X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=c753cae133e1a105047c9d84aea0ee8310263453;hb=d559b47886de6427219011e6e355320a0babd757;hp=c89a9d5bfe00b45a041dd77216b5614c7e089813;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c89a9d5..c753cae 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -161,17 +161,17 @@ public class IdCanvas extends JPanel
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    int ss = av.getStartSeq();
+    int es = av.getEndSeq();
     int transY = 0;
 
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < av.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
@@ -182,9 +182,9 @@ public class IdCanvas extends JPanel
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -204,6 +204,7 @@ public class IdCanvas extends JPanel
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
@@ -239,7 +240,7 @@ public class IdCanvas extends JPanel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
 
-    drawIds(av.getStartSeq(), av.endSeq);
+    drawIds(av.getStartSeq(), av.getEndSeq());
 
     g.drawImage(image, 0, 0, this);
   }
@@ -316,7 +317,7 @@ public class IdCanvas extends JPanel
       int rowSize = av.getEndRes() - av.getStartRes();
 
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getHeight())
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
@@ -479,7 +480,7 @@ public class IdCanvas extends JPanel
     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);
     }