Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 0e2773d..6bb54f2 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -20,9 +20,16 @@
  */
 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
 {
@@ -510,49 +517,52 @@ public class SeqCanvas extends Panel
   void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
           int endSeq, int offset)
   {
+
+
     if (!av.hasHiddenColumns())
     {
       draw(g1, startRes, endRes, startSeq, endSeq, offset);
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
 
       int screenY = 0;
       int blockStart = startRes;
       int blockEnd = endRes;
 
-      for (int i = 0; i < regions.size(); i++)
+      if (av.hasHiddenColumns())
       {
-        int[] region = (int[]) regions.elementAt(i);
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
+        for (int[] region : av.getColumnSelection().getHiddenColumns())
         {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
+          int hideStart = region[0];
+          int hideEnd = region[1];
 
-        blockEnd = hideStart - 1;
+          if (hideStart <= blockStart)
+          {
+            blockStart += (hideEnd - hideStart) + 1;
+            continue;
+          }
 
-        g1.translate(screenY * av.charWidth, 0);
+          blockEnd = hideStart - 1;
 
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+          g1.translate(screenY * av.charWidth, 0);
 
-        if (av.getShowHiddenMarkers())
-        {
-          g1.setColor(Color.blue);
-          g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
-                  0 + offset, (blockEnd - blockStart + 1) * av.charWidth
-                          - 1, (endSeq - startSeq) * av.charHeight + offset);
-        }
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-        g1.translate(-screenY * av.charWidth, 0);
-        screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-      }
+          if (av.getShowHiddenMarkers())
+          {
+            g1.setColor(Color.blue);
+            g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
+                    0 + offset, (blockEnd - blockStart + 1) * av.charWidth
+                            - 1, (endSeq - startSeq) * av.charHeight
+                            + offset);
+          }
 
+          g1.translate(-screenY * av.charWidth, 0);
+          screenY += blockEnd - blockStart + 1;
+          blockStart = hideEnd + 1;
+        }
+      }
       if (screenY <= (endRes - startRes))
       {
         blockEnd = blockStart + (endRes - startRes) - screenY;
@@ -589,7 +599,7 @@ 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));
@@ -646,7 +656,7 @@ 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;
     }
 
@@ -803,7 +813,7 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups()
+        group = av.getAlignment().getGroups()
                 .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());