Merge branch 'develop' into merged_2_11_2_0_to_2_12

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

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index eaa3413..b4fa934 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -20,6 +20,8 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Dimension;
+
 import jalview.api.AlignmentColsCollectionI;
 import jalview.api.AlignmentRowsCollectionI;
 import jalview.datamodel.AlignmentI;
@@ -38,6 +40,18 @@ public class OverviewDimensionsShowHidden 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 OverviewDimensionsShowHidden(ViewportRanges vpranges, boolean showAnnotationPanel) {
+    this(vpranges, showAnnotationPanel, null);
+  }
+
   /**
    * Create an OverviewDimensions object
    * 
@@ -47,9 +61,9 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
    *          true if the annotation panel is to be shown, false otherwise
    */
   public OverviewDimensionsShowHidden(ViewportRanges vpranges,
-          boolean showAnnotationPanel)
+          boolean showAnnotationPanel, Dimension dim)
   {
-    super(vpranges, showAnnotationPanel);
+    super(vpranges, showAnnotationPanel, dim);
     ranges = vpranges;
     resetAlignmentDims();
   }
@@ -80,7 +94,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
 
     // convert to visible positions
-    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+    int visXAsRes = hiddenCols.absoluteToVisibleColumn(xAsRes);
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
             hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
     yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
@@ -101,8 +115,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     // get mouse location in viewport coords, add translation in viewport
     // coords,
     // convert back to pixel coords
-    int vpx = Math.round(mousex * widthRatio);
-    int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
+    int vpx = Math.round((float) mousex * alwidth / width);
+    int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff;
 
     int vpy = Math.round(mousey * heightRatio);
     int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
@@ -143,7 +157,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int vpwidth = ranges.getViewportWidth();
 
     // check in case we went off the edge of the alignment
-    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    int visAlignWidth = hiddenCols.absoluteToVisibleColumn(alwidth - 1);
     if (visXAsRes + vpwidth - 1 > visAlignWidth)
     {
       // went past the end of the alignment, adjust backwards
@@ -151,8 +165,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       // if last position was before the end of the alignment, need to update
       if (ranges.getEndRes() < visAlignWidth)
       {
-        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
-                .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+        visXAsRes = hiddenCols.absoluteToVisibleColumn(hiddenCols
+                .offsetByVisibleColumns(-(vpwidth - 1), alwidth - 1));
       }
       else
       {
@@ -202,8 +216,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
           HiddenColumns hiddenCols)
   {
     // work with absolute values of startRes and endRes
-    int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
-    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+    int startRes = hiddenCols.visibleToAbsoluteColumn(ranges.getStartRes());
+    int endRes = hiddenCols.visibleToAbsoluteColumn(ranges.getEndRes());
 
     // work with absolute values of startSeq and endSeq
     int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
@@ -237,7 +251,6 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     heightRatio = (float) alheight / sequencesHeight;
   }
 
-
   /**
    * {@inheritDoc} Callers should have already called resetAlignmentDims to
    * refresh widthRatio
@@ -245,8 +258,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   @Override
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
-    int vpx = Math.round(mousex * widthRatio);
-    return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+    int vpx = Math.round((float) mousex * alwidth / width);
+    return hidden.offsetByVisibleColumns(-ranges.getViewportWidth() / 2,
             vpx);
   }
 
@@ -272,7 +285,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int vpx = Math.round(x * widthRatio);
     int vpy = Math.round(y * heightRatio);
 
-    xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
+    xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx);
     ydiff = ranges.getStartSeq()
             - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
   }