formatting

[jalview.git] / src / jalview / appletgui / ScalePanel.java

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index d888d25..ab76f7f 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -60,7 +60,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
     final int res;
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(x);
     }
@@ -122,8 +122,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
           {
             av.hideColumns(res, res);
             if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av.alignment
-                            .getHeight())
+                    && av.getSelectionGroup().getSize() == av
+                            .getAlignment().getHeight())
             {
               av.setSelectionGroup(null);
             }
@@ -150,9 +150,9 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
       av.getColumnSelection().addElement(res);
       SequenceGroup sg = new SequenceGroup();
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
+      for (int i = 0; i < av.getAlignment().getSequences().size(); i++)
       {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
+        sg.addSequence(av.getAlignment().getSequenceAt(i), false);
       }
 
       sg.setStartRes(res);
@@ -173,6 +173,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     }
 
     ap.paintAlignment(true);
+    av.sendSelection();
   }
 
   public void mouseReleased(MouseEvent evt)
@@ -181,12 +182,12 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if (res > av.alignment.getWidth())
+    if (res > av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
@@ -211,6 +212,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     stretchingGroup = false;
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   public void mouseDragged(MouseEvent evt)
@@ -223,14 +225,14 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       res = 0;
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (res > av.alignment.getWidth())
+    if (res > av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
     if (res < min)
@@ -305,7 +307,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
   public void mouseMoved(MouseEvent evt)
   {
-    if (!av.hasHiddenColumns)
+    if (!av.hasHiddenColumns())
     {
       return;
     }
@@ -358,7 +360,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     for (int i = 0; i < cs.size(); i++)
     {
       int sel = cs.columnAt(i);
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         sel = av.getColumnSelection().findColumnPosition(sel);
       }
@@ -398,26 +400,24 @@ public class ScalePanel extends Panel 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));
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       gg.setColor(Color.blue);
       int res;