X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=fd0127e432cd7cf73537285f65341a7933db438e;hb=876ced97014fafe54ff51dcc17da8bf25913fec7;hp=d3414a7e486ae1579d222fa0a8027db72e960d05;hpb=b819fa043cac2722618af63f0d4752ffa1a40890;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index d3414a7..fd0127e 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -29,6 +29,7 @@ package org.forester.application; import java.io.File; import java.io.IOException; +import java.math.RoundingMode; import java.util.ArrayList; import java.util.List; @@ -56,7 +57,7 @@ public class rio { final static private String PRG_NAME = "rio"; final static private String PRG_VERSION = "4.000 beta 10"; - final static private String PRG_DATE = "130325"; + final static private String PRG_DATE = "140211"; final static private String E_MAIL = "phyloxml@gmail.com"; final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; final static private String HELP_OPTION_1 = "help"; @@ -88,7 +89,7 @@ public class rio { if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { printHelp(); } - if ( ( args.length < 3 ) || ( args.length > 11 ) ) { + if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) { System.out.println(); System.out.println( "error: incorrect number of arguments" ); System.out.println(); @@ -160,7 +161,7 @@ public class rio { } else { ForesterUtil - .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); + .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); } } if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) { @@ -287,6 +288,7 @@ public class rio { } if ( return_gene_tree != null ) { System.out.println( "Write best gene tree to : " + return_gene_tree ); + System.out.println( "Transfer taxonomic data : " + transfer_taxonomy ); } time = System.currentTimeMillis(); final ALGORITHM algorithm; @@ -318,13 +320,13 @@ public class rio { final NHXParser nhx = ( NHXParser ) p; nhx.setReplaceUnderscores( false ); nhx.setIgnoreQuotes( true ); - nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE ); + nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else if ( p instanceof NexusPhylogeniesParser ) { final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p; nex.setReplaceUnderscores( false ); nex.setIgnoreQuotes( true ); - nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE ); + nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else { throw new RuntimeException( "unknown parser type: " + p ); @@ -369,22 +371,26 @@ public class rio { writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" ); } if ( return_gene_tree != null ) { + String tt = ""; + if ( transfer_taxonomy ) { + tt = "(with transferred taxonomic data) "; + } writeTree( rio.getMinDuplicationsGeneTree(), return_gene_tree, - "Wrote (one) minimal duplication gene tree to" ); + "Wrote (one) minimal duplication gene tree " + tt + "to" ); } final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" ); System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: " + df.format( stats.sampleStandardDeviation() ) + ") (" - + df.format( 100.0 * stats.arithmeticMean() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); if ( stats.getN() > 3 ) { System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " (" - + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + + df.format( ( 100.0 * stats.median() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); } System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " (" - + df.format( 100.0 * stats.getMin() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + + df.format( ( 100.0 * stats.getMin() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " (" - + df.format( 100.0 * stats.getMax() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + + df.format( ( 100.0 * stats.getMax() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); System.out.println( "Gene tree internal nodes : " + rio.getIntNodesOfAnalyzedGeneTrees() ); System.out.println( "Gene tree external nodes : " + rio.getExtNodesOfAnalyzedGeneTrees() ); } @@ -416,37 +422,37 @@ public class rio { System.out.println( "Usage" ); System.out.println(); System.out - .println( PRG_NAME - + " [options] [logfile]" ); + .println( PRG_NAME + + " [options] [logfile]" ); System.out.println(); System.out.println( " Options" ); System.out.println( " -" + GT_FIRST + "= : first gene tree to analyze (0-based index)" ); System.out.println( " -" + GT_LAST + "= : last gene tree to analyze (0-based index)" ); System.out.println( " -" + REROOTING_OPT - + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); + + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); System.out.println( " or 'outgroup' (default: by minizming duplications)" ); System.out.println( " -" + OUTGROUP - + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); + + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); System.out - .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); + .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); System.out.println( " -" + RETURN_BEST_GENE_TREE - + "= : to write (one) minimal duplication gene tree to file" ); + + "= : to write (one) minimal duplication gene tree to file" ); System.out - .println( " -" - + TRANSFER_TAXONOMY_OPTION - + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" - + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); + .println( " -" + + TRANSFER_TAXONOMY_OPTION + + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" + + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); System.out.println( " -" + USE_SDIR - + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); + + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); System.out.println( " disallowed, as are most options)" ); System.out.println(); System.out.println( " Formats" ); System.out - .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); + .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); System.out - .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); + .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); System.out - .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); + .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); System.out.println( " in the species tree." ); System.out.println(); System.out.println( " Examples" ); @@ -484,8 +490,9 @@ public class rio { private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m ) throws IOException { final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile ); - final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" ); + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" ); df.setDecimalSeparatorAlwaysShown( false ); + df.setRoundingMode( RoundingMode.HALF_UP ); for( int i = 0; i < m.size(); ++i ) { w.print( "\t" ); w.print( m.getLabel( i ) );