From 1ab6f120162b85abfb50046444199f2638f966ac Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 14 Mar 2017 16:42:01 +0000
Subject: [PATCH 1/1] JAL-2388 Working overview panel

---
 src/jalview/viewmodel/OverviewDimensions.java |   47 ++++++++++++++-----------
 1 file changed, 27 insertions(+), 20 deletions(-)

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 4af4175..60b4ee9 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -162,22 +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
-    // subtract 1 because the width includes endRes
-    int endRes = xAsRes + vpwidth - 1;
+    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
 
     // check in case we went off the edge of the alignment
-    int visAlignWidth = hiddenCols.findColumnPosition(alwidth);
-    if (endRes > visAlignWidth - 1)
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    if (visXAsRes + vpwidth - 1 > visAlignWidth)
     {
       // went past the end of the alignment, adjust backwards
-      endRes = visAlignWidth - 1;
-      // recalc xAsRes backwards from endRes
-      // add 1 because width includes xAsRes
-      xAsRes = hiddenCols.adjustForHiddenColumns(endRes - vpwidth + 1);
+
+      // 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;
+      }
     }
 
     //
@@ -203,18 +204,26 @@ public class OverviewDimensions
 
     // check in case we went off the edge of the alignment
     int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
-    if (hiddenSeqs.findIndexWithoutHiddenSeqs(endSeq) > visAlignHeight - 1)
+    int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    if (hiddenSeqs.findIndexWithoutHiddenSeqs(endSeq) > visAlignHeight)
     {
       // went past the end of the alignment, adjust backwards
-      endSeq = visAlignHeight - 1;
-      // 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);
+
   }
 
   /**
@@ -252,8 +261,6 @@ public class OverviewDimensions
     boxWidth = Math
             .round((float) (endRes - startRes + 1) * width / alwidth);
     // boxHeight is the height in sequences translated to pixels
-    // since the box includes both the start and end sequences, add 1 to the
-    // difference
     boxHeight = Math.round((float) (endSeq - startSeq + 1)
             * sequencesHeight
             / alheight);
-- 
1.7.10.2