X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHidden.java;h=eaa3413ce9444303997058524aa2c5157e67f931;hb=e7a03b66f3e11f7383f721a61d22a50c26ae18fe;hp=c4b69a86e37d1fc124b7fcc79163e59eea2cafa6;hpb=58fb14c48ecb086be7422f92addf14f930656523;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index c4b69a8..eaa3413 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -72,6 +72,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   public void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // convert mousex and mousey to alignment units as well as
     // translating to top left corner of viewport - this is an absolute position
     int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
@@ -81,7 +83,9 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
             hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
+    yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
     int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
 
     // update viewport accordingly
     updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
@@ -91,29 +95,32 @@ public class OverviewDimensionsShowHidden 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,
     // convert back to pixel coords
-    int vpx = Math.round((float) mousex * alwidth / width);
+    int vpx = Math.round(mousex * widthRatio);
     int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
 
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpy = Math.round(mousey * heightRatio);
     int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
 
     // update viewport accordingly
-    updateViewportFromTopLeft(visXAsRes, visYAsRes,
-            hiddenSeqs,
-            hiddenCols);
+    updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
   }
 
+  /**
+   * {@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 visXAsRes = leftx;
     int visYAsSeq = topy;
-    resetAlignmentDims();
 
     if (visXAsRes < 0)
     {
@@ -125,6 +132,11 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       visYAsSeq = 0;
     }
 
+    if (ranges.isWrappedMode())
+    {
+      visYAsSeq = 0; // sorry, no vertical scroll when wrapped
+    }
+
     // Determine where scrollCol should be, given visXAsRes
 
     // get viewport width in residues
@@ -161,8 +173,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       // went past the end of the alignment, adjust backwards
       if (ranges.getEndSeq() < visAlignHeight)
       {
-        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
-                .subtractVisibleRows(vpheight - 1, alheight - 1));
+        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(
+                hiddenSeqs.subtractVisibleRows(vpheight - 1, alheight - 1));
       }
       else
       {
@@ -171,8 +183,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     }
 
     // update viewport
-    ranges.setStartRes(visXAsRes);
-    ranges.setStartSeq(visYAsSeq);
+    ranges.setStartResAndSeq(visXAsRes, visYAsSeq);
   }
 
   /**
@@ -198,22 +209,21 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
     int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
 
-    setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
-            - startSeq + 1);
+    setBoxPosition(startRes, startSeq, endRes - startRes + 1,
+            endSeq - startSeq + 1);
   }
 
   @Override
   public AlignmentColsCollectionI getColumns(AlignmentI al)
   {
-    return new AllColsCollection(0,
-            ranges.getAbsoluteAlignmentWidth() - 1, al);
+    return new AllColsCollection(0, ranges.getAbsoluteAlignmentWidth() - 1,
+            al);
   }
 
   @Override
   public AlignmentRowsCollectionI getRows(AlignmentI al)
   {
-    return new AllRowsCollection(0,
-            ranges.getAbsoluteAlignmentHeight() - 1,
+    return new AllRowsCollection(0, ranges.getAbsoluteAlignmentHeight() - 1,
             al);
   }
 
@@ -222,20 +232,32 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   {
     alwidth = ranges.getAbsoluteAlignmentWidth();
     alheight = ranges.getAbsoluteAlignmentHeight();
+
+    widthRatio = (float) alwidth / width;
+    heightRatio = (float) alheight / sequencesHeight;
   }
 
+
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh widthRatio
+   */
   @Override
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
-    int vpx = Math.round((float) mousex * alwidth / width);
+    int vpx = Math.round(mousex * widthRatio);
     return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
             vpx);
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh heightRatio
+   */
   @Override
   protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
   {
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpy = Math.round(mousey * heightRatio);
     return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
   }
 
@@ -243,10 +265,12 @@ public class OverviewDimensionsShowHidden 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((float) x * alwidth / width);
-    int vpy = Math.round((float) y * alheight / sequencesHeight);
+    int vpx = Math.round(x * widthRatio);
+    int vpy = Math.round(y * heightRatio);
 
     xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
     ydiff = ranges.getStartSeq()