JAL-1551 JAL-962 formatting and code change ripples from changing HiddenColumns ...

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index c7a8232..81e5dae 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,25 +1,35 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
 
 public class SeqCanvas extends Panel
 {
@@ -348,7 +358,7 @@ public class SeqCanvas extends Panel
     String mask = "0";
     int maxWidth = 0;
     int tmp;
-    AlignmentI alignment=av.getAlignment();
+    AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       tmp = alignment.getSequenceAt(i).getEnd();
@@ -513,7 +523,8 @@ public class SeqCanvas extends Panel
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      java.util.List<int[]> regions = av.getColumnSelection()
+              .getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
@@ -521,7 +532,7 @@ public class SeqCanvas extends Panel
 
       for (int i = 0; i < regions.size(); i++)
       {
-        int[] region = (int[]) regions.elementAt(i);
+        int[] region = regions.get(i);
         int hideStart = region[0];
         int hideEnd = region[1];
 
@@ -586,7 +597,7 @@ public class SeqCanvas extends Panel
       sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
               startRes, endRes, offset + ((i - startSeq) * av.charHeight));
 
-      if (av.showSequenceFeatures)
+      if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
                 + ((i - startSeq) * av.charHeight));
@@ -643,7 +654,7 @@ public class SeqCanvas extends Panel
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+      group = av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -675,7 +686,8 @@ public class SeqCanvas extends Panel
           {
             if ((bottom == -1)
                     && (i >= alHeight || !group.getSequences(null)
-                            .contains(av.getAlignment().getSequenceAt(i + 1))))
+                            .contains(
+                                    av.getAlignment().getSequenceAt(i + 1))))
             {
               bottom = sy + av.charHeight;
             }
@@ -799,8 +811,8 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups().get(
-                groupIndex);
+        group = av.getAlignment().getGroups()
+                .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());
 
     }