JAL-1925 update source version in license

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5617bcf..65567dc 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -540,7 +540,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return isDataset;
   }
 
-
   private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
 
   protected ColumnSelection colSel = new ColumnSelection();
@@ -553,12 +552,11 @@ 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
@@ -630,7 +628,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
     }
-
   }
 
   @Override
@@ -979,7 +976,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean sortByTree = false;
 
-
   /**
    * 
    * 
@@ -1061,7 +1057,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return alignment.getHiddenSequences().getSize() > 0;
   }
 
-
   protected SequenceGroup selectionGroup;
 
   public void setSequenceSetId(String newid)
@@ -1310,8 +1305,7 @@ 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)
@@ -1412,8 +1406,9 @@ 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)
@@ -1435,7 +1430,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     colSel.invertColumnSelection(0, alignment.getWidth());
   }
 
-
   @Override
   public SequenceI[] getSelectionAsNewSequence()
   {
@@ -1463,7 +1457,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sequences;
   }
 
-
   @Override
   public SequenceI[] getSequenceSelection()
   {
@@ -1479,16 +1472,13 @@ 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)
@@ -1496,7 +1486,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return getAlignmentView(selectedOnly, false);
   }
 
-
   @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
@@ -1506,7 +1495,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
             markGroups);
   }
 
-
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
@@ -1544,7 +1532,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selection;
   }
 
-
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
@@ -1572,8 +1559,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
 
-      regions.add(new int[]
-      { start, end });
+      regions.add(new int[] { start, end });
 
       if (colSel != null && colSel.hasHiddenColumns())
       {
@@ -1588,19 +1574,23 @@ 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);
@@ -1609,14 +1599,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ala;
   }
 
-
   @Override
   public boolean isPadGaps()
   {
     return padGaps;
   }
 
-
   @Override
   public void setPadGaps(boolean padGaps)
   {
@@ -1944,6 +1932,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     oldrfs.clear();
   }
+
   @Override
   public boolean isDisplayReferenceSeq()
   {
@@ -2052,7 +2041,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean areFeaturesDisplayed()
   {
-    return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+    return featuresDisplayed != null
+            && featuresDisplayed.getRegisterdFeaturesCount() > 0;
   }
 
   /**
@@ -2066,6 +2056,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     viewStyle.setShowSequenceFeatures(b);
   }
+
   @Override
   public boolean isShowSequenceFeatures()
   {
@@ -2084,8 +2075,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return viewStyle.isShowSequenceFeaturesHeight();
   }
 
-
-
   @Override
   public void setShowAnnotation(boolean b)
   {
@@ -2330,7 +2319,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected void broadcastCommand(CommandI command, boolean undo)
   {
-    getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+    getStructureSelectionManager().commandPerformed(command, undo,
+            getVamsasSource());
   }
 
   /**
@@ -2501,21 +2491,21 @@ 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
@@ -2531,7 +2521,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     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))
@@ -2549,7 +2545,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         break;
       }
     }
-  
+
     if (sequence == null)
     {
       /*