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 c385ca9..33254a5 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -10,8 +10,8 @@ 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_compactor.MsaCompactor;
 import org.forester.msa.MsaMethods;
+import org.forester.msa_compactor.MsaCompactor;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.ForesterUtil;
 
@@ -28,7 +28,7 @@ public class msa_compactor {
     final static private String PRG_NAME                               = "msa_compactor";
     final static private String PRG_DESC                               = "multiple sequnce aligment compactor";
     final static private String PRG_VERSION                            = "0.01";
-    final static private String PRG_DATE                               = "140221";
+    final static private String PRG_DATE                               = "140314";
     final static private String E_MAIL                                 = "phylosoft@gmail.com";
     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/forester";
 
@@ -128,7 +128,8 @@ public class msa_compactor {
         System.out.println();
         System.out.println( " options: " );
         System.out.println();
-        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
+        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>  number of sequences to remove" );
+        System.out.println( "   -" + REALIGN_OPTION + " to realign using " );
         System.out.println();
         System.out.println();
         System.out.println();