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 7457b3e..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;
@@ -25,10 +26,10 @@ public class msa_compactor {
     final static private String REALIGN_OPTION                = "r";
     final static private String PRG_NAME                      = "msa_compactor";
     final static private String PRG_DESC                      = "multiple sequnce aligment compactor";
-    final static private String PRG_VERSION                   = "0.90";
-    final static private String PRG_DATE                      = "2012.07.11";
+    final static private String PRG_VERSION                   = "0.01";
+    final static private String PRG_DATE                      = "140221";
     final static private String E_MAIL                        = "phylosoft@gmail.com";
-    final static private String WWW                           = "www.phylosoft.org/forester/";
+    final static private String WWW                           = "https://sites.google.com/site/cmzmasek/home/software/forester";
 
     public static void main( final String args[] ) {
         try {
@@ -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();
@@ -120,10 +122,6 @@ public class msa_compactor {
         System.out.println();
         System.out.println( " options: " );
         System.out.println();
-        //        System.out.println( "   -" + FROM_OPTION + "=<integer>: from (msa column)" );
-        //        System.out.println( "   -" + TO_OPTION + "=<integer>: to (msa column)" );
-        //        System.out.println( "    or" );
-        //        System.out.println( "   -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );
         System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
         System.out.println();
         System.out.println();