Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d5dd927..ba963ec 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -34,6 +34,7 @@ import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
+import java.util.List;
 
 import javax.swing.JComponent;
 
@@ -573,7 +574,7 @@ public class SeqCanvas extends JComponent
 
       drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
-      if (av.showAnnotation)
+      if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 3);
         if (annotations == null)
@@ -598,7 +599,7 @@ public class SeqCanvas extends JComponent
 
   int getAnnotationHeight()
   {
-    if (!av.showAnnotation)
+    if (!av.isShowAnnotation())
     {
       return 0;
     }
@@ -627,7 +628,8 @@ public class SeqCanvas extends JComponent
    * @param offset
    *          DOCUMENT ME!
    */
-  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+  public void drawPanel(Graphics g1, int startRes, int endRes,
+          int startSeq,
           int endSeq, int offset)
   {
     if (!av.hasHiddenColumns())
@@ -636,7 +638,7 @@ public class SeqCanvas extends JComponent
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
@@ -644,7 +646,7 @@ public class SeqCanvas extends JComponent
 
       for (int i = 0; regions != null && i < regions.size(); i++)
       {
-        int[] region = (int[]) regions.elementAt(i);
+        int[] region = regions.get(i);
         int hideStart = region[0];
         int hideEnd = region[1];
 
@@ -710,7 +712,7 @@ public class SeqCanvas extends JComponent
       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));