X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensions.java;h=b34c85d352b4bdc5d053f2b116e31ba5c60d5138;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=34b7aff51f4f76065b8d5391fee09cee57cfae83;hpb=cb72ab56f740256004ad15c56514528b34d79b43;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 34b7aff..b34c85d 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -91,7 +91,7 @@ public class OverviewDimensions
     {
       // wider
       width = MAX_WIDTH;
-      sequencesHeight = (int) (MAX_WIDTH / initialScale);
+      sequencesHeight = Math.round(MAX_WIDTH / initialScale);
       if (sequencesHeight < MIN_SEQ_HEIGHT)
       {
         sequencesHeight = MIN_SEQ_HEIGHT;
@@ -100,7 +100,7 @@ public class OverviewDimensions
     else
     {
       // taller
-      width = (int) (MAX_WIDTH * initialScale);
+      width = Math.round(MAX_WIDTH * initialScale);
       sequencesHeight = MAX_SEQ_HEIGHT;
 
       if (width < MIN_WIDTH)
@@ -138,19 +138,11 @@ public class OverviewDimensions
     {
       x = 0;
     }
-    else if (x >= alwidth)
-    {
-      x = alwidth - 1;
-    }
 
     if (y < 0)
     {
       y = 0;
     }
-    else if (y >= alheight)
-    {
-      y = alheight - 1;
-    }
 
     //
     // Convert x value to residue position
@@ -170,19 +162,24 @@ public class OverviewDimensions
     // if x is in a hidden col region, shift to left - but we still need
     // absolute position
     // so convert back after getting visible region position
-    xAsRes = hiddenCols.adjustForHiddenColumns(hiddenCols
-            .findColumnPosition(xAsRes));
-
-    // get where end res should be by adding the viewport width on
-    int endRes = xAsRes + vpwidth;
+    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
 
     // check in case we went off the edge of the alignment
-    if (endRes > alwidth)
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    if (visXAsRes + vpwidth - 1 > visAlignWidth)
     {
       // went past the end of the alignment, adjust backwards
-      endRes = alwidth;
-      // recalc xAsRes backwards from endRes
-      xAsRes = endRes - vpwidth;
+
+      // if last position was before the end of the alignment, need to update
+      if ((scrollCol + vpwidth - 1) < visAlignWidth)
+      {
+        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
+                .findColumnNToLeft(vpwidth - 1, alwidth - 1));
+      }
+      else
+      {
+        visXAsRes = scrollCol;
+      }
     }
 
     //
@@ -193,7 +190,8 @@ public class OverviewDimensions
     int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
 
     // get viewport height in sequences
-    int vpheight = props.getEndSeq() - props.getStartSeq();
+    // add 1 because height includes both endSeq and startSeq
+    int vpheight = props.getEndSeq() - props.getStartSeq() + 1;
 
     // get where y should be when accounting for hidden rows
     // if y is in a hidden row region, shift up - but we still need absolute
@@ -202,22 +200,27 @@ public class OverviewDimensions
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
             .findIndexWithoutHiddenSeqs(yAsSeq));
 
-    // get where end seq should be by adding the viewport height on
-    int endSeq = yAsSeq + vpheight;
-
     // check in case we went off the edge of the alignment
-    if (endSeq > alheight)
+    int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+    int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    if (visYAsRes + vpheight - 1 > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
-      endSeq = alheight;
-      // recalc yAsSeq backwards from endSeq
-      yAsSeq = endSeq - vpheight;
+      if ((scrollRow + vpheight - 1) < visAlignHeight)
+      {
+        visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
+                .findIndexNAboveRow(vpheight - 1, alheight - 1));
+      }
+      else
+      {
+        visYAsRes = scrollRow;
+      }
     }
 
-    // convert absolute positions back to visible alignment positions for
-    // viewport scrolling
-    scrollCol = hiddenCols.findColumnPosition(xAsRes);
-    scrollRow = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    // update scroll values
+    scrollCol = visXAsRes;
+    scrollRow = visYAsRes;
+
   }
 
   /**
@@ -250,10 +253,13 @@ public class OverviewDimensions
     boxY = Math.round((float) startSeq * sequencesHeight / alheight);
 
     // boxWidth is the width in residues translated to pixels
+    // since the box includes both the start and end residues, add 1 to the
+    // difference
     boxWidth = Math
             .round((float) (endRes - startRes + 1) * width / alwidth);
     // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
+    boxHeight = Math.round((float) (endSeq - startSeq + 1)
+            * sequencesHeight
             / alheight);
   }
 
@@ -269,7 +275,6 @@ public class OverviewDimensions
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
-  // don't like this, scroll vals are separate from setting code
   public int getScrollCol()
   {
     return scrollCol;