X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FBasicMsa.java;h=bf215d81bfbaac8c376180288cccf8a840e00a9c;hb=50c2ff100214fbb04b5f9665466e6d98d26b051d;hp=02da257664a0817e2a58a9a5a094e847a0dd8a99;hpb=917fdd32a745f77a8b70d7779e44b8b36e11185f;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index 02da257..bf215d8 100644
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -143,7 +143,7 @@ public class BasicMsa implements Msa {
         }
         if ( _identifiers_set.contains( id ) ) {
             throw new IllegalArgumentException( "illegal attempt to create msa with non-unique identifiers [" + id
-                                                + "]" );
+                    + "]" );
         }
         _identifiers_set.add( id );
         _identifiers[ row ] = id;
@@ -200,13 +200,32 @@ public class BasicMsa implements Msa {
 
     private void writeToNexus( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
+        TYPE t = null;
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            t = ForesterUtil.guessMolecularSequenceType( getSequence( row ).getMolecularSequenceAsString() );
+            if ( t != null ) {
+                break;
+            }
+        }
+        String type_str = "Protein";
+        if ( t != null ) {
+            if ( t == TYPE.DNA ) {
+                type_str = "DNA";
+            }
+            else if ( t == TYPE.RNA ) {
+                type_str = "RNA";
+            }
+            else if ( t == TYPE.GENERAL ) {
+                type_str = "Standard";
+            }
+        }
         w.write( "Begin Data;" );
         w.write( ForesterUtil.LINE_SEPARATOR );
         w.write( "   Dimensions NTax=" + getNumberOfSequences() );
         w.write( " NChar=" + getLength() );
         w.write( ";" );
         w.write( ForesterUtil.LINE_SEPARATOR );
-        w.write( "   Format DataType=Protein Interleave=No gap=-;" );
+        w.write( "   Format DataType=" + type_str + " Interleave=No gap=-;" );
         w.write( ForesterUtil.LINE_SEPARATOR );
         w.write( "   Matrix" );
         w.write( ForesterUtil.LINE_SEPARATOR );