colours in viewport

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 12ae05c..0012ec4 100755 (executable)
--- 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(),\r
                         Font.ITALIC,\r
                         av.getFont().getSize()));\r
+    SequenceI seq;\r
     for (int i = startSeq; i < endSeq; i++)\r
     {\r
+      seq = av.getAlignment().getSequenceAt(i);\r
       if ( (av.getSelectionGroup() != null) &&\r
-          av.getSelectionGroup().getSequences(false).contains(\r
-              av.getAlignment().getSequenceAt(i)))\r
+          av.getSelectionGroup().getSequences(false).contains(seq))\r
       {\r
         currentColor = Color.gray;\r
         currentTextColor = Color.black;\r
       }\r
       else\r
       {\r
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+        currentColor = av.getSequenceColour(seq);\r
         currentTextColor = Color.black;\r
       }\r
 \r
@@ -735,10 +736,8 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
       pg.setColor(currentTextColor);\r
 \r
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
-          ( av.getShowJVSuffix());\r
-\r
-      pg.drawString(string, 0,\r
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),\r
+                    0,\r
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
                     (av.getCharHeight() / 5));\r
     }\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 32cbfb5..c9ed305 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -86,7 +86,7 @@ public class IdCanvas extends JPanel
         }\r
         else\r
         {\r
-            gg.setColor(s.getColor());\r
+            gg.setColor(av.getSequenceColour(s));\r
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),\r
                 charHeight);\r
             gg.setColor(Color.black);\r
@@ -310,7 +310,7 @@ public class IdCanvas extends JPanel
                 }\r
                 else\r
                 {\r
-                  currentColor = sequence.getColor();\r
+                  currentColor = av.getSequenceColour(sequence);\r
                   currentTextColor = Color.black;\r
                 }\r
 \r