From bb99b11825ccc8f9d7dd7b4b0dfcc2f64ebe0b75 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:50:47 +0000
Subject: [PATCH] isNucleotide

---
 src/jalview/datamodel/Alignment.java  |   30 +++++++++++++++++++++++++++++-
 src/jalview/datamodel/AlignmentI.java |   15 +++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 61735ee..ac8f47a 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -33,6 +33,8 @@ public class Alignment implements AlignmentI
     protected Vector groups = new Vector();
     protected Vector superGroup = new Vector();
     protected char gapCharacter = '-';
+    protected boolean isNucleotide = true;
+
 
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
@@ -46,9 +48,25 @@ public class Alignment implements AlignmentI
      */
     public Alignment(SequenceI[] seqs)
     {
+        int i=0, iSize = seqs.length, j, jSize;
+        while(isNucleotide && i<iSize)
+        {
+            jSize = seqs[i].getLength();
+            for(j=0; j<jSize; j++)
+            {
+              if(!jalview.schemes.ResidueProperties.nucleotideHash.containsKey(seqs[i].getSequence(j, j+1))
+              && !jalview.util.Comparison.isGap(seqs[i].getSequence().charAt(j)))
+              {
+                isNucleotide = false;
+                break;
+              }
+            }
+            i++;
+        }
+
         sequences = new Vector();
 
-        for (int i = 0; i < seqs.length; i++)
+        for (i = 0; i < seqs.length; i++)
         {
             sequences.addElement(seqs[i]);
         }
@@ -683,4 +701,14 @@ public class Alignment implements AlignmentI
     {
         return annotations;
     }
+
+    public void setNucleotide(boolean b)
+    {
+      isNucleotide = b;
+    }
+
+    public boolean isNucleotide()
+    {
+      return isNucleotide;
+    }
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 416be69..4399b39 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -289,4 +289,19 @@ public interface AlignmentI
      * @return DOCUMENT ME!
      */
     public Vector getAAFrequency();
+
+    /**
+     * Returns true if alignment is nucleotide sequence
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isNucleotide();
+
+    /**
+     * Set true if the alignment is a nucleotide sequence
+     *
+     * @return
+     */
+    public void setNucleotide(boolean b);
+
 }
-- 
1.7.10.2