JAL-2388 Renamed viewport position props to viewport ranges

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 6cdc998..c6312ab 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -33,7 +33,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.util.Hashtable;
@@ -47,7 +47,7 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  ViewportPositionProps getPosProps();
+  ViewportRanges getRanges();
   
   int getEndRes();
 

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index f5d6ce7..30817d5 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -39,7 +39,7 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 
@@ -75,13 +75,10 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
-    posProps = new ViewportPositionProps(this.alignment);
+    ranges = new ViewportRanges(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
-    this.setStartRes(0);
-    this.setEndRes(al.getWidth() - 1);
-    this.setStartSeq(0);
-    this.setEndSeq(al.getHeight() - 1);
+
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index dd7c8fa..e864337 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -724,7 +724,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       x = 0;
     }
-    ;
+
 
     hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
     vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
@@ -763,14 +763,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
 
     av.setStartSeq(y);
-
-    int endSeq = y + vextent;
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
-
-    av.setEndSeq(endSeq);
+    av.setEndSeq(y + vextent);
     av.setStartRes(x);
     av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
             .getCharWidth())) - 1);

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 1d11b67..e2d986e 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -76,7 +76,7 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -143,7 +143,7 @@ public class OverviewPanel extends Panel implements Runnable,
   {
     od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av
-            .getPosProps());
+            .getRanges());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
@@ -339,7 +339,7 @@ public class OverviewPanel extends Panel implements Runnable,
   public void setBoxPosition()
   {
     od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
 

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 598bd69..11321eb 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -51,7 +51,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -238,7 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    posProps = new ViewportPositionProps(this.alignment);
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 2c77942..1c49b8a 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -89,7 +89,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(alPanel);
 
-    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
 
     addComponentListener(new ComponentAdapter()
     {
@@ -113,7 +113,7 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                   .getAlignment().getHiddenSequences(), av
-                  .getColumnSelection(), av.getPosProps());
+                  .getColumnSelection(), av.getRanges());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -128,7 +128,7 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                   .getAlignment().getHiddenSequences(), av
-                  .getColumnSelection(), av.getPosProps());
+                  .getColumnSelection(), av.getRanges());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -327,7 +327,7 @@ public class OverviewPanel extends JPanel implements Runnable
   public void setBoxPosition()
   {
     od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
 

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 47f7d9d..1f91935 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -78,7 +78,7 @@ import java.util.Map;
 public abstract class AlignmentViewport implements AlignViewportI,
         CommandListener, VamsasSource
 {
-  protected ViewportPositionProps posProps;
+  protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -2647,54 +2647,53 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public ViewportPositionProps getPosProps()
+  public ViewportRanges getRanges()
   {
-    return posProps;
+    return ranges;
   }
 
   @Override
   public int getStartRes()
   {
-    return posProps.getStartRes();
+    return ranges.getStartRes();
   }
 
   @Override
   public int getEndRes()
   {
-    return posProps.getEndRes();
+    return ranges.getEndRes();
   }
 
   @Override
   public int getStartSeq()
   {
-    return posProps.getStartSeq();
+    return ranges.getStartSeq();
   }
 
   public void setStartRes(int res)
   {
-    posProps.setStartRes(res);
-    // this.startRes = res;
+    ranges.setStartRes(res);
   }
 
   public void setStartSeq(int seq)
   {
-    posProps.setStartSeq(seq);
+    ranges.setStartSeq(seq);
   }
 
   public void setEndRes(int res)
   {
-    posProps.setEndRes(res);
+    ranges.setEndRes(res);
   }
 
   public void setEndSeq(int seq)
   {
-    posProps.setEndSeq(seq);
+    ranges.setEndSeq(seq);
   }
 
   @Override
   public int getEndSeq()
   {
-    return posProps.getEndSeq();
+    return ranges.getEndSeq();
   }
 
   /**

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index b34c85d..1e9eaf7 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -69,24 +69,24 @@ public class OverviewDimensions
   /**
    * Create an OverviewDimensions object
    * 
-   * @param props
+   * @param ranges
    *          positional properties of the viewport
    * @param showAnnotationPanel
    *          true if the annotation panel is to be shown, false otherwise
    */
-  public OverviewDimensions(ViewportPositionProps props,
+  public OverviewDimensions(ViewportRanges ranges,
           boolean showAnnotationPanel)
   {
     // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) props.getAbsoluteAlignmentWidth()
-            / (float) props.getAbsoluteAlignmentHeight();
+    float initialScale = (float) ranges.getAbsoluteAlignmentWidth()
+            / (float) ranges.getAbsoluteAlignmentHeight();
 
     if (!showAnnotationPanel)
     {
       graphHeight = 0;
     }
 
-    if (props.getAbsoluteAlignmentWidth() > props
+    if (ranges.getAbsoluteAlignmentWidth() > ranges
             .getAbsoluteAlignmentHeight())
     {
       // wider
@@ -121,18 +121,18 @@ public class OverviewDimensions
    *          hidden sequences
    * @param hiddenCols
    *          hidden columns
-   * @param props
+   * @param ranges
    *          viewport position properties
    */
   public void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
-          ViewportPositionProps props)
+          ViewportRanges ranges)
   {
     int x = mousex;
     int y = mousey;
 
-    int alwidth = props.getAbsoluteAlignmentWidth();
-    int alheight = props.getAbsoluteAlignmentHeight();
+    int alwidth = ranges.getAbsoluteAlignmentWidth();
+    int alheight = ranges.getAbsoluteAlignmentHeight();
 
     if (x < 0)
     {
@@ -156,7 +156,7 @@ public class OverviewDimensions
     int xAsRes = Math.round((float) x * alwidth / width);
 
     // get viewport width in residues
-    int vpwidth = props.getEndRes() - props.getStartRes() + 1;
+    int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
 
     // get where x should be when accounting for hidden cols
     // if x is in a hidden col region, shift to left - but we still need
@@ -191,7 +191,7 @@ public class OverviewDimensions
 
     // get viewport height in sequences
     // add 1 because height includes both endSeq and startSeq
-    int vpheight = props.getEndSeq() - props.getStartSeq() + 1;
+    int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
 
     // get where y should be when accounting for hidden rows
     // if y is in a hidden row region, shift up - but we still need absolute
@@ -231,22 +231,22 @@ public class OverviewDimensions
    *          hidden sequences
    * @param hiddenCols
    *          hidden columns
-   * @param props
+   * @param ranges
    *          viewport position properties
    */
   public void setBoxPosition(HiddenSequences hiddenSeqs,
-          ColumnSelection hiddenCols, ViewportPositionProps props)
+          ColumnSelection hiddenCols, ViewportRanges ranges)
   {
-    int alwidth = props.getAbsoluteAlignmentWidth();
-    int alheight = props.getAbsoluteAlignmentHeight();
+    int alwidth = ranges.getAbsoluteAlignmentWidth();
+    int alheight = ranges.getAbsoluteAlignmentHeight();
 
     // work with absolute values of startRes and endRes
-    int startRes = hiddenCols.adjustForHiddenColumns(props.getStartRes());
-    int endRes = hiddenCols.adjustForHiddenColumns(props.getEndRes());
+    int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
+    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
 
     // work with absolute values of startSeq and endSeq
-    int startSeq = hiddenSeqs.adjustForHiddenSeqs(props.getStartSeq());
-    int endSeq = hiddenSeqs.adjustForHiddenSeqs(props.getEndSeq());
+    int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
+    int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
 
     // boxX, boxY is the x,y location equivalent to startRes, startSeq
     boxX = Math.round((float) startRes * width / alwidth);

diff --git a/src/jalview/viewmodel/ViewportPositionProps.java b/src/jalview/viewmodel/ViewportRanges.java
similarity index 89%
rename from src/jalview/viewmodel/ViewportPositionProps.java
rename to src/jalview/viewmodel/ViewportRanges.java
index 61dd18c..5c8cdb6 100644 (file)
--- a/src/jalview/viewmodel/ViewportPositionProps.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -23,10 +23,11 @@ package jalview.viewmodel;
 import jalview.datamodel.AlignmentI;
 
 /**
- * Supplies and updates viewport properties relating to position such as: start
- * and end residues and sequences
+ * Embryonic class which: Supplies and updates viewport properties relating to
+ * position such as: start and end residues and sequences; ideally will serve
+ * hidden columns/rows too
  */
-public class ViewportPositionProps extends ViewportProperties
+public class ViewportRanges extends ViewportProperties
 {
   // start residue of viewport
   private int startRes;
@@ -49,7 +50,7 @@ public class ViewportPositionProps extends ViewportProperties
    * @param alignment
    *          the viewport's alignment
    */
-  public ViewportPositionProps(AlignmentI alignment)
+  public ViewportRanges(AlignmentI alignment)
   {
     // initial values of viewport settings
     this.startRes = 0;
@@ -59,12 +60,6 @@ public class ViewportPositionProps extends ViewportProperties
     this.al = alignment;
   }
 
-  // ways to update values
-
-  // ways to notify of changes
-
-  // ways to supply positional information
-
   /**
    * Get alignment width in cols, including hidden cols
    */
@@ -112,9 +107,9 @@ public class ViewportPositionProps extends ViewportProperties
     {
       res = al.getWidth() - 1;
     }
-    else if (res < 1)
+    else if (res < 0)
     {
-      res = 1;
+      res = 0;
     }
     this.endRes = res;
   }
@@ -150,9 +145,9 @@ public class ViewportPositionProps extends ViewportProperties
     {
       seq = al.getHeight() - 1;
     }
-    else if (seq < 1)
+    else if (seq < 0)
     {
-      seq = 1;
+      seq = 0;
     }
     this.endSeq = seq;
   }

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index a1d9f31..398fec3 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -52,7 +52,7 @@ public class OverviewDimensionsTest
   int alheight;
   int alwidth;
 
-  ViewportPositionProps posProps;
+  ViewportRanges vpranges;
 
   Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
 
@@ -75,33 +75,33 @@ public class OverviewDimensionsTest
     }
     hiddenCols.revealAllHiddenColumns();
     
-    posProps = new ViewportPositionProps(al);
-    posProps.setStartRes(0);
-    posProps.setEndRes(62);
-    posProps.setStartSeq(0);
-    posProps.setEndSeq(17);
+    vpranges = new ViewportRanges(al);
+    vpranges.setStartRes(0);
+    vpranges.setEndRes(62);
+    vpranges.setStartSeq(0);
+    vpranges.setEndSeq(17);
 
-    viewHeight = posProps.getEndSeq() - posProps.getStartSeq() + 1;
-    viewWidth = posProps.getEndRes() - posProps.getStartRes() + 1;
+    viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
+    viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
 
     ColumnSelection hiddenCols = new ColumnSelection();
 
-    od = new OverviewDimensions(posProps, true);
+    od = new OverviewDimensions(vpranges, true);
     // Initial box sizing - default path through code
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
 
     mouseClick(od, 0, 0);
     moveViewport(0, 0);
 
     // calculate before hidden columns so we get absolute values
-    alheight = posProps.getAbsoluteAlignmentHeight();
-    alwidth = posProps.getAbsoluteAlignmentWidth();
+    alheight = vpranges.getAbsoluteAlignmentHeight();
+    alwidth = vpranges.getAbsoluteAlignmentWidth();
 
-    boxWidth = Math.round((float) (posProps.getEndRes()
-            - posProps.getStartRes() + 1)
+    boxWidth = Math.round((float) (vpranges.getEndRes()
+            - vpranges.getStartRes() + 1)
             * od.getWidth() / alwidth);
-    boxHeight = Math.round((float) (posProps.getEndSeq()
-            - posProps.getStartSeq() + 1)
+    boxHeight = Math.round((float) (vpranges.getEndSeq()
+            - vpranges.getStartSeq() + 1)
             * od.getSequencesHeight() / alheight);
   }
 
@@ -134,7 +134,7 @@ public class OverviewDimensionsTest
     // test for alignment with width > height
     SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
     Alignment al1 = new Alignment(seqs1);
-    ViewportPositionProps props = new ViewportPositionProps(al1);
+    ViewportRanges props = new ViewportRanges(al1);
 
     OverviewDimensions od = new OverviewDimensions(props, true);
     int scaledHeight = 267;
@@ -146,7 +146,7 @@ public class OverviewDimensionsTest
     // test for alignment with width < height
     SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
     Alignment al2 = new Alignment(seqs2);
-    props = new ViewportPositionProps(al2);
+    props = new ViewportRanges(al2);
 
     od = new OverviewDimensions(props, true);
     int scaledWidth = 300;
@@ -159,7 +159,7 @@ public class OverviewDimensionsTest
     // min value
     SequenceI[] seqs3 = new SequenceI[] { seqe };
     Alignment al3 = new Alignment(seqs3);
-    props = new ViewportPositionProps(al3);
+    props = new ViewportRanges(al3);
 
     od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
@@ -171,7 +171,7 @@ public class OverviewDimensionsTest
     SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
         seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
     Alignment al4 = new Alignment(seqs4);
-    props = new ViewportPositionProps(al4);
+    props = new ViewportRanges(al4);
 
     od = new OverviewDimensions(props, true);
     assertEquals(od.getGraphHeight(), defaultGraphHeight);
@@ -180,7 +180,7 @@ public class OverviewDimensionsTest
     assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
 
     Alignment al5 = new Alignment(seqs4);
-    props = new ViewportPositionProps(al5);
+    props = new ViewportRanges(al5);
 
     od = new OverviewDimensions(props, false);
     assertEquals(od.getGraphHeight(), 0);
@@ -198,7 +198,7 @@ public class OverviewDimensionsTest
   public void testSetBoxFromMouseClick()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -297,7 +297,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenColsAtStart()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -309,7 +309,7 @@ public class OverviewDimensionsTest
     int lastHiddenCol = 30;
     hiddenCols.hideColumns(0, lastHiddenCol);
 
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
     assertEquals(od.getBoxX(),
             Math.round((float) (lastHiddenCol + 1) * od.getWidth()
                     / alwidth));
@@ -362,7 +362,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenColsInMiddle()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -374,7 +374,7 @@ public class OverviewDimensionsTest
     int lastHidden = 73;
     hiddenCols.hideColumns(firstHidden, lastHidden);
 
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -464,7 +464,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenColsAtEnd()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -475,7 +475,7 @@ public class OverviewDimensionsTest
     int firstHidden = 140;
     int lastHidden = 164;
     hiddenCols.hideColumns(firstHidden, lastHidden);
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -791,7 +791,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenRowsAtStart()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -804,7 +804,7 @@ public class OverviewDimensionsTest
     int lastHiddenRow = 30;
     hideSequences(0, lastHiddenRow);
 
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
             Math.round((float) (lastHiddenRow + 1)
@@ -838,7 +838,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenRowsInMiddle()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -853,7 +853,7 @@ public class OverviewDimensionsTest
     int lastHiddenRow = 54;
     hideSequences(firstHiddenRow, lastHiddenRow);
 
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
 
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
@@ -897,7 +897,7 @@ public class OverviewDimensionsTest
   public void testFromMouseWithHiddenRowsAtEnd()
   {
     od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -911,7 +911,7 @@ public class OverviewDimensionsTest
     int lastHidden = 524;
     hideSequences(firstHidden, lastHidden);
 
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -958,9 +958,9 @@ public class OverviewDimensionsTest
    */
   private void moveViewportH(int startRes)
   {
-    posProps.setStartRes(startRes);
-    posProps.setEndRes(startRes + viewWidth - 1);
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    vpranges.setStartRes(startRes);
+    vpranges.setEndRes(startRes + viewWidth - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
   /*
@@ -968,9 +968,9 @@ public class OverviewDimensionsTest
    */
   private void moveViewportV(int startSeq)
   {
-    posProps.setStartSeq(startSeq);
-    posProps.setEndSeq(startSeq + viewHeight - 1);
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    vpranges.setStartSeq(startSeq);
+    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
   /*
@@ -978,11 +978,11 @@ public class OverviewDimensionsTest
    */
   private void moveViewport(int startRes, int startSeq)
   {
-    posProps.setStartRes(startRes);
-    posProps.setEndRes(startRes + viewWidth - 1);
-    posProps.setStartSeq(startSeq);
-    posProps.setEndSeq(startSeq + viewHeight - 1);
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    vpranges.setStartRes(startRes);
+    vpranges.setEndRes(startRes + viewWidth - 1);
+    vpranges.setStartSeq(startSeq);
+    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
 
   /*
@@ -991,17 +991,17 @@ public class OverviewDimensionsTest
   private void mouseClick(OverviewDimensions od, int x, int y)
   {
     od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols,
-            posProps);
+            vpranges);
 
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally
 
-    posProps.setStartRes(od.getScrollCol());
-    posProps.setEndRes(od.getScrollCol() + viewWidth - 1);
-    posProps.setStartSeq(od.getScrollRow());
-    posProps.setEndSeq(od.getScrollRow() + viewHeight - 1);
-    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+    vpranges.setStartRes(od.getScrollCol());
+    vpranges.setEndRes(od.getScrollCol() + viewWidth - 1);
+    vpranges.setStartSeq(od.getScrollRow());
+    vpranges.setEndSeq(od.getScrollRow() + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
   }
   
   /*