X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=18281d9d4a1b7659d3f74d12a70be5af53bda7fa;hb=f20144e54bcecee1a25b94dddf6c9bf802012b38;hp=5c6e510c9e0257138912c489e91f948385f596cc;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 5c6e510..18281d9 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -106,25 +106,26 @@ public class IdCanvas extends Panel
     gg.copyArea(0, 0, getSize().width, imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq, es = av.endSeq, transY = 0;
+    int ss = av.getStartSeq(), es = av.getEndSeq(), transY = 0;
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
-        transY = imgHeight - vertical * av.getCharHeight();
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -138,11 +139,13 @@ public class IdCanvas extends Panel
     repaint();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (getSize().height < 0 || getSize().width < 0)
@@ -178,7 +181,7 @@ public class IdCanvas extends Panel
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.startSeq, av.endSeq);
+    drawIds(av.getStartSeq(), av.getEndSeq());
     g.drawImage(image, 0, 0, this);
   }
 
@@ -233,7 +236,7 @@ public class IdCanvas extends Panel
 
       int rowSize = av.getEndRes() - av.getStartRes();
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
@@ -261,7 +264,7 @@ public class IdCanvas extends Panel
     {
       // Now draw the id strings
       SequenceI seq;
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
 
         seq = av.getAlignment().getSequenceAt(i);
@@ -378,7 +381,7 @@ public class IdCanvas extends Panel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.isHiddenRepSequence(seq))
+    if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
       return true;