From 4edb2cfcc271458aaa7898e3ccb3be4c05a650ea Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 8 Jun 2012 16:37:41 +0000 Subject: [PATCH] phylotastic hackathon at NESCENT 120608 --- .../java/src/org/forester/application/gsdi.java | 36 +++++++++----------- 1 file changed, 17 insertions(+), 19 deletions(-) diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 3f39fb8..b61d896 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -31,7 +31,6 @@ import java.util.ArrayList; import java.util.Date; import java.util.List; - import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.nhx.NHXParser; import org.forester.io.parsers.phyloxml.PhyloXmlParser; @@ -50,19 +49,19 @@ import org.forester.util.ForesterUtil; public final class gsdi { final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true; - final static private String STRIP_OPTION = "s"; - final static private String SDI_OPTION = "b"; - final static private String MOST_PARSIMONIOUS_OPTION = "m"; - final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String DEFAULT_OUTFILE = "gsdi_out.phylo.xml"; - final static private String PRG_NAME = "gsdi"; - final static private String PRG_VERSION = "0.5"; - final static private String PRG_DATE = "120608"; - final static private String PRG_DESC = "general speciation duplication inference"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String WWW = "www.phylosoft.org/forester"; + final static private String STRIP_OPTION = "s"; + final static private String SDI_OPTION = "b"; + final static private String MOST_PARSIMONIOUS_OPTION = "m"; + final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.phylo.xml"; + final static private String PRG_NAME = "gsdi"; + final static private String PRG_VERSION = "0.901"; + final static private String PRG_DATE = "120608"; + final static private String PRG_DESC = "general speciation duplication inference"; + final static private String E_MAIL = "phylosoft@gmail.com"; + final static private String WWW = "www.phylosoft.org/forester"; public static void main( final String args[] ) { ForesterUtil.printProgramInformation( PRG_NAME, @@ -131,7 +130,8 @@ public final class gsdi { out_file = cla.getFile( 2 ); } else { - out_file = new File( gsdi.DEFAULT_OUTFILE ); + out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX ); + //out_file = new File( gsdi.DEFAULT_OUTFILE ); } } catch ( final IllegalArgumentException e ) { @@ -153,20 +153,18 @@ public final class gsdi { } else { final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true ); - if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && p instanceof NHXParser ) { - (( NHXParser ) p ).setReplaceUnderscores( true ); + if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) { + ( ( NHXParser ) p ).setReplaceUnderscores( true ); } species_tree = factory.create( species_tree_file, p )[ 0 ]; PhylogenyMethods.transferNodeNameToField( species_tree, PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ); - } } catch ( final IOException e ) { ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() ); } - try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ]; -- 1.7.10.2