JAL-845 code/refactoring/tests related to linking DNA and protein

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 903c694..9c2fd73 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -6,21 +6,31 @@
  * 
  * 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;
+import java.util.List;
 
 public class SeqCanvas extends Panel
 {
@@ -514,15 +524,14 @@ public class SeqCanvas extends Panel
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
       int blockEnd = endRes;
 
-      for (int i = 0; i < regions.size(); i++)
+      for (int[] region : regions)
       {
-        int[] region = (int[]) regions.elementAt(i);
         int hideStart = region[0];
         int hideEnd = region[1];
 
@@ -644,7 +653,7 @@ 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;
     }
 
@@ -801,7 +810,7 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups()
+        group = av.getAlignment().getGroups()
                 .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());