gsdi work

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

diff --git a/forester/java/src/org/forester/application/count_support.java b/forester/java/src/org/forester/application/count_support.java
index 67dfc1b..96a7596 100644 (file)
--- a/forester/java/src/org/forester/application/count_support.java
+++ b/forester/java/src/org/forester/application/count_support.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -32,6 +32,7 @@ import java.util.Arrays;
 import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
@@ -49,11 +50,13 @@ public class count_support {
     final static private String  PRG_NAME                = "count_support";
     final static private String  PRG_VERSION             = "1.0";
     final static private String  PRG_DATE                = "2008.03.04";
+    final static private String E_MAIL        = "phylosoft@gmail.com";
+    final static private String WWW           = "www.phylosoft.org/forester/";
     private final static boolean WRITE_EVALUATORS_AS_NHX = false;
 
     public static void main( final String args[] ) {
-        ForesterUtil
-                .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
+         ForesterUtil.printProgramInformation( PRG_NAME, null, PRG_VERSION, PRG_DATE, E_MAIL, WWW, ForesterUtil.getForesterLibraryInformation() );
+        
         if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
             System.out.println();
             System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
@@ -104,21 +107,21 @@ public class count_support {
         Phylogeny[] ev = null;
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
             p = factory.create( phylogeny_infile, pp )[ 0 ];
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" ["
-                    + e.getMessage() + "]" );
+            ForesterUtil.fatalError( count_support.PRG_NAME,
+                                     "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]" );
         }
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( evaluators_infile, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( evaluators_infile, true );
             ev = factory.create( evaluators_infile, pp );
         }
         catch ( final Exception e ) {
-            ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + evaluators_infile + "\" ["
-                    + e.getMessage() + "]" );
+            ForesterUtil.fatalError( count_support.PRG_NAME,
+                                     "Could not read \"" + evaluators_infile + "\" [" + e.getMessage() + "]" );
         }
         boolean strip = false;
         if ( cla.isOptionSet( "s" ) ) {
@@ -187,8 +190,9 @@ public class count_support {
                 else {
                     System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
                     if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
-                        w.toNewHampshireX( Arrays.asList( ev ), evaluators_outfile, ";"
-                                + ForesterUtil.getLineSeparator() );
+                        w.toNewHampshireX( Arrays.asList( ev ),
+                                           evaluators_outfile,
+                                           ";" + ForesterUtil.getLineSeparator() );
                     }
                     else {
                         w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"