X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensions.java;h=d2912d8996be680821b48c109f6e0193c4dd690e;hb=93cdde7955263e9c0fc81621d73cd3157c02b944;hp=a837d53b83d6d435b9d4218ea160c5505acc09c2;hpb=460c037bef9ec113c2a46010c443d85e73347592;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index a837d53..d2912d8 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -31,24 +31,41 @@ import java.awt.Graphics;
 public abstract class OverviewDimensions
 {
   protected static final int MAX_WIDTH = 400;
+
   protected static final int MIN_WIDTH = 120;
+
   protected static final int MIN_SEQ_HEIGHT = 40;
+
   protected static final int MAX_SEQ_HEIGHT = 300;
 
   private static final int DEFAULT_GRAPH_HEIGHT = 20;
 
   protected int width;
+
   protected int sequencesHeight;
+
   protected int graphHeight = DEFAULT_GRAPH_HEIGHT;
+
   protected int boxX = -1;
+
   protected int boxY = -1;
+
   protected int boxWidth = -1;
+
   protected int boxHeight = -1;
-  protected int scrollCol = -1;
-  protected int scrollRow = -1;
+
   protected int alwidth;
+
   protected int alheight;
 
+  /**
+   * Create an OverviewDimensions object
+   * 
+   * @param ranges
+   *          positional properties of the viewport
+   * @param showAnnotationPanel
+   *          true if the annotation panel is to be shown, false otherwise
+   */
   public OverviewDimensions(ViewportRanges ranges,
           boolean showAnnotationPanel)
   {
@@ -97,16 +114,6 @@ public abstract class OverviewDimensions
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
-  public int getScrollCol()
-  {
-    return scrollCol;
-  }
-
-  public int getScrollRow()
-  {
-    return scrollRow;
-  }
-
   public int getBoxX()
   {
     return boxX;
@@ -218,8 +225,8 @@ public abstract class OverviewDimensions
    */
   protected abstract void resetAlignmentDims();
 
-  protected void setBoxPosition(int startRes, int endRes, int startSeq,
-          int endSeq)
+  protected void setBoxPosition(int startRes, int startSeq, int vpwidth,
+          int vpheight)
   {
     resetAlignmentDims();
 
@@ -228,12 +235,9 @@ public abstract class OverviewDimensions
     boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
     // boxWidth is the width in residues translated to pixels
-    // since the box includes both the start and end residues, add 1 to the
-    // difference
-    boxWidth = Math
-            .round((float) (endRes - startRes + 1) * width / alwidth);
+    boxWidth = Math.round((float) vpwidth * width / alwidth);
+
     // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) (endSeq - startSeq + 1)
-            * sequencesHeight / alheight);
+    boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
   }
 }
\ No newline at end of file