X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=51a36bf9a99011b540fdbb110ef1173ade4370df;hb=504b2b133e9814ac9ee966dc04a1408c455c6a2f;hp=b56c289718e6cdaa5964ca39ba1ae35f731de6e3;hpb=4160636eeed0e0c07397f062fa9f990f6a30eef4;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index b56c289..51a36bf 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -23,21 +23,26 @@ // 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.io.File; import java.io.IOException; +import java.math.RoundingMode; import java.util.ArrayList; import java.util.List; import org.forester.datastructures.IntMatrix; +import org.forester.io.parsers.IteratingPhylogenyParser; +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlParser; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.rio.RIO; import org.forester.rio.RIO.REROOTING; import org.forester.rio.RIOException; @@ -50,18 +55,21 @@ import org.forester.util.ForesterUtil; public class rio { - final static private String PRG_NAME = "rio"; - final static private String PRG_VERSION = "4.000 beta 3"; - final static private String PRG_DATE = "2012.12.18"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String GT_FIRST = "f"; - final static private String GT_LAST = "l"; - final static private String REROOTING_OPT = "r"; - final static private String OUTGROUP = "o"; - final static private String USE_SDIR = "b"; + final static private String PRG_NAME = "rio"; + final static private String PRG_VERSION = "4.000 beta 10"; + 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"; + final static private String HELP_OPTION_2 = "h"; + final static private String GT_FIRST = "f"; + final static private String GT_LAST = "l"; + final static private String REROOTING_OPT = "r"; + final static private String OUTGROUP = "o"; + final static private String RETURN_SPECIES_TREE = "s"; + final static private String RETURN_BEST_GENE_TREE = "g"; + final static private String USE_SDIR = "b"; + final static private String TRANSFER_TAXONOMY_OPTION = "t"; public static void main( final String[] args ) { ForesterUtil.printProgramInformation( PRG_NAME, @@ -76,14 +84,14 @@ public class rio { cla = new CommandLineArguments( args ); } catch ( final Exception e ) { - ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( e.getMessage() ); } if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) { printHelp(); } - if ( ( args.length < 3 ) || ( args.length > 8 ) ) { + if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) { System.out.println(); - System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" ); + System.out.println( "error: incorrect number of arguments" ); System.out.println(); printHelp(); } @@ -93,9 +101,12 @@ public class rio { allowed_options.add( REROOTING_OPT ); allowed_options.add( OUTGROUP ); allowed_options.add( USE_SDIR ); + allowed_options.add( RETURN_SPECIES_TREE ); + allowed_options.add( RETURN_BEST_GENE_TREE ); + allowed_options.add( TRANSFER_TAXONOMY_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); + ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options ); } final File gene_trees_file = cla.getFile( 0 ); final File species_tree_file = cla.getFile( 1 ); @@ -104,7 +115,7 @@ public class rio { if ( cla.getNumberOfNames() > 3 ) { logfile = cla.getFile( 3 ); if ( logfile.exists() ) { - ForesterUtil.fatalError( PRG_NAME, "\"" + logfile + "\" already exists" ); + ForesterUtil.fatalError( "\"" + logfile + "\" already exists" ); } } else { @@ -113,30 +124,30 @@ public class rio { boolean sdir = false; if ( cla.isOptionSet( USE_SDIR ) ) { if ( cla.isOptionHasAValue( USE_SDIR ) ) { - ForesterUtil.fatalError( PRG_NAME, "no value allowed for -" + USE_SDIR ); + ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR ); } sdir = true; if ( logfile != null ) { - ForesterUtil.fatalError( PRG_NAME, "no logfile output for SDIR algorithm" ); + ForesterUtil.fatalError( "no logfile output for SDIR algorithm" ); } } String outgroup = null; if ( cla.isOptionSet( OUTGROUP ) ) { if ( !cla.isOptionHasAValue( OUTGROUP ) ) { - ForesterUtil.fatalError( PRG_NAME, "no value for -" + OUTGROUP ); + ForesterUtil.fatalError( "no value for -" + OUTGROUP ); } if ( sdir ) { - ForesterUtil.fatalError( PRG_NAME, "no outgroup option for SDIR algorithm" ); + ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" ); } outgroup = cla.getOptionValueAsCleanString( OUTGROUP ); } REROOTING rerooting = REROOTING.BY_ALGORITHM; if ( cla.isOptionSet( REROOTING_OPT ) ) { if ( !cla.isOptionHasAValue( REROOTING_OPT ) ) { - ForesterUtil.fatalError( PRG_NAME, "no value for -" + REROOTING_OPT ); + ForesterUtil.fatalError( "no value for -" + REROOTING_OPT ); } if ( sdir ) { - ForesterUtil.fatalError( PRG_NAME, "no re-rooting option for SDIR algorithm" ); + ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" ); } final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase(); if ( rerooting_str.equals( "none" ) ) { @@ -150,60 +161,88 @@ public class rio { } else { ForesterUtil - .fatalError( PRG_NAME, - "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 ) ) { - ForesterUtil.fatalError( PRG_NAME, "selected re-rooting by outgroup, but outgroup not set" ); + ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" ); } if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) { - ForesterUtil.fatalError( PRG_NAME, "outgroup set, but selected re-rooting by other approach" ); + ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" ); } int gt_first = RIO.DEFAULT_RANGE; int gt_last = RIO.DEFAULT_RANGE; if ( cla.isOptionSet( GT_FIRST ) ) { if ( !cla.isOptionHasAValue( GT_FIRST ) ) { - ForesterUtil.fatalError( PRG_NAME, "no value for -" + GT_FIRST ); + ForesterUtil.fatalError( "no value for -" + GT_FIRST ); } if ( sdir ) { - ForesterUtil.fatalError( PRG_NAME, "no gene tree range option for SDIR algorithm" ); + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); } try { gt_first = cla.getOptionValueAsInt( GT_FIRST ); } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "could not parse integer for -" + GT_FIRST + " option" ); + ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" ); } if ( gt_first < 0 ) { - ForesterUtil.fatalError( PRG_NAME, "attempt to set index of first tree to analyze to: " + gt_first ); + ForesterUtil.fatalError( "attempt to set index of first tree to analyze to: " + gt_first ); } } if ( cla.isOptionSet( GT_LAST ) ) { if ( !cla.isOptionHasAValue( GT_LAST ) ) { - ForesterUtil.fatalError( PRG_NAME, "no value for -" + GT_LAST ); + ForesterUtil.fatalError( "no value for -" + GT_LAST ); } if ( sdir ) { - ForesterUtil.fatalError( PRG_NAME, "no gene tree range option for SDIR algorithm" ); + ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" ); } try { gt_last = cla.getOptionValueAsInt( GT_LAST ); } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "could not parse integer for -" + GT_LAST + " option" ); + ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" ); } if ( gt_last < 0 ) { - ForesterUtil.fatalError( PRG_NAME, "attempt to set index of last tree to analyze to: " + gt_last ); + ForesterUtil.fatalError( "attempt to set index of last tree to analyze to: " + gt_last ); } } if ( ( ( gt_last != RIO.DEFAULT_RANGE ) && ( gt_first != RIO.DEFAULT_RANGE ) ) && ( ( gt_last < gt_first ) ) ) { - ForesterUtil.fatalError( PRG_NAME, "attempt to set range (0-based) of gene to analyze to: from " + gt_first - + " to " + gt_last ); + ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to " + + gt_last ); } - ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, gene_trees_file ); - ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file ); + File return_species_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_SPECIES_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_SPECIES_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_SPECIES_TREE ); + } + final String s = cla.getOptionValueAsCleanString( RETURN_SPECIES_TREE ); + return_species_tree = new File( s ); + if ( return_species_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_species_tree + "\" already exists" ); + } + } + File return_gene_tree = null; + if ( !sdir && cla.isOptionSet( RETURN_BEST_GENE_TREE ) ) { + if ( !cla.isOptionHasAValue( RETURN_BEST_GENE_TREE ) ) { + ForesterUtil.fatalError( "no value for -" + RETURN_BEST_GENE_TREE ); + } + final String s = cla.getOptionValueAsCleanString( RETURN_BEST_GENE_TREE ); + return_gene_tree = new File( s ); + if ( return_gene_tree.exists() ) { + ForesterUtil.fatalError( "\"" + return_gene_tree + "\" already exists" ); + } + } + boolean transfer_taxonomy = false; + if ( !sdir && cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) { + if ( return_gene_tree == null ) { + ForesterUtil.fatalError( "no point in transferring taxonomy data without returning best gene tree" ); + } + transfer_taxonomy = true; + } + ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file ); + ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); if ( orthology_outtable.exists() ) { - ForesterUtil.fatalError( PRG_NAME, "\"" + orthology_outtable + "\" already exists" ); + ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); } long time = 0; System.out.println( "Gene trees : " + gene_trees_file ); @@ -244,28 +283,14 @@ public class rio { else { System.out.println( "Non binary species tree : disallowed" ); } - time = System.currentTimeMillis(); - Phylogeny species_tree = null; - try { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ]; - } - catch ( final Exception e ) { - e.printStackTrace(); - System.exit( -1 ); + if ( return_species_tree != null ) { + System.out.println( "Write used species tree to: " + return_species_tree ); } - if ( !species_tree.isRooted() ) { - ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" ); - } - final int o = PhylogenyMethods.countNumberOfOneDescendantNodes( species_tree ); - if ( o > 0 ) { - ForesterUtil.printWarningMessage( PRG_NAME, "species tree has " + o - + " internal nodes with only one descendent! Going to strip them." ); - PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree ); - if ( PhylogenyMethods.countNumberOfOneDescendantNodes( species_tree ) > 0 ) { - ForesterUtil.unexpectedFatalError( PRG_NAME, "stripping of one-desc nodes failed" ); - } + 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; if ( sdir ) { algorithm = ALGORITHM.SDIR; @@ -274,19 +299,63 @@ public class rio { algorithm = ALGORITHM.GSDIR; } try { - final RIO rio = RIO.executeAnalysis( gene_trees_file, - species_tree, - algorithm, - rerooting, - outgroup, - gt_first, - gt_last, - logfile != null, - true ); + final RIO rio; + boolean iterating = false; + final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true ); + if ( p instanceof PhyloXmlParser ) { + rio = RIO.executeAnalysis( gene_trees_file, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); + } + else { + iterating = true; + if ( p instanceof NHXParser ) { + final NHXParser nhx = ( NHXParser ) p; + nhx.setReplaceUnderscores( false ); + nhx.setIgnoreQuotes( true ); + 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.AGGRESSIVE ); + } + else { + throw new RuntimeException( "unknown parser type: " + p ); + } + final IteratingPhylogenyParser ip = ( IteratingPhylogenyParser ) p; + ip.setSource( gene_trees_file ); + rio = RIO.executeAnalysis( ip, + species_tree_file, + algorithm, + rerooting, + outgroup, + gt_first, + gt_last, + logfile != null, + true, + transfer_taxonomy ); + } if ( algorithm == ALGORITHM.GSDIR ) { - ForesterUtil.programMessage( PRG_NAME, "taxonomy linking based on: " + rio.getGSDIRtaxCompBase() ); + System.out.println( "Taxonomy linking based on : " + rio.getGSDIRtaxCompBase() ); + } + final IntMatrix m; + if ( iterating ) { + m = rio.getOrthologTable(); + } + else { + m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); } - tableOutput( orthology_outtable, rio ); + final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics(); + writeTable( orthology_outtable, stats.getN(), m ); if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) { writeLogFile( logfile, rio, @@ -298,32 +367,54 @@ public class rio { PRG_DATE, ForesterUtil.getForesterLibraryInformation() ); } - final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics(); + if ( return_species_tree != null ) { + 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 " + tt + "to" ); + } final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" ); - ForesterUtil.programMessage( PRG_NAME, - "Mean number of duplications : " + df.format( stats.arithmeticMean() ) - + " (sd: " + df.format( stats.sampleStandardDeviation() ) + ")" ); + System.out.println( "Mean number of duplications : " + df.format( stats.arithmeticMean() ) + " (sd: " + + df.format( stats.sampleStandardDeviation() ) + ") (" + + df.format( 100.0 * stats.arithmeticMean() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); if ( stats.getN() > 3 ) { - ForesterUtil.programMessage( PRG_NAME, "Median number of duplications: " + df.format( stats.median() ) ); + System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " (" + + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); } - ForesterUtil.programMessage( PRG_NAME, "Minimum duplications : " + ( int ) stats.getMin() ); - ForesterUtil.programMessage( PRG_NAME, "Maximum duplications : " + ( int ) stats.getMax() ); + System.out.println( "Minimum duplications : " + ( int ) stats.getMin() + " (" + + df.format( 100.0 * stats.getMin() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); + System.out.println( "Maximum duplications : " + ( int ) stats.getMax() + " (" + + 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() ); } catch ( final RIOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + ForesterUtil.fatalError( e.getLocalizedMessage() ); } catch ( final SDIException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + ForesterUtil.fatalError( e.getLocalizedMessage() ); } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + catch ( final OutOfMemoryError e ) { + ForesterUtil.outOfMemoryError( e ); } catch ( final Exception e ) { - ForesterUtil.unexpectedFatalError( PRG_NAME, e ); + ForesterUtil.unexpectedFatalError( e ); + } + catch ( final Error e ) { + ForesterUtil.unexpectedFatalError( e ); } time = System.currentTimeMillis() - time; - ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" ); - ForesterUtil.programMessage( PRG_NAME, "OK" ); + System.out.println( "Time: " + time + "ms" ); + System.out.println( "OK" ); System.exit( 0 ); } @@ -342,16 +433,27 @@ public class rio { System.out.println( " or 'outgroup' (default: by minizming duplications)" ); System.out.println( " -" + OUTGROUP + "= : 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" ); + System.out.println( " -" + RETURN_BEST_GENE_TREE + + "= : 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)" ); System.out.println( " -" + USE_SDIR + " : 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 species tree is expected to be in phyloXML format." ); System.out - .println( " The gene trees ideally are in phyloXML as well, but can also be in New Hamphshire (Newick)" ); - System.out.println( " or Nexus format as long as species information can be extracted from the gene names" ); - System.out.println( " (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." ); + .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" ); + System.out + .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" ); System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" ); @@ -361,11 +463,6 @@ public class rio { System.exit( -1 ); } - private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException, RIOException { - final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true ); - writeTable( table_outfile, rio, m ); - } - private static void writeLogFile( final File logfile, final RIO rio, final File species_tree_file, @@ -387,13 +484,15 @@ public class rio { out.flush(); out.println( rio.getLog().toString() ); out.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote log to \"" + logfile + "\"" ); + System.out.println( "Wrote log to \"" + logfile + "\"" ); } - private static void writeTable( final File table_outfile, final RIO rio, final IntMatrix m ) throws IOException { + 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 ) ); @@ -404,18 +503,24 @@ public class rio { for( int y = 0; y < m.size(); ++y ) { w.print( "\t" ); if ( x == y ) { - if ( m.get( x, y ) != rio.getAnalyzedGeneTrees().length ) { - ForesterUtil.unexpectedFatalError( PRG_NAME, "diagonal value is off" ); + if ( m.get( x, y ) != gene_trees_analyzed ) { + ForesterUtil.unexpectedFatalError( "diagonal value is off" ); } w.print( "-" ); } else { - w.print( df.format( ( ( double ) m.get( x, y ) ) / rio.getAnalyzedGeneTrees().length ) ); + w.print( df.format( ( ( double ) m.get( x, y ) ) / gene_trees_analyzed ) ); } } w.println(); } w.close(); - ForesterUtil.programMessage( PRG_NAME, "wrote table to \"" + table_outfile + "\"" ); + System.out.println( "Wrote table to \"" + table_outfile + "\"" ); + } + + private static void writeTree( final Phylogeny p, final File f, final String comment ) throws IOException { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( f, p, 0 ); + System.out.println( comment + " \"" + f + "\"" ); } }