X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fcount_support.java;h=9be5f899a23ae9eeff3ad3803dd958076e42d41f;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=e094f69ed4313b6948f5cd4fdfb8e8968a7243c5;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/application/count_support.java b/forester/java/src/org/forester/application/count_support.java
index e094f69..9be5f89 100644
--- a/forester/java/src/org/forester/application/count_support.java
+++ b/forester/java/src/org/forester/application/count_support.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.application;
 
@@ -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 +50,18 @@ 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" );
@@ -104,7 +112,7 @@ 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 ) {
@@ -113,7 +121,7 @@ public class count_support {
         }
         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 ) {
@@ -178,7 +186,6 @@ public class count_support {
                     }
                     else {
                         w.toNewHampshire( evaluator_phylogenies_above_threshold,
-                                          true,
                                           branch_lengths_in_ev_out,
                                           evaluators_outfile,
                                           ";" + ForesterUtil.getLineSeparator() );
@@ -192,7 +199,7 @@ public class count_support {
                                            ";" + ForesterUtil.getLineSeparator() );
                     }
                     else {
-                        w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
+                        w.toNewHampshire( Arrays.asList( ev ), branch_lengths_in_ev_out, evaluators_outfile, ";"
                                 + ForesterUtil.getLineSeparator() );
                     }
                 }