JAL-3626 from JAL-3253-applet web page embedding

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

diff --git a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
index 1cc42bb..598b989 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
@@ -20,6 +20,8 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Dimension;
+
 import jalview.api.AlignmentColsCollectionI;
 import jalview.api.AlignmentRowsCollectionI;
 import jalview.datamodel.AlignmentI;
@@ -38,10 +40,21 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   private int ydiff; // when dragging, difference in alignment units between
                      // start sequence and original mouse click position
 
+  /**
+   * for testng only
+   * 
+   * @param vpranges
+   * @param showAnnotationPanel
+   */  
+  @Deprecated
+  public OverviewDimensionsHideHidden(ViewportRanges vpranges, boolean showAnnotationPanel) {
+    this(vpranges, showAnnotationPanel, null);
+  }
+
   public OverviewDimensionsHideHidden(ViewportRanges vpranges,
-          boolean showAnnotationPanel)
+          boolean showAnnotationPanel, Dimension dim)
   {
-    super(vpranges, showAnnotationPanel);
+    super(vpranges, showAnnotationPanel, dim);
     ranges = vpranges;
     resetAlignmentDims();
   }
@@ -50,6 +63,8 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
     int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
 
@@ -61,6 +76,8 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void adjustViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // calculate translation in pixel terms:
     // get mouse location in viewport coords, add translation in viewport
     // coords, and update viewport as usual
@@ -72,13 +89,16 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
 
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh alwidth, alheight and width/height ratios
+   */
   @Override
   protected void updateViewportFromTopLeft(int leftx, int topy,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
     int xAsRes = leftx;
     int yAsSeq = topy;
-    resetAlignmentDims();
 
     if (xAsRes < 0)
     {
@@ -147,7 +167,7 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public AlignmentColsCollectionI getColumns(AlignmentI al)
   {
     return new VisibleColsCollection(0,
-            ranges.getAbsoluteAlignmentWidth() - 1, al);
+            ranges.getAbsoluteAlignmentWidth() - 1, al.getHiddenColumns());
   }
 
   @Override
@@ -167,6 +187,10 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
     heightRatio = (float) alheight / sequencesHeight;
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh widthRatio
+   */
   @Override
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
@@ -174,6 +198,10 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
     return vpx - ranges.getViewportWidth() / 2;
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh heightRatio
+   */
   @Override
   protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
   {
@@ -185,6 +213,8 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
           HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // get alignment position of x and box (can get directly from vpranges) and
     // calculate difference between the positions
     int vpx = Math.round(x * widthRatio);