X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FBasicMsa.java;h=5fc25908f118587b8ab53945b12ec314af49826f;hb=656be28debec520e0e35a8b311114398a40ea366;hp=1fdef107de80aa97c7d6dd8e6d06a47334bc71b0;hpb=b1a74bd076c917d428002284a53a2c6f390226fb;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index 1fdef10..5fc2590 100644
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.msa;
 
@@ -32,6 +32,8 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
 import org.forester.sequence.BasicSequence;
 import org.forester.sequence.Sequence;
 import org.forester.sequence.Sequence.TYPE;
@@ -152,7 +154,24 @@ public class BasicMsa implements Msa {
     }
 
     @Override
-    public void write( final Writer w ) throws IOException {
+    public void write( final Writer w, final MSA_FORMAT format ) throws IOException {
+        switch ( format ) {
+            case PHYLIP:
+                writeToPhylip( w );
+                break;
+            case FASTA:
+                writeToFasta( w );
+                break;
+            default:
+                throw new RuntimeException( "unknown format " + format );
+        }
+    }
+
+    private void writeToFasta( final Writer w ) throws IOException {
+        SequenceWriter.writeSeqs( asSequenceList(), w, SEQ_FORMAT.FASTA, 100 );
+    }
+
+    private void writeToPhylip( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
         for( int row = 0; row < _data.length; ++row ) {
             w.write( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ).toString() );