From 236efa0d06562386ba9a5e44764143298e0306d2 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 17 Jul 2017 16:02:03 +0100
Subject: [PATCH] JAL-2611 Still not happy with behaviour

---
 src/jalview/gui/OverviewPanel.java                 |    5 +-
 .../viewmodel/OverviewDimensionsShowHidden.java    |  105 +++++++++++++++++++-
 2 files changed, 103 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 0f276d7..5fbefb5 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -28,6 +28,7 @@ import jalview.viewmodel.OverviewDimensionsShowHidden;
 import jalview.viewmodel.ViewportListenerI;
 
 import java.awt.BorderLayout;
+import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -134,12 +135,12 @@ public class OverviewPanel extends JPanel implements Runnable,
         if (od.isPositionInBox(evt.getX(), evt.getY()))
         {
           // display drag cursor at mouse position
-
+          setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
         }
         else
         {
           // reset cursor
-
+          setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
         }
       }
     });
diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index af95c45..4ab27de 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -81,14 +81,109 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     // coords,
     // convert back to pixel coords
     int vpx = Math.round((float) mousex * alwidth / width);
-    int visXAsRes = hiddenCols.findColumnPosition(vpx);
+    // int visXAsRes = hiddenCols.findColumnPosition(vpx);
 
     int vpy = Math.round((float) mousey * alheight / sequencesHeight);
-    int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
+    // int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
 
-    updateViewportFromTopLeft(visXAsRes + transX, visYAsRes + transY,
-            hiddenSeqs,
-            hiddenCols);
+    System.out.println("vpx: " + vpx);
+    // System.out.println("VisXAsRes: " + visXAsRes);
+    System.out.println("transX: " + transX);
+    // updateViewportFromTopLeft(vpx + transX, vpy + transY,
+    // hiddenSeqs,
+    // hiddenCols);
+
+    int xAsRes = vpx + transX;
+    int yAsSeq = vpy + transY;
+
+    resetAlignmentDims();
+
+    if (xAsRes < 0)
+    {
+      xAsRes = 0;
+    }
+
+    if (yAsSeq < 0)
+    {
+      yAsSeq = 0;
+    }
+
+    //
+    // Convert x value to residue position
+    //
+
+    // need to determine where scrollCol should be, given x
+    // to do this also need to know width of viewport, and some hidden column
+    // correction
+
+    // convert x to residues - this is an absolute position
+    // int xAsRes = Math.round((float) x * alwidth / width);
+
+    // get viewport width in residues
+    int vpwidth = ranges.getViewportWidth();
+
+    // get where x should be when accounting for hidden cols
+    // 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
+    // int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+    int visXAsRes = xAsRes;
+
+    // check in case we went off the edge of the alignment
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    /*    if (visXAsRes + vpwidth - 1 > visAlignWidth)
+    {
+      // went past the end of the alignment, adjust backwards
+    
+      // 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));
+      }
+      else
+      {
+        visXAsRes = ranges.getStartRes();
+      }
+    }*/
+
+    //
+    // Convert y value to sequence position
+    //
+
+    // convert y to residues
+    // int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+
+    // get viewport height in sequences
+    int vpheight = ranges.getViewportHeight();
+
+    // 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
+    // position,
+    // so convert back after getting visible region position
+    yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
+            hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
+
+    // check in case we went off the edge of the alignment
+    int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+    int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    if (visYAsSeq + vpheight - 1 > visAlignHeight)
+    {
+      // went past the end of the alignment, adjust backwards
+      if (ranges.getEndSeq() < visAlignHeight)
+      {
+        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(
+                hiddenSeqs.subtractVisibleRows(vpheight - 1, alheight - 1));
+      }
+      else
+      {
+        visYAsSeq = ranges.getStartSeq();
+      }
+    }
+
+    // update viewport
+    ranges.setStartRes(visXAsRes);
+    ranges.setStartSeq(visYAsSeq);
   }
 
   @Override
-- 
1.7.10.2