JAL-2388 Initial removal of hidden cols/seqs out of overview

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

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index b4c7c6d..fe9f4db 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -77,8 +77,8 @@ public class OverviewDimensions
     this.posProps = av.getPosProps();
 
     // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.getAlignment().getWidth()
-            / (float) av.getAlignment().getHeight();
+    float initialScale = (float) posProps.getAlignmentWidthInCols()
+            / (float) posProps.getAlignmentHeightInRows();
 
     // TODO: in applet this was getSequenceConsensusHash()
     // check if it makes any functional difference
@@ -116,6 +116,9 @@ public class OverviewDimensions
    */
   public void setBoxPositionByMouse(int x, int y)
   {
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
+
     boxX = x;
     boxY = y;
     if (boxY < 0)
@@ -124,7 +127,7 @@ public class OverviewDimensions
     }
     else if (boxY > (sequencesHeight - boxHeight))
     {
-      boxY = sequencesHeight - boxHeight + 1;
+      boxY = sequencesHeight - boxHeight;
     }
 
     if (boxX < 0)
@@ -136,28 +139,23 @@ public class OverviewDimensions
       if (av.hasHiddenColumns())
       {
         // Try smallest possible box
-        boxWidth = (int) (posProps.convertResiduesToPixels(posProps
-                .getEndRes() - posProps.getStartRes() + 1) * scalew);
-
-        // boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
-        // * av.getCharWidth() * scalew);
+        boxWidth = Math.round((float) (posProps.getEndRes()
+                - posProps.getStartRes() + 1)
+                * width / alwidth);
       }
       boxX = width - boxWidth;
     }
 
-    scrollCol = posProps.convertPixelsToResidues(Math.round(boxX / scalew));
-    scrollRow = posProps
-            .convertPixelsToSequences(Math.round(boxY / scaleh));
-
-    // scrollCol = (int) (boxX / scalew / av.getCharWidth());
-    // scrollRow = (int) (boxY / scaleh / av.getCharHeight());
+    scrollCol = Math.round((float) boxX * alwidth / width);
+    scrollRow = Math.round((float) boxY * alheight / sequencesHeight);
 
     if (av.hasHiddenColumns())
     {
-      if (!av.getColumnSelection().isVisible(scrollCol))
+      // doesn't seem to do anything useful
+      /*if (!av.getColumnSelection().isVisible(scrollCol))
       {
         return;
-      }
+      }*/
 
       scrollCol = av.getColumnSelection().findColumnPosition(scrollCol);
     }
@@ -176,60 +174,22 @@ public class OverviewDimensions
    */
   public void setBoxPosition()
   {
-    updateScales();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns())
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.getStartSeq();
-    int endSeq = av.getEndSeq();
-
-    if (av.hasHiddenRows())
-    {
-      startSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(startSeq);
-
-      endSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
-    }
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
-    boxX = Math.round(posProps.convertResiduesToPixels(startRes) * scalew);
-    boxY = Math.round(posProps.convertSequencesToPixels(startSeq) * scaleh);
+    int startRes = av.getPosProps().getAbsoluteStartRes();
+    int endRes = av.getPosProps().getAbsoluteEndRes();
 
-    // boxX = (int) (startRes * av.getCharWidth() * scalew);
-    // boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+    int startSeq = av.getPosProps().getAbsoluteStartSeq();
+    int endSeq = av.getPosProps().getAbsoluteEndSeq();
 
-    boxWidth = Math.round(posProps.convertResiduesToPixels(endRes
-            - startRes
-            + 1) * scalew);
-    boxHeight = Math.round(posProps.convertSequencesToPixels(endSeq
-            - startSeq)
-            * scaleh);
+    boxX = Math.round((float) startRes * width / alwidth);
+    boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
-    // boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-    // boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-  }
-
-  /**
-   * Update width and height scales in terms of the alignment width and height
-   */
-  public void updateScales()
-  {
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / fullsizeWidth;
-    scaleh = (float) sequencesHeight / fullsizeHeight;
+    boxWidth = Math
+            .round((float) (endRes - startRes + 1) * width / alwidth);
+    boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
+            / alheight);
   }
 
   /**
@@ -269,11 +229,13 @@ public class OverviewDimensions
     return boxY;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
   public int getBoxWidth()
   {
     return boxWidth;
   }
 
+  // TODO should be removed, when unit test has mock Graphics object available
   public int getBoxHeight()
   {
     return boxHeight;