X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=a1bc8732a64dad55ee57f70331d5d6e1a9dbfb25;hb=b61f2d9b571c4e4ab3285257c6ddbd39da61fa05;hp=dd057a347e4a3839445d9742282026c87d63874e;hpb=da144cfa9b7997a6e8dd04ef10d55bcea3b02c71;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index dd057a3..a1bc873 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -43,7 +43,7 @@ public class IdCanvas
   {
     setLayout(null);
     this.av = av;
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
@@ -59,7 +59,7 @@ public class IdCanvas
       gg.setColor(Color.white);
     }
     else if (av.getSelectionGroup() != null &&
-             av.getSelectionGroup().getSequences(false).contains(s))
+             av.getSelectionGroup().getSequences(null).contains(s))
     {
       gg.setColor(Color.lightGray);
       gg.fillRect(0, ((i - starty) * charHeight) + ypos,
@@ -68,7 +68,7 @@ public class IdCanvas
     }
     else
     {
-      gg.setColor(s.getColor());
+      gg.setColor(av.getSequenceColour(s));
       gg.fillRect(0, ((i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.black);
@@ -240,6 +240,7 @@ public class IdCanvas
       //Now draw the id strings
 
       //Now draw the id strings
+      SequenceI seq;
       for (int i = starty; i < endy; i++)
       {
         if (av.hasHiddenRows)
@@ -247,23 +248,26 @@ public class IdCanvas
           setHiddenFont(i);
         }
 
+        seq = av.alignment.getSequenceAt(i);
+        if(seq==null)
+          continue;
+
         // Selected sequence colours
         if ( (searchResults != null) &&
-            searchResults.contains(av.alignment.getSequenceAt(i)))
+            searchResults.contains(seq))
         {
           currentColor = Color.black;
           currentTextColor = Color.white;
         }
         else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().getSequences(false).contains(
-                     av.alignment.getSequenceAt(i)))
+                 av.getSelectionGroup().getSequences(null).contains(seq))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
+          currentColor =  av.getSequenceColour(seq);
           currentTextColor = Color.black;
         }
 
@@ -274,10 +278,9 @@ public class IdCanvas
 
         gg.setColor(currentTextColor);
 
-        String string = av.alignment.getSequenceAt(i).getDisplayId(av.
-            getShowJVSuffix());
 
-        gg.drawString(string, 0,
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
+                      0,
                       ( ( (i - starty) * av.charHeight) + av.charHeight) -
                       (av.charHeight / 5));