JAL-2388 Applied ViewportRanges to code

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1f91935..5f84a5d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1287,14 +1287,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean followHighlight = true;
 
-  /*private int startRes;
-
-  private int endRes;
-
-  private int startSeq;
-
-  private int endSeq;*/
-
   /**
    * Property change listener for changes in alignment
    * 
@@ -2652,50 +2644,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ranges;
   }
 
-  @Override
-  public int getStartRes()
-  {
-    return ranges.getStartRes();
-  }
-
-  @Override
-  public int getEndRes()
-  {
-    return ranges.getEndRes();
-  }
-
-  @Override
-  public int getStartSeq()
-  {
-    return ranges.getStartSeq();
-  }
-
-  public void setStartRes(int res)
-  {
-    ranges.setStartRes(res);
-  }
-
-  public void setStartSeq(int seq)
-  {
-    ranges.setStartSeq(seq);
-  }
-
-  public void setEndRes(int res)
-  {
-    ranges.setEndRes(res);
-  }
-
-  public void setEndSeq(int seq)
-  {
-    ranges.setEndSeq(seq);
-  }
-
-  @Override
-  public int getEndSeq()
-  {
-    return ranges.getEndSeq();
-  }
-
   /**
    * Helper method to populate the SearchResults with the location in the
    * complementary alignment to scroll to, in order to match this one.
@@ -2733,7 +2681,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * locate 'middle' column (true middle if an odd number visible, left of
      * middle if an even number visible)
      */
-    int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+    int middleColumn = ranges.getStartRes()
+            + (ranges.getEndRes() - ranges.getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
 
@@ -2743,7 +2692,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))