X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=c4ae76d1060f9c88418600834fbefb0eeeff86b7;hb=8d44c38e7028bcce53c0370dec67baa5d8d209c9;hp=d6aa400e9daa425449fc1d360734bf40d164edbd;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d6aa400..c4ae76d 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,17 +20,6 @@
  */
 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;
@@ -67,6 +56,17 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+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;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -75,7 +75,7 @@ import jalview.workers.StrucConsensusThread;
  * 
  */
 public abstract class AlignmentViewport implements AlignViewportI,
-        ViewStyleI, CommandListener, VamsasSource
+        CommandListener, VamsasSource
 {
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -95,6 +95,7 @@ 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 +105,7 @@ 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 +115,7 @@ 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 +125,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontStyle()
    */
+  @Override
   public int getFontStyle()
   {
     return viewStyle.getFontStyle();
@@ -131,6 +135,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontName()
    */
+  @Override
   public String getFontName()
   {
     return viewStyle.getFontName();
@@ -140,6 +145,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getFontSize()
    */
+  @Override
   public int getFontSize()
   {
     return viewStyle.getFontSize();
@@ -149,6 +155,7 @@ 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 +165,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isUpperCasebold()
    */
+  @Override
   public boolean isUpperCasebold()
   {
     return viewStyle.isUpperCasebold();
@@ -167,6 +175,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isSeqNameItalics()
    */
+  @Override
   public boolean isSeqNameItalics()
   {
     return viewStyle.isSeqNameItalics();
@@ -176,6 +185,7 @@ 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 +195,7 @@ 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 +205,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
    */
+  @Override
   public boolean getColourAppliesToAllGroups()
   {
     return viewStyle.getColourAppliesToAllGroups();
@@ -203,6 +215,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
    */
+  @Override
   public boolean getAbovePIDThreshold()
   {
     return viewStyle.getAbovePIDThreshold();
@@ -212,6 +225,7 @@ 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 +235,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIncrement()
    */
+  @Override
   public int getIncrement()
   {
     return viewStyle.getIncrement();
@@ -230,6 +245,7 @@ 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 +255,7 @@ 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 +265,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
    */
+  @Override
   public boolean getShowHiddenMarkers()
   {
     return viewStyle.getShowHiddenMarkers();
@@ -257,6 +275,7 @@ 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 +285,7 @@ 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 +295,7 @@ 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 +305,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
    */
+  @Override
   public boolean getScaleLeftWrapped()
   {
     return viewStyle.getScaleLeftWrapped();
@@ -293,6 +315,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
    */
+  @Override
   public boolean getScaleAboveWrapped()
   {
     return viewStyle.getScaleAboveWrapped();
@@ -302,6 +325,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getScaleRightWrapped()
    */
+  @Override
   public boolean getScaleRightWrapped()
   {
     return viewStyle.getScaleRightWrapped();
@@ -311,6 +335,7 @@ 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 +345,7 @@ 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 +355,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThreshold()
    */
+  @Override
   public int getThreshold()
   {
     return viewStyle.getThreshold();
@@ -338,6 +365,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowJVSuffix()
    */
+  @Override
   public boolean getShowJVSuffix()
   {
     return viewStyle.getShowJVSuffix();
@@ -347,6 +375,7 @@ 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 +385,7 @@ 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 +395,7 @@ 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 +405,7 @@ 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 +415,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getColourText()
    */
+  @Override
   public boolean getColourText()
   {
     return viewStyle.getColourText();
@@ -392,6 +425,7 @@ 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 +435,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrapAlignment()
    */
+  @Override
   public boolean getWrapAlignment()
   {
     return viewStyle.getWrapAlignment();
@@ -410,6 +445,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowText()
    */
+  @Override
   public boolean getShowText()
   {
     return viewStyle.getShowText();
@@ -419,6 +455,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getWrappedWidth()
    */
+  @Override
   public int getWrappedWidth()
   {
     return viewStyle.getWrappedWidth();
@@ -428,6 +465,7 @@ 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 +475,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharHeight()
    */
+  @Override
   public int getCharHeight()
   {
     return viewStyle.getCharHeight();
@@ -446,6 +485,7 @@ 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 +495,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getCharWidth()
    */
+  @Override
   public int getCharWidth()
   {
     return viewStyle.getCharWidth();
@@ -464,6 +505,7 @@ 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 +515,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowBoxes()
    */
+  @Override
   public boolean getShowBoxes()
   {
     return viewStyle.getShowBoxes();
@@ -482,6 +525,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getShowUnconserved()
    */
+  @Override
   public boolean getShowUnconserved()
   {
     return viewStyle.getShowUnconserved();
@@ -491,6 +535,7 @@ 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 +545,13 @@ 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 +586,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return isDataset;
   }
 
-
   private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
 
   protected ColumnSelection colSel = new ColumnSelection();
@@ -562,12 +598,11 @@ 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 +674,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
     }
-
   }
 
   @Override
@@ -988,7 +1022,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean sortByTree = false;
 
-
   /**
    * 
    * 
@@ -1064,12 +1097,10 @@ 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;
@@ -1162,7 +1193,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
             .hashCode();
     if (hc != -1 && hc != colselhash)
     {
@@ -1257,7 +1288,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void hideSelectedColumns()
   {
-    if (colSel.size() < 1)
+    if (colSel.isEmpty())
     {
       return;
     }
@@ -1308,7 +1339,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         setSequenceAnnotationsVisible(seq, true);
       }
 
-      hasHiddenRows = false;
       hiddenRepSequences = null;
 
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1321,8 +1351,7 @@ 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 +1365,6 @@ 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();
     }
@@ -1370,7 +1393,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
-      hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -1430,8 +1452,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return alignment.getSeqrep()==seq || (hiddenRepSequences != null
-            && hiddenRepSequences.containsKey(seq));
+    return alignment.getSeqrep() == seq
+            || (hiddenRepSequences != null && hiddenRepSequences
+                    .containsKey(seq));
   }
 
   public SequenceGroup getRepresentedSequences(SequenceI seq)
@@ -1453,7 +1476,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     colSel.invertColumnSelection(0, alignment.getWidth());
   }
 
-
   @Override
   public SequenceI[] getSelectionAsNewSequence()
   {
@@ -1481,7 +1503,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
   public SequenceI[] getSequenceSelection()
   {
@@ -1497,16 +1518,13 @@ 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 +1532,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return getAlignmentView(selectedOnly, false);
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
@@ -1524,7 +1541,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
             markGroups);
   }
 
-
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
@@ -1562,7 +1578,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selection;
   }
 
-
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
@@ -1590,8 +1605,7 @@ 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 +1620,23 @@ 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 +1645,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ala;
   }
 
-
   @Override
   public boolean isPadGaps()
   {
     return padGaps;
   }
 
-
   @Override
   public void setPadGaps(boolean padGaps)
   {
@@ -1962,6 +1978,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     oldrfs.clear();
   }
+
   @Override
   public boolean isDisplayReferenceSeq()
   {
@@ -2070,7 +2087,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean areFeaturesDisplayed()
   {
-    return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+    return featuresDisplayed != null
+            && featuresDisplayed.getRegisterdFeaturesCount() > 0;
   }
 
   /**
@@ -2084,6 +2102,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     viewStyle.setShowSequenceFeatures(b);
   }
+
   @Override
   public boolean isShowSequenceFeatures()
   {
@@ -2093,7 +2112,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
-    viewStyle.setShowSeqFeaturesHeight(selected);
+    viewStyle.setShowSequenceFeaturesHeight(selected);
   }
 
   @Override
@@ -2102,8 +2121,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return viewStyle.isShowSequenceFeaturesHeight();
   }
 
-
-
   @Override
   public void setShowAnnotation(boolean b)
   {
@@ -2144,6 +2161,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour()
    */
+  @Override
   public Color getTextColour()
   {
     return viewStyle.getTextColour();
@@ -2153,6 +2171,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getTextColour2()
    */
+  @Override
   public Color getTextColour2()
   {
     return viewStyle.getTextColour2();
@@ -2162,6 +2181,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getThresholdTextColour()
    */
+  @Override
   public int getThresholdTextColour()
   {
     return viewStyle.getThresholdTextColour();
@@ -2171,6 +2191,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isConservationColourSelected()
    */
+  @Override
   public boolean isConservationColourSelected()
   {
     return viewStyle.isConservationColourSelected();
@@ -2180,6 +2201,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isRenderGaps()
    */
+  @Override
   public boolean isRenderGaps()
   {
     return viewStyle.isRenderGaps();
@@ -2189,23 +2211,17 @@ 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 +2232,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param showColourText
    * @see jalview.api.ViewStyleI#setShowColourText(boolean)
    */
+  @Override
   public void setShowColourText(boolean showColourText)
   {
     viewStyle.setShowColourText(showColourText);
@@ -2225,6 +2242,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour
    * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
    */
+  @Override
   public void setTextColour(Color textColour)
   {
     viewStyle.setTextColour(textColour);
@@ -2234,6 +2252,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param thresholdTextColour
    * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
    */
+  @Override
   public void setThresholdTextColour(int thresholdTextColour)
   {
     viewStyle.setThresholdTextColour(thresholdTextColour);
@@ -2243,6 +2262,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @param textColour2
    * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
    */
+  @Override
   public void setTextColour2(Color textColour2)
   {
     viewStyle.setTextColour2(textColour2);
@@ -2270,6 +2290,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#getIdWidth()
    */
+  @Override
   public int getIdWidth()
   {
     return viewStyle.getIdWidth();
@@ -2279,6 +2300,7 @@ 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 +2310,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isCentreColumnLabels()
    */
+  @Override
   public boolean isCentreColumnLabels()
   {
     return viewStyle.isCentreColumnLabels();
@@ -2297,6 +2320,7 @@ 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 +2330,7 @@ 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 +2340,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowDBRefs()
    */
+  @Override
   public boolean isShowDBRefs()
   {
     return viewStyle.isShowDBRefs();
@@ -2324,6 +2350,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * @return
    * @see jalview.api.ViewStyleI#isShowNPFeats()
    */
+  @Override
   public boolean isShowNPFeats()
   {
     return viewStyle.isShowNPFeats();
@@ -2333,6 +2360,7 @@ 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 +2384,8 @@ 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 +2493,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return startRes;
   }
 
+  @Override
   public int getEndRes()
   {
     return endRes;
@@ -2527,21 +2557,21 @@ 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
             .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 +2579,21 @@ 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;
+    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2570,7 +2611,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         break;
       }
     }
-  
+
     if (sequence == null)
     {
       /*