X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=c50330b93a5b0700def7f4988f8cdf8eeec38b5e;hb=7c28880430765f06ccd5ec8ad3caf17871336e97;hp=2acd92cd3595e3e6766800772196bac042bec801;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 2acd92c..c50330b 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -72,7 +72,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (av.hasHiddenColumns)
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(x);
+      x = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+
+    if (x >= av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
     }
     else
     {
@@ -169,7 +174,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       iVec = null;
       sg.setStartRes(res);
       sg.setEndRes(res);
-      av.setSelectionGroup(sg);
 
       if (evt.isShiftDown())
       {
@@ -182,7 +186,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         sg.setStartRes(min);
         sg.setEndRes(max);
       }
-
+      av.setSelectionGroup(sg);
     }
 
     ap.paintAlignment(false);
@@ -201,14 +205,14 @@ 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 +261,7 @@ 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 +299,7 @@ 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()))
         {
@@ -351,8 +355,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       {
         reveal = region;
         ToolTipManager.sharedInstance().registerComponent(this);
-        this
-                .setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+        this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
         break;
       }
       else
@@ -398,6 +401,7 @@ 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 +411,14 @@ 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))
@@ -445,22 +456,20 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
         }
 
-        gg
-                .drawLine(
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + 2,
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + (fm.getDescent() * 2));
+        gg.drawLine(
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + 2,
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + (fm.getDescent() * 2));
 
       }
       else
       {
-        gg
-                .drawLine(
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + fm.getDescent(),
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + (fm.getDescent() * 2));
+        gg.drawLine(
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + fm.getDescent(),
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + (fm.getDescent() * 2));
       }
     }