X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensions.java;h=60b4ee988a031030bce8fc22a0abfa0307183759;hb=f20144e54bcecee1a25b94dddf6c9bf802012b38;hp=1f18a1022fc4327a0fa26e1b6a24a7a94a3fc35a;hpb=1f015ae6034c51f7e7ab619fe428943899755d1c;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 1f18a10..60b4ee9 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -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 +162,23 @@ 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.findColumnNToLeft(vpwidth - 1, alwidth - 1);
+      }
+      else
+      {
+        visXAsRes = scrollCol;
+      }
     }
 
     //
@@ -193,6 +189,7 @@ public class OverviewDimensions
     int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
 
     // get viewport height in sequences
+    // 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
@@ -203,21 +200,30 @@ public class OverviewDimensions
             .findIndexWithoutHiddenSeqs(yAsSeq));
 
     // get where end seq should be by adding the viewport height on
-    int endSeq = yAsSeq + vpheight;
+    int endSeq = yAsSeq + vpheight - 1;
 
     // 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 (hiddenSeqs.findIndexWithoutHiddenSeqs(endSeq) > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
-      endSeq = alheight;
-      // recalc yAsSeq backwards from endSeq
-      yAsSeq = endSeq - vpheight + 1;
+      if ((scrollRow + vpheight - 1) < visAlignHeight)
+      {
+        visYAsRes = 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);
+    scrollCol = visXAsRes;
+    scrollRow = visYAsRes; // hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+
   }
 
   /**
@@ -250,6 +256,8 @@ 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