X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fcount_support.java;h=8e8526342c2d905d8376e1dcd9b32eed54fb19aa;hb=f7f0102d3e7eb2fd254f7d22d75a88495133449c;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..8e85263 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;
@@ -49,20 +50,27 @@ 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" );
             System.out.println();
             System.out
-                    .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
-                            + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
+            .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
+                    + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
             System.out
-                    .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
+            .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
             System.out.println( "        : -t=<d> threshold for similarity (0.0 to 1.0)" );
             System.out.println( "        : -n no branch lengths in outfile for evaluator phylogenies" );
             System.out.println();
@@ -97,14 +105,14 @@ public class count_support {
         else {
             if ( !branch_lengths_in_ev_out ) {
                 ForesterUtil.fatalError( count_support.PRG_NAME,
-                                         "Cannot use -n option if no outfile for evaluators specified" );
+                        "Cannot use -n option if no outfile for evaluators specified" );
             }
         }
         Phylogeny p = null;
         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 ) {
@@ -134,7 +142,7 @@ public class count_support {
             }
             if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) {
                 ForesterUtil.fatalError( count_support.PRG_NAME,
-                                         "support threshold has to be between 0.0 and 1.0 (inclusive)" );
+                        "support threshold has to be between 0.0 and 1.0 (inclusive)" );
             }
         }
         List<Phylogeny> evaluator_phylogenies_above_threshold = null;
@@ -155,7 +163,7 @@ public class count_support {
         if ( threshhold >= 0 ) {
             count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() );
             System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length
-                    + " evaluator phylogenies are above threshold of " + threshhold );
+                                + " evaluator phylogenies are above threshold of " + threshhold );
         }
         try {
             final PhylogenyWriter w = new PhylogenyWriter();
@@ -171,14 +179,13 @@ public class count_support {
                 final PhylogenyWriter w = new PhylogenyWriter();
                 if ( evaluator_phylogenies_above_threshold != null ) {
                     System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size()
-                            + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
+                                        + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
                     if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
                         w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";"
                                 + ForesterUtil.getLineSeparator() );
                     }
                     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() );
                     }
                 }