X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=eaa3a501251888160f22220e98b25ebb348ba858;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=c7a82326607d81b6e4ffdf6fee738fa46f6080d0;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index c7a8232..eaa3a50 100755
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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();
@@ -507,49 +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];
+
+          if (hideStart <= blockStart)
+          {
+            blockStart += (hideEnd - hideStart) + 1;
+            continue;
+          }
 
-        blockEnd = hideStart - 1;
+          blockEnd = hideStart - 1;
 
-        g1.translate(screenY * av.charWidth, 0);
+          g1.translate(screenY * av.charWidth, 0);
 
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-        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);
-        }
+          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;
+          g1.translate(-screenY * av.charWidth, 0);
+          screenY += blockEnd - blockStart + 1;
+          blockStart = hideEnd + 1;
+        }
       }
-
       if (screenY <= (endRes - startRes))
       {
         blockEnd = blockStart + (endRes - startRes) - screenY;
@@ -586,7 +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));
@@ -643,7 +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;
     }
 
@@ -675,7 +688,8 @@ 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 +813,8 @@ 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());
 
     }