// 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
// 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
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
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;
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();
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 ) {
- 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" ) ) {
}
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;
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();
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() );
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, ";"
+ w.toNewHampshire( Arrays.asList( ev ), branch_lengths_in_ev_out, evaluators_outfile, ";"
+ ForesterUtil.getLineSeparator() );
}
}
git://source.jalview.org / jalview.git / blobdiff