X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=850c68eec9c9ff6cbf960121864e0d69109f7cf5;hb=16d109024847af92482237e43f99b82fd997451a;hp=fdad0ceb3df052f6695bee968ceb450dd190c7cc;hpb=bf8275c621048462bd0275e31bf490dca443b477;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fdad0ce..850c68e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -67,6 +67,7 @@ import java.util.BitSet;
 import java.util.Deque;
 import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -661,7 +662,7 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs);
+        sg.setColourScheme(cs.getInstance(this, sg));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
@@ -1338,7 +1339,10 @@ public abstract class AlignmentViewport
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    if (changeSupport != null)
+    {
+      changeSupport.removePropertyChangeListener(listener);
+    }
   }
 
   /**
@@ -1632,6 +1636,7 @@ public abstract class AlignmentViewport
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -1737,8 +1742,12 @@ public abstract class AlignmentViewport
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns()
-              .getVisibleSequenceStrings(start, end, seqs);
+      for (i = 0; i < iSize; i++)
+      {
+        Iterator<int[]> blocks = alignment.getHiddenColumns()
+                .getVisContigsIterator(start, end + 1, false);
+        selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+      }
     }
     else
     {
@@ -1765,10 +1774,10 @@ public abstract class AlignmentViewport
       {
         if (start == 0)
         {
-          start = hidden.adjustForHiddenColumns(start);
+          start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = hidden.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1783,8 +1792,8 @@ public abstract class AlignmentViewport
 
       if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = hidden.adjustForHiddenColumns(end);
-        start = hidden.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.visibleToAbsoluteColumn(end);
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
@@ -1806,13 +1815,13 @@ public abstract class AlignmentViewport
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(
+          clone.makeVisibleAnnotation(
                   selectionGroup.getStartRes(), selectionGroup.getEndRes(),
-                  clone);
+                  alignment.getHiddenColumns());
         }
         else
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+          clone.makeVisibleAnnotation(alignment.getHiddenColumns());
         }
         ala.add(clone);
       }
@@ -2778,7 +2787,7 @@ public abstract class AlignmentViewport
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = ranges
-            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2946,4 +2955,68 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  /**
+   * flag set to indicate if structure views might be out of sync with sequences
+   * in the alignment
+   */
+
+  private boolean needToUpdateStructureViews = false;
+
+  @Override
+  public boolean isUpdateStructures()
+  {
+    return needToUpdateStructureViews;
+  }
+
+  @Override
+  public void setUpdateStructures(boolean update)
+  {
+    needToUpdateStructureViews = update;
+  }
+
+  @Override
+  public boolean needToUpdateStructureViews()
+  {
+    boolean update = needToUpdateStructureViews;
+    needToUpdateStructureViews = false;
+    return update;
+  }
+
+  @Override
+  public void addSequenceGroup(SequenceGroup sequenceGroup)
+  {
+    alignment.addGroup(sequenceGroup);
+
+    Color col = sequenceGroup.idColour;
+    if (col != null)
+    {
+      col = col.brighter();
+
+      for (SequenceI sq : sequenceGroup.getSequences())
+      {
+        setSequenceColour(sq, col);
+      }
+    }
+
+    if (codingComplement != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils
+              .mapSequenceGroup(sequenceGroup, this, codingComplement);
+      if (mappedGroup.getSequences().size() > 0)
+      {
+        codingComplement.getAlignment().addGroup(mappedGroup);
+
+        if (col != null)
+        {
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+      // propagate the structure view update flag according to our own setting
+      codingComplement.setUpdateStructures(needToUpdateStructureViews);
+    }
+  }
 }