From bf22060aa91d40c9d6f7e3c7f518b6bd0457921e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:49:05 +0000
Subject: [PATCH] Display nucleotides

---
 src/jalview/appletgui/SeqPanel.java |   31 +++++++++++++++++++++---------
 src/jalview/gui/SeqPanel.java       |   36 ++++++++++++++++++++++-------------
 2 files changed, 45 insertions(+), 22 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index fb11579..9c3a1e8 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -244,19 +244,32 @@ public class SeqPanel
       return;
     }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    String aa = "";
-    if (obj != null)
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+            sequence.getName());
+
+    Object obj = null;
+    if (av.alignment.isNucleotide())
+    {
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+          "");
+      if(obj!=null)
+        text.append(" Nucleotide: ");
+    }
+    else
     {
-      aa = obj.toString();
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if(obj!=null)
+        text.append("  Residue: ");
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-    if (aa != "")
+    if (obj != null)
     {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+
+      if (obj != "")
+      {
+        text.append(obj + " (" +
+                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      }
     }
 
     ap.alignFrame.statusBar.setText(text.toString());
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8486ac1..ab5ed30 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -342,25 +342,35 @@ public class SeqPanel extends JPanel
 
       if (res > sequence.getLength())
       {
-          return;
-        }
+        return;
+      }
 
-        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                "");
-        String aa = "";
+        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                sequence.getName());
 
-        if (obj != null)
+        Object obj = null;
+        if (av.alignment.isNucleotide())
         {
-            aa = obj.toString();
+          obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+              "");
+          if(obj!=null)
+            text.append(" Nucleotide: ");
+        }
+        else
+        {
+          obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+          if(obj!=null)
+            text.append("  Residue: ");
         }
 
-        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                sequence.getName());
-
-        if (aa != "")
+        if (obj != null)
         {
-            text.append("  Residue: " + aa + " (" +
-                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+
+          if (obj != "")
+          {
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
         }
 
         ap.alignFrame.statusBar.setText(text.toString());
-- 
1.7.10.2