X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=ea6c6f8c401a7c06f55e810dc744554dedc045f1;hb=83be20f1d8274aa0044acc72c427abef766d8dd1;hp=44dfe8d0fe96b969b81b0bdc0329485fca68348f;hpb=62086b8b7a0b9436c445a94bfab5eff253adb6d5;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 44dfe8d..ea6c6f8 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;
 
@@ -1740,8 +1741,12 @@ 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
     {
@@ -1771,7 +1776,7 @@ public abstract class AlignmentViewport
           start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = hidden.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1787,7 +1792,7 @@ public abstract class AlignmentViewport
       if (hidden != null && hidden.hasHiddenColumns())
       {
         start = hidden.visibleToAbsoluteColumn(end);
-        start = hidden.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
@@ -2781,7 +2786,7 @@ 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))
@@ -2949,4 +2954,25 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  List<SequenceI> highlightedSeqs = null;
+
+  /**
+   * Highlight the IDs for the given sequences call alignPanel.repaint() to
+   * update view after setting.
+   * 
+   * @param list
+   *          List<SequenceI>
+   */
+  @Override
+  public void setHighlightedSeqs(List<SequenceI> list)
+  {
+    highlightedSeqs = list;
+  }
+
+  @Override
+  public List<SequenceI> getHighlightedSeqs()
+  {
+    return highlightedSeqs;
+  }
 }