From ca3387f2bb9cd5b39ff89949ce3698af505f05fc Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 8 Jun 2010 14:25:35 +0000
Subject: [PATCH] Patch for incorrect column selection when hidden regions are
 present * JAL-558

---
 src/jalview/datamodel/ColumnSelection.java |   20 ++++++++---------
 src/jalview/gui/ScalePanel.java            |   32 ++++++++++++++++++----------
 2 files changed, 31 insertions(+), 21 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4371994..63a5700 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -508,8 +508,8 @@ public class ColumnSelection
   }
 
   /**
-   * Use this method to find out where a visible column is in the alignment when
-   * hidden columns exist
+   * Use this method to find out where a column will appear in the visible alignment when
+   * hidden columns exist. If the column is not visible, then the left-most visible column will always be returned.
    * 
    * @param hiddenColumn
    *          int
@@ -521,21 +521,21 @@ public class ColumnSelection
     if (hiddenColumns != null)
     {
       int index = 0;
-      int gaps = 0;
+      int[] region;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        region = (int[]) hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
         }
-        index++;
-      } while (index < hiddenColumns.size());
-
-      result -= gaps;
+      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+      if (hiddenColumn>region[0] && hiddenColumn<region[1])
+      {
+        return region[0]+hiddenColumn-result;
+      }
     }
-
-    return result;
+    return result; // return the shifted position after removing hidden columns.
   }
 
   /**
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 2acd92c..64daf1f 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -72,10 +72,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (av.hasHiddenColumns)
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(x);
+      x = av.getColumnSelection().adjustForHiddenColumns(x);
     }
-    else
+
+    if (x >= av.alignment.getWidth())
     {
+      res = av.alignment.getWidth() - 1;
+    } else {
       res = x;
     }
 
@@ -169,7 +172,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       iVec = null;
       sg.setStartRes(res);
       sg.setEndRes(res);
-      av.setSelectionGroup(sg);
 
       if (evt.isShiftDown())
       {
@@ -182,7 +184,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         sg.setStartRes(min);
         sg.setEndRes(max);
       }
-
+      av.setSelectionGroup(sg);
     }
 
     ap.paintAlignment(false);
@@ -201,14 +203,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if (res > av.alignment.getWidth())
+    if (av.hasHiddenColumns)
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (av.hasHiddenColumns)
+    if (res >= av.alignment.getWidth())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.alignment.getWidth() - 1;
     }
 
     if (!stretchingGroup)
@@ -257,7 +259,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (res > av.alignment.getWidth())
+    if (res >= av.alignment.getWidth())
     {
       res = av.alignment.getWidth() - 1;
     }
@@ -295,7 +297,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       int col;
       for (int i = min; i <= max; i++)
       {
-        col = av.getColumnSelection().adjustForHiddenColumns(i);
+        col = i; // av.getColumnSelection().adjustForHiddenColumns(i);
 
         if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
         {
@@ -398,6 +400,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
+    int s;
     if (cs != null)
     {
       gg.setColor(new Color(220, 0, 0));
@@ -407,7 +410,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         int sel = cs.columnAt(i);
         if (av.hasHiddenColumns)
         {
-          sel = cs.findColumnPosition(sel);
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
         }
 
         if ((sel >= startx) && (sel <= endx))
-- 
1.7.10.2