From b149069ca631eb2e2c56c900ff4f490af1e98972 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 13 Nov 2006 11:12:51 +0000
Subject: [PATCH] colours in viewport

---
 src/jalview/gui/AlignmentPanel.java |   13 ++++++-------
 src/jalview/gui/IdCanvas.java       |    4 ++--
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 12ae05c..0012ec4 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -714,18 +714,19 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setFont(new Font(av.getFont().getName(),
                         Font.ITALIC,
                         av.getFont().getSize()));
+    SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
+      seq = av.getAlignment().getSequenceAt(i);
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().getSequences(false).contains(
-              av.getAlignment().getSequenceAt(i)))
+          av.getSelectionGroup().getSequences(false).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentColor = av.getSequenceColour(seq);
         currentTextColor = Color.black;
       }
 
@@ -735,10 +736,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
-
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    0,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 32cbfb5..c9ed305 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -86,7 +86,7 @@ public class IdCanvas extends JPanel
         }
         else
         {
-            gg.setColor(s.getColor());
+            gg.setColor(av.getSequenceColour(s));
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
                 charHeight);
             gg.setColor(Color.black);
@@ -310,7 +310,7 @@ public class IdCanvas extends JPanel
                 }
                 else
                 {
-                  currentColor = sequence.getColor();
+                  currentColor = av.getSequenceColour(sequence);
                   currentTextColor = Color.black;
                 }
 
-- 
1.7.10.2