X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHidden.java;h=4c36cfa1d06fc22de6ccd219eeddf88051112222;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=0bda56ecca1ed046f91b2134035f0a275eaa100e;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index 0bda56e..4c36cfa 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -72,13 +72,15 @@ 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);
     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
@@ -93,27 +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 visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
+    int visXAsRes = hiddenCols.absoluteToVisibleColumn(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);
   }
 
+  /**
+   * {@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)
     {
@@ -136,7 +143,7 @@ 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
@@ -144,8 +151,8 @@ 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
       {
@@ -176,8 +183,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     }
 
     // update viewport
-    ranges.setStartRes(visXAsRes);
-    ranges.setStartSeq(visYAsSeq);
+    ranges.setStartResAndSeq(visXAsRes, visYAsSeq);
   }
 
   /**
@@ -196,8 +202,8 @@ 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());
@@ -226,20 +232,31 @@ 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);
-    return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+    return hidden.offsetByVisibleColumns(-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);
   }
 
@@ -247,12 +264,14 @@ 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);
+    xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx);
     ydiff = ranges.getStartSeq()
             - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
   }