X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=67bba3239cc1c30cae971b65b0c187caf8bd38ba;hb=2a5cbe264ec842c1a0f93e6bd78294607a94e686;hp=58a4af155c9926991dd989e459e6de139a347e8d;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 58a4af1..67bba32 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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -80,7 +80,7 @@ public class IdCanvas extends Panel
             ((i - starty) * charHeight) + ypos + charHeight
                     - (charHeight / 5));
 
-    if (av.hasHiddenRows && av.showHiddenMarkers)
+    if (av.hasHiddenRows() && av.showHiddenMarkers)
     {
       drawMarker(i, starty, ypos);
     }
@@ -186,10 +186,10 @@ public class IdCanvas extends Panel
 
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
-      int alheight = av.alignment.getHeight();
+      int maxwidth = av.getAlignment().getWidth();
+      int alheight = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
@@ -221,9 +221,9 @@ public class IdCanvas extends Panel
         for (int i = starty; i < alheight; i++)
         {
 
-          SequenceI s = av.alignment.getSequenceAt(i);
+          SequenceI s = av.getAlignment().getSequenceAt(i);
           gg.setFont(italic);
-          if (av.hasHiddenRows)
+          if (av.hasHiddenRows())
           {
             setHiddenFont(s);
           }
@@ -246,14 +246,14 @@ public class IdCanvas extends Panel
       for (int i = starty; i < endy; i++)
       {
 
-        seq = av.alignment.getSequenceAt(i);
+        seq = av.getAlignment().getSequenceAt(i);
         if (seq == null)
         {
           continue;
         }
         gg.setFont(italic);
         // boolean isrep=false;
-        if (av.hasHiddenRows)
+        if (av.hasHiddenRows())
         {
           // isrep =
           setHiddenFont(seq);
@@ -288,7 +288,7 @@ public class IdCanvas extends Panel
                 (((i - starty) * av.charHeight) + av.charHeight)
                         - (av.charHeight / 5));
 
-        if (av.hasHiddenRows && av.showHiddenMarkers)
+        if (av.hasHiddenRows() && av.showHiddenMarkers)
         {
           drawMarker(i, starty, 0);
         }
@@ -304,7 +304,7 @@ public class IdCanvas extends Panel
 
   void drawMarker(int i, int starty, int yoffset)
   {
-    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
     // Use this method here instead of calling hiddenSeq adjust
     // 3 times.
     int hSize = hseqs.length;
@@ -362,8 +362,8 @@ public class IdCanvas extends Panel
     Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
             .getSize());
 
-    if (av.hiddenRepSequences != null
-            && av.hiddenRepSequences.containsKey(seq))
+    if (av.getHiddenRepSequences() != null
+            && av.getHiddenRepSequences().containsKey(seq))
     {
       gg.setFont(bold);
       return true;