@ -437,6 +476,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharHeight()
    */
+  @Override
   public int getCharHeight()
   {
     return viewStyle.getCharHeight();
@@ -446,6 +486,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param h
    * @see jalview.api.ViewStyleI#setCharHeight(int)
    */
+  @Override
   public void setCharHeight(int h)
   {
     viewStyle.setCharHeight(h);
@@ -455,6 +496,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharWidth()
    */
+  @Override
   public int getCharWidth()
   {
     return viewStyle.getCharWidth();
@@ -464,6 +506,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param w
    * @see jalview.api.ViewStyleI#setCharWidth(int)
    */
+  @Override
   public void setCharWidth(int w)
   {
     viewStyle.setCharWidth(w);
@@ -473,6 +516,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowBoxes()
    */
+  @Override
   public boolean getShowBoxes()
   {
     return viewStyle.getShowBoxes();
@@ -482,6 +526,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowUnconserved()
    */
+  @Override
   public boolean getShowUnconserved()
   {
     return viewStyle.getShowUnconserved();
@@ -491,6 +536,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showunconserved
    * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
    */
+  @Override
   public void setShowUnconserved(boolean showunconserved)
   {
     viewStyle.setShowUnconserved(showunconserved);
@@ -500,21 +546,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param default1
    * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
    */
+  @Override
   public void setSeqNameItalics(boolean default1)
   {
     viewStyle.setSeqNameItalics(default1);
   }
 
   /**
-   * @param selected
-   * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
-   */
-  public void setShowSeqFeaturesHeight(boolean selected)
-  {
-    viewStyle.setShowSeqFeaturesHeight(selected);
-  }
-
-  /**
    * alignment displayed in the viewport. Please use get/setter
    */
   protected AlignmentI alignment;
@@ -549,7 +587,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return isDataset;
   }
 
-
   private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
 
   protected ColumnSelection colSel = new ColumnSelection();
@@ -562,12 +599,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected ColourSchemeI globalColourScheme = null;
 
-
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
     // TODO: logic refactored from AlignFrame changeColour -
-    // autorecalc stuff should be changed to rely on the worker system
+    // TODO: autorecalc stuff should be changed to rely on the worker system
     // check to see if we should implement a changeColour(cs) method rather than
     // put th logic in here
     // - means that caller decides if they want to just modify state and defer
@@ -639,7 +675,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
     }
-
   }
 
   @Override
@@ -803,15 +838,36 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     /*
      * A separate thread to compute cDNA consensus for a protein alignment
+     * which has mapping to cDNA
      */
     final AlignmentI al = this.getAlignment();
     if (!al.isNucleotide() && al.getCodonFrames() != null
             && !al.getCodonFrames().isEmpty())
     {
-      if (calculator
-              .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+      /*
+       * fudge - check first for protein-to-nucleotide mappings
+       * (we don't want to do this for protein-to-protein)
+       */
+      boolean doConsensus = false;
+      for (AlignedCodonFrame mapping : al.getCodonFrames())
+      {
+        // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+        MapList[] mapLists = mapping.getdnaToProt();
+        // mapLists can be empty if project load has not finished resolving seqs
+        if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+        {
+          doConsensus = true;
+          break;
+        }
+      }
+      if (doConsensus)
       {
-        calculator.registerWorker(new ComplementConsensusThread(this, ap));
+        if (calculator
+                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        {
+          calculator
+                  .registerWorker(new ComplementConsensusThread(this, ap));
+        }
       }
     }
   }
@@ -988,7 +1044,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean sortByTree = false;
 
-
   /**
    * 
    * 
@@ -1032,6 +1087,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       updateHiddenColumns();
     }
+    isColSelChanged(true);
   }
 
   /**
@@ -1052,6 +1108,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public boolean hasSelectedColumns()
+  {
+    ColumnSelection columnSelection = getColumnSelection();
+    return columnSelection != null && columnSelection.hasSelectedColumns();
+  }
+
+  @Override
   public boolean hasHiddenColumns()
   {
     return colSel != null && colSel.hasHiddenColumns();
@@ -1064,12 +1127,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
-  protected boolean hasHiddenRows = false;
-
   @Override
   public boolean hasHiddenRows()
   {
-    return hasHiddenRows;
+    return alignment.getHiddenSequences().getSize() > 0;
   }
 
   protected SequenceGroup selectionGroup;
@@ -1162,8 +1223,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
-            .hashCode();
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
       if (b)
@@ -1193,7 +1253,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showConsensus = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  private Map<SequenceI, ColorI> sequenceColours = new HashMap<SequenceI, ColorI>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1257,14 +1317,14 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void hideSelectedColumns()
   {
-    if (colSel.size() < 1)
+    if (colSel.isEmpty())
     {
       return;
     }
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
-
+    isColSelChanged(true);
   }
 
   public void hideColumns(int start, int end)
@@ -1277,17 +1337,19 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       colSel.hideColumns(start, end);
     }
+    isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-
+    isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
+    isColSelChanged(true);
   }
 
   // common hide/show seq stuff
@@ -1308,7 +1370,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         setSequenceAnnotationsVisible(seq, true);
       }
 
-      hasHiddenRows = false;
       hiddenRepSequences = null;
 
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1321,8 +1382,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void showSequence(int index)
   {
     List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
-            index,
-            hiddenRepSequences);
+            index, hiddenRepSequences);
     if (tmp.size() > 0)
     {
       if (selectionGroup == null)
@@ -1336,12 +1396,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup.addSequence(seq, false);
         setSequenceAnnotationsVisible(seq, true);
       }
-      // JBPNote: refactor: only update flag if we modified visiblity (used to
-      // do this regardless)
-      if (alignment.getHiddenSequences().getSize() < 1)
-      {
-        hasHiddenRows = false;
-      }
       firePropertyChange("alignment", null, alignment.getSequences());
       sendSelection();
     }
@@ -1370,12 +1424,44 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
-      hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
 
   /**
+   * Hides the specified sequence, or the sequences it represents
+   * 
+   * @param sequence
+   *          the sequence to hide, or keep as representative
+   * @param representGroup
+   *          if true, hide the current selection group except for the
+   *          representative sequence
+   */
+  public void hideSequences(SequenceI sequence, boolean representGroup)
+  {
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
+    {
+      hideSequence(new SequenceI[] { sequence });
+      return;
+    }
+
+    if (representGroup)
+    {
+      hideRepSequences(sequence, selectionGroup);
+      setSelectionGroup(null);
+      return;
+    }
+
+    int gsize = selectionGroup.getSize();
+    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+            new SequenceI[gsize]);
+
+    hideSequence(hseqs);
+    setSelectionGroup(null);
+    sendSelection();
+  }
+
+  /**
    * Set visibility for any annotations for the given sequence.
    * 
    * @param sequenceI
@@ -1383,11 +1469,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
           boolean visible)
   {
-    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (ann.sequenceRef == sequenceI)
+      for (AlignmentAnnotation ann : anns)
       {
-        ann.visible = visible;
+        if (ann.sequenceRef == sequenceI)
+        {
+          ann.visible = visible;
+        }
       }
     }
   }
@@ -1402,7 +1492,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable();
+      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1428,12 +1518,42 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  /**
+   * 
+   * @return null or the current reference sequence
+   */
+  public SequenceI getReferenceSeq()
+  {
+    return alignment.getSeqrep();
+  }
+
+  /**
+   * @param seq
+   * @return true iff seq is the reference for the alignment
+   */
+  public boolean isReferenceSeq(SequenceI seq)
+  {
+    return alignment.getSeqrep() == seq;
+  }
+
+  /**
+   * 
+   * @param seq
+   * @return true if there are sequences represented by this sequence that are
+   *         currently hidden
+   */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return alignment.getSeqrep()==seq || (hiddenRepSequences != null
-            && hiddenRepSequences.containsKey(seq));
+    return (hiddenRepSequences != null && hiddenRepSequences
+                    .containsKey(seq));
   }
 
+  /**
+   * 
+   * @param seq
+   * @return null or a sequence group containing the sequences that seq
+   *         represents
+   */
   public SequenceGroup getRepresentedSequences(SequenceI seq)
   {
     return (SequenceGroup) (hiddenRepSequences == null ? null
@@ -1453,7 +1573,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     colSel.invertColumnSelection(0, alignment.getWidth());
   }
 
-
   @Override
   public SequenceI[] getSelectionAsNewSequence()
   {
@@ -1481,7 +1600,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
   public SequenceI[] getSequenceSelection()
   {
@@ -1497,16 +1615,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
-  public CigarArray getViewAsCigars(
-          boolean selectedRegionOnly)
+  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
   {
     return new CigarArray(alignment, colSel,
             (selectedRegionOnly ? selectionGroup : null));
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
@@ -1514,7 +1629,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return getAlignmentView(selectedOnly, false);
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
@@ -1524,10 +1638,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
             markGroups);
   }
 
-
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
+    return getViewAsString(selectedRegionOnly, true);
+  }
+
+  @Override
+  public String[] getViewAsString(boolean selectedRegionOnly,
+          boolean exportHiddenSeqs)
+  {
     String[] selection = null;
     SequenceI[] seqs = null;
     int i, iSize;
@@ -1541,9 +1661,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth();
+      if (hasHiddenRows() && exportHiddenSeqs)
+      {
+        AlignmentI fullAlignment = alignment.getHiddenSequences()
+                .getFullAlignment();
+        iSize = fullAlignment.getHeight();
+        seqs = fullAlignment.getSequencesArray();
+        end = fullAlignment.getWidth();
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth();
+      }
     }
 
     selection = new String[iSize];
@@ -1562,7 +1693,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selection;
   }
 
-
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
@@ -1590,8 +1720,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
 
-      regions.add(new int[]
-      { start, end });
+      regions.add(new int[] { start, end });
 
       if (colSel != null && colSel.hasHiddenColumns())
       {
@@ -1606,19 +1735,23 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+  public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+          boolean selectedOnly)
   {
     ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
     AlignmentAnnotation[] aa;
-    if ((aa=alignment.getAlignmentAnnotation())!=null)
+    if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
-      for (AlignmentAnnotation annot:aa)
+      for (AlignmentAnnotation annot : aa)
       {
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
-        if (selectedOnly && selectionGroup!=null)
+        if (selectedOnly && selectionGroup != null)
+        {
+          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+                  selectionGroup.getEndRes(), clone);
+        }
+        else
         {
-          colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
-        } else {
           colSel.makeVisibleAnnotation(clone);
         }
         ala.add(clone);
@@ -1627,14 +1760,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ala;
   }
 
-
   @Override
   public boolean isPadGaps()
   {
     return padGaps;
   }
 
-
   @Override
   public void setPadGaps(boolean padGaps)
   {
@@ -1753,14 +1884,30 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (!alignment.isNucleotide())
     {
-      final Set<AlignedCodonFrame> codonMappings = alignment
+      final List<AlignedCodonFrame> codonMappings = alignment
               .getCodonFrames();
       if (codonMappings != null && !codonMappings.isEmpty())
       {
-        complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                "PID for cDNA", new Annotation[1], 0f, 100f,
-                AlignmentAnnotation.BAR_GRAPH);
-        initConsensus(complementConsensus);
+        boolean doConsensus = false;
+        for (AlignedCodonFrame mapping : codonMappings)
+        {
+          // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+          MapList[] mapLists = mapping.getdnaToProt();
+          // mapLists can be empty if project load has not finished resolving
+          // seqs
+          if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+          {
+            doConsensus = true;
+            break;
+          }
+        }
+        if (doConsensus)
+        {
+          complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  AlignmentAnnotation.BAR_GRAPH);
+          initConsensus(complementConsensus);
+        }
       }
     }
   }
@@ -1962,6 +2109,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     oldrfs.clear();
   }
+
   @Override
   public boolean isDisplayReferenceSeq()
   {
@@ -1981,14 +2129,14 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Color getSequenceColour(SequenceI seq)
+  public ColorI getSequenceColour(SequenceI seq)
   {
-    Color sqc = sequenceColours.get(seq);
-    return (sqc == null ? Color.white : sqc);
+    ColorI sqc = sequenceColours.get(seq);
+    return (sqc == null ? Colour.white : sqc);
   }
 
   @Override
-  public void setSequenceColour(SequenceI seq, Color col)
+  public void setSequenceColour(SequenceI seq, ColorI col)
   {
     if (col == null)
     {
@@ -2070,7 +2218,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean areFeaturesDisplayed()
   {
-    return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+    return featuresDisplayed != null
+            && featuresDisplayed.getRegisteredFeaturesCount() > 0;
   }
 
   /**
@@ -2084,6 +2233,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     viewStyle.setShowSequenceFeatures(b);
   }
+
   @Override
   public boolean isShowSequenceFeatures()
   {
@@ -2093,7 +2243,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
-    viewStyle.setShowSeqFeaturesHeight(selected);
+    viewStyle.setShowSequenceFeaturesHeight(selected);
   }
 
   @Override
@@ -2102,8 +2252,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return viewStyle.isShowSequenceFeaturesHeight();
   }
 
-
-
   @Override
   public void setShowAnnotation(boolean b)
   {
@@ -2144,7 +2292,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour()
    */
-  public Color getTextColour()
+  @Override
+  public ColorI getTextColour()
   {
     return viewStyle.getTextColour();
   }
@@ -2153,7 +2302,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour2()
    */
-  public Color getTextColour2()
+  @Override
+  public ColorI getTextColour2()
   {
     return viewStyle.getTextColour2();
   }
@@ -2162,6 +2312,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThresholdTextColour()
    */
+  @Override
   public int getThresholdTextColour()
   {
     return viewStyle.getThresholdTextColour();
@@ -2171,6 +2322,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isConservationColourSelected()
    */
+  @Override
   public boolean isConservationColourSelected()
   {
     return viewStyle.isConservationColourSelected();
@@ -2180,6 +2332,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isRenderGaps()
    */
+  @Override
   public boolean isRenderGaps()
   {
     return viewStyle.isRenderGaps();
@@ -2189,23 +2342,17 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowColourText()
    */
+  @Override
   public boolean isShowColourText()
   {
     return viewStyle.isShowColourText();
   }
-  /**
-   * @return
-   * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
-   */
-  public boolean isShowSeqFeaturesHeight()
-  {
-    return viewStyle.isShowSeqFeaturesHeight();
-  }
 
   /**
    * @param conservationColourSelected
    * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
    */
+  @Override
   public void setConservationColourSelected(
           boolean conservationColourSelected)
   {
@@ -2216,6 +2363,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showColourText
    * @see jalview.api.ViewStyleI#setShowColourText(boolean)
    */
+  @Override
   public void setShowColourText(boolean showColourText)
   {
     viewStyle.setShowColourText(showColourText);
@@ -2225,7 +2373,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour
    * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
    */
-  public void setTextColour(Color textColour)
+  @Override
+  public void setTextColour(ColorI textColour)
   {
     viewStyle.setTextColour(textColour);
   }
@@ -2234,6 +2383,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresholdTextColour
    * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
    */
+  @Override
   public void setThresholdTextColour(int thresholdTextColour)
   {
     viewStyle.setThresholdTextColour(thresholdTextColour);
@@ -2243,7 +2393,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour2
    * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
    */
-  public void setTextColour2(Color textColour2)
+  @Override
+  public void setTextColour2(ColorI textColour2)
   {
     viewStyle.setTextColour2(textColour2);
   }
@@ -2270,6 +2421,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIdWidth()
    */
+  @Override
   public int getIdWidth()
   {
     return viewStyle.getIdWidth();
@@ -2279,6 +2431,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param i
    * @see jalview.api.ViewStyleI#setIdWidth(int)
    */
+  @Override
   public void setIdWidth(int i)
   {
     viewStyle.setIdWidth(i);
@@ -2288,6 +2441,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isCentreColumnLabels()
    */
+  @Override
   public boolean isCentreColumnLabels()
   {
     return viewStyle.isCentreColumnLabels();
@@ -2297,6 +2451,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param centreColumnLabels
    * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
    */
+  @Override
   public void setCentreColumnLabels(boolean centreColumnLabels)
   {
     viewStyle.setCentreColumnLabels(centreColumnLabels);
@@ -2306,6 +2461,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showdbrefs
    * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
    */
+  @Override
   public void setShowDBRefs(boolean showdbrefs)
   {
     viewStyle.setShowDBRefs(showdbrefs);
@@ -2315,6 +2471,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowDBRefs()
    */
+  @Override
   public boolean isShowDBRefs()
   {
     return viewStyle.isShowDBRefs();
@@ -2324,6 +2481,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowNPFeats()
    */
+  @Override
   public boolean isShowNPFeats()
   {
     return viewStyle.isShowNPFeats();
@@ -2333,6 +2491,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param shownpfeats
    * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
    */
+  @Override
   public void setShowNPFeats(boolean shownpfeats)
   {
     viewStyle.setShowNPFeats(shownpfeats);
@@ -2356,7 +2515,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected void broadcastCommand(CommandI command, boolean undo)
   {
-    getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+    getStructureSelectionManager().commandPerformed(command, undo,
+            getVamsasSource());
   }
 
   /**
@@ -2464,6 +2624,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return startRes;
   }
 
+  @Override
   public int getEndRes()
   {
     return endRes;
@@ -2527,21 +2688,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   protected int findComplementScrollTarget(SearchResults sr)
   {
-    final AlignViewportI codingComplement = getCodingComplement();
-    if (codingComplement == null || !codingComplement.isFollowHighlight())
+    final AlignViewportI complement = getCodingComplement();
+    if (complement == null || !complement.isFollowHighlight())
     {
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
-            : codingComplement.getAlignment();
+    AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
+            .getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
     }
-    final Set<AlignedCodonFrame> mappings = proteinAlignment
+    final List<AlignedCodonFrame> mappings = proteinAlignment
             .getCodonFrames();
-  
+
     /*
      * Heuristic: find the first mapped sequence (if any) with a non-gapped
      * residue in the middle column of the visible region. Scroll the
@@ -2549,10 +2710,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int seqOffset = 0;
     SequenceI sequence = null;
+
+    /*
+     * locate 'middle' column (true middle if an odd number visible, left of
+     * middle if an even number visible)
+     */
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-    for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
+
+    /*
+     * searching to the bottom of the alignment gives smoother scrolling across
+     * all gapped visible regions
+     */
+    int lastSeq = alignment.getHeight() - 1;
+    List<AlignedCodonFrame> seqMappings = null;
+    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2563,15 +2736,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      List<AlignedCodonFrame> seqMappings = MappingUtils
-              .findMappingsForSequence(sequence, mappings);
+      seqMappings = MappingUtils
+              .findMappingsForSequenceAndOthers(sequence, mappings,
+                      getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
       }
     }
-  
-    if (sequence == null)
+
+    if (sequence == null || seqMappings == null || seqMappings.isEmpty())
     {
       /*
        * No ungapped mapped sequence in middle column - do nothing
@@ -2579,7 +2753,68 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     MappingUtils.addSearchResults(sr, sequence,
-            sequence.findPosition(middleColumn), mappings);
+            sequence.findPosition(middleColumn), seqMappings);
     return seqOffset;
   }
+
+  /**
+   * 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())
+            && !this.hasSelectedColumns())
+    {
+      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);
+      }
+    }
+  }
+
+  /**
+   * hold status of current selection group - defined on alignment or not.
+   */
+  private boolean selectionIsDefinedGroup = false;
+
+  @Override
+  public boolean isSelectionDefinedGroup()
+  {
+    if (selectionGroup == null)
+    {
+      return false;
+    }
+    if (isSelectionGroupChanged(true))
+    {
+      selectionIsDefinedGroup = false;
+      List<SequenceGroup> gps = alignment.getGroups();
+      if (gps == null || gps.size() == 0)
+      {
+        selectionIsDefinedGroup = false;
+      }
+      else
+      {
+        selectionIsDefinedGroup = gps.contains(selectionGroup);
+      }
+    }
+    return selectionGroup.getContext() == alignment
+            || selectionIsDefinedGroup;
+  }
 }