From dd645839efa022cd15c6247398692412b7c2ceaa Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 14 Apr 2010 14:39:18 +0000
Subject: [PATCH] todo and disable selection sharing between views on same
 alignment

---
 src/jalview/gui/SeqPanel.java              |    8 +++----
 src/jalview/schemes/ResidueProperties.java |   35 +++++++++++++++++++++-------
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a961928..f260ec2 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1863,16 +1863,15 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
-    if (av == source)
+    // TODO: extend config options to allow user to control if selections may be shared between viewports.
+    if (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport)source).getSequenceSetId().equals(av.getSequenceSetId())))
     {
       return;
     }
     // do we want to thread this ? (contention with seqsel and colsel locks, I
     // suspect)
     boolean repaint = false;
-    if (av.followSelection)
-    {
-      if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+    if (av.selectionGroup == null || !av.isSelectionGroupChanged())
       {
         SequenceGroup sgroup = null;
         if (seqsel != null)
@@ -1917,7 +1916,6 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         repaint |= av.isColSelChanged();
       }
-    }
     if (av.hasHiddenColumns && (av.colSel==null || av.colSel.getHiddenColumns()==null))
     {
       System.err.println("Bad things");
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a53b95f..48a9272 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -101,7 +101,7 @@ public class ResidueProperties
     nucleotideIndex = new int[255];
     for (int i = 0; i < 255; i++)
     {
-      nucleotideIndex[i] = -1;
+      nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps.
     }
 
     nucleotideIndex['A'] = 0;
@@ -280,7 +280,13 @@ public class ResidueProperties
       new Color(255, 179, 64), // C
       new Color(235, 65, 60), // G
       new Color(60, 136, 238), // T
-      new Color(60, 136, 238) // U
+      new Color(60, 136, 238), // U
+  Color.white, // I
+  Color.white, // X
+  Color.white, // R
+  Color.white, // Y
+  Color.white, // N
+  Color.white, // Gap
   };
 
   // Zappo
@@ -504,14 +510,27 @@ public class ResidueProperties
     ssHash.put("I", Color.pink);
     ssHash.put("B", Color.yellow);
   }
-
+/*      new Color(60, 136, 238), // U
+  Color.white, // I
+  Color.white, // X
+  Color.white, // R
+  Color.white, // Y
+  Color.white, // N
+  Color.white, // Gap
+*/
   static final int[][] DNA =
   {
-  { 5, -4, -4, -4, 1 }, // C
-      { -4, 5, -4, -4, 1 }, // T
-      { -4, -4, 5, -4, 1 }, // A
-      { -4, -4, -4, 5, 1 }, // G
-      { 1, 1, 1, 1, 1 }, // -
+  { 10, -8, -8, -8, 1, 0  ,0  ,0  ,0  ,0 ,1 }, // C
+  { -8, 10, -8, -8, 1, 0  ,0  ,0  ,0  ,0 ,1 }, // T
+  { -8, -8, 10, -8, 1, 0  ,0  ,0  ,0  ,0 ,1 }, // A
+  { -8, -8, -8, 10, 1, 0  ,0  ,0  ,0  ,0 ,1 }, // G
+  { 1,   1,  1, 1, 10,0  ,0  ,0  ,0  ,0 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,10 ,0  ,0  ,0  ,0 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,0  ,10 ,0  ,0  ,0 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,0  ,0  ,10 ,0  ,0 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,0  ,0  ,0  ,10 ,0 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,0  ,0  ,0  ,0 ,10 ,1 }, // -
+  { 1,   1,  1, 1, 1 ,1  ,1  ,1  ,1  ,1 ,1 }, // -
   };
   /**
    * register matrices in list
-- 
1.7.10.2