inprogress

[jalview.git] / forester / java / src / org / forester / application / msa_compactor.java

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 5d83681..9ed5e20 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -9,6 +9,7 @@ import java.util.List;
 import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.msa.Msa;
+import org.forester.msa.Msa.MSA_FORMAT;
 import org.forester.msa.MsaCompactor;
 import org.forester.msa.MsaMethods;
 import org.forester.util.CommandLineArguments;
@@ -99,6 +100,7 @@ public class msa_compactor {
             for( final String id : mc.getRemovedSeqIds() ) {
                 System.out.println( id );
             }
+            mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
         }
         catch ( final Exception e ) {
             e.printStackTrace();