X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FRIO.java;h=f2056408b97c8e983afec2ecd13b6e99437f7b88;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=b19d32703a76c3e89462839daab37a8a11f82c4b;hpb=b819fa043cac2722618af63f0d4752ffa1a40890;p=jalview.git diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java index b19d327..f205640 100644 --- a/forester/java/src/org/forester/rio/RIO.java +++ b/forester/java/src/org/forester/rio/RIO.java @@ -30,12 +30,12 @@ package org.forester.rio; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; -import java.text.DecimalFormat; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.List; +import java.util.Map; import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; @@ -80,6 +80,7 @@ public final class RIO { private final REROOTING _rerooting; private final Phylogeny _species_tree; private Phylogeny _min_dub_gene_tree; + private Map _dup_to_tree_map; private RIO( final IteratingPhylogenyParser p, final Phylogeny species_tree, @@ -90,7 +91,8 @@ public final class RIO { int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { if ( ( last == DEFAULT_RANGE ) && ( first >= 0 ) ) { last = END_OF_GT; } @@ -124,7 +126,8 @@ public final class RIO { int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { if ( ( last == DEFAULT_RANGE ) && ( first >= 0 ) ) { last = gene_trees.length - 1; } @@ -158,7 +161,7 @@ public final class RIO { /** * Returns the numbers of number of ext nodes in gene trees analyzed (after * stripping). - * + * * @return number of ext nodes in gene trees analyzed (after stripping) */ public final int getExtNodesOfAnalyzedGeneTrees() { @@ -172,7 +175,7 @@ public final class RIO { /** * Returns the numbers of number of int nodes in gene trees analyzed (after * stripping). - * + * * @return number of int nodes in gene trees analyzed (after stripping) */ public final int getIntNodesOfAnalyzedGeneTrees() { @@ -205,8 +208,8 @@ public final class RIO { final String outgroup, int first, final int last, - final boolean transfer_taxonomy ) throws SDIException, RIOException, - FileNotFoundException, IOException { + final boolean transfer_taxonomy ) + throws SDIException, RIOException, FileNotFoundException, IOException { if ( !parser.hasNext() ) { throw new RIOException( "no gene trees to analyze" ); } @@ -216,7 +219,6 @@ public final class RIO { if ( _verbose ) { System.out.println(); } - final DecimalFormat pf = new java.text.DecimalFormat( "000" ); int gene_tree_ext_nodes = 0; int i = 0; int counter = 0; @@ -231,7 +233,7 @@ public final class RIO { throw new RIOException( "gene tree #" + i + " has only one external node" ); } if ( _verbose ) { - ForesterUtil.updateProgress( i, pf ); + System.out.print( "\r" + i ); } if ( counter == 0 ) { if ( algorithm == ALGORITHM.SDIR ) { @@ -266,6 +268,9 @@ public final class RIO { } ++i; } + if ( _verbose ) { + System.out.print( "\rGene trees analyzed :\t" + counter ); + } if ( ( first >= 0 ) && ( counter == 0 ) && ( i > 0 ) ) { throw new RIOException( "attempt to analyze first gene tree #" + first + " in a set of " + i ); } @@ -273,7 +278,7 @@ public final class RIO { first = 0; } if ( log() ) { - postLog( species_tree, first, first + counter - 1 ); + postLog( species_tree, first, ( first + counter ) - 1 ); } if ( _verbose ) { System.out.println(); @@ -287,8 +292,8 @@ public final class RIO { final String outgroup, final int first, final int last, - final boolean transfer_taxonomy ) throws SDIException, RIOException, - FileNotFoundException, IOException { + final boolean transfer_taxonomy ) + throws SDIException, RIOException, FileNotFoundException, IOException { if ( algorithm == ALGORITHM.SDIR ) { // Removes from species_tree all species not found in gene_tree. PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree ); @@ -367,7 +372,6 @@ public final class RIO { } private final void logRemovedGeneTreeNodes() { - log( "Species stripped from gene trees:" ); final SortedSet rn = new TreeSet(); for( final PhylogenyNode n : getRemovedGeneTreeNodes() ) { final Taxonomy t = n.getNodeData().getTaxonomy(); @@ -386,10 +390,12 @@ public final class RIO { } } } + final StringBuilder sb = new StringBuilder(); for( final String s : rn ) { - log( s ); + sb.append( '\t' ); + sb.append( s ); } - log( "" ); + log( "Species stripped from gene trees :" + sb ); } private final Phylogeny performOrthologInference( final Phylogeny gene_tree, @@ -397,8 +403,8 @@ public final class RIO { final ALGORITHM algorithm, final String outgroup, final int i, - final boolean transfer_taxonomy ) throws SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws SDIException, RIOException { final Phylogeny assigned_tree; switch ( algorithm ) { case SDIR: { @@ -406,7 +412,11 @@ public final class RIO { break; } case GSDIR: { - assigned_tree = performOrthologInferenceByGSDI( gene_tree, species_tree, outgroup, i, transfer_taxonomy ); + assigned_tree = performOrthologInferenceByGSDI( gene_tree, + species_tree, + outgroup, + i, + transfer_taxonomy ); break; } default: { @@ -429,8 +439,8 @@ public final class RIO { final Phylogeny species_tree, final String outgroup, final int i, - final boolean transfer_taxonomy ) throws SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws SDIException, RIOException { final Phylogeny assigned_tree; final int dups; if ( _rerooting == REROOTING.BY_ALGORITHM ) { @@ -472,48 +482,101 @@ public final class RIO { } dups = gsdi.getDuplicationsSum(); } + assigned_tree.setRerootable( false ); + double new_dist = -1; if ( ( i == 0 ) || ( dups < _duplications_stats.getMin() ) ) { _min_dub_gene_tree = assigned_tree; } + else if ( dups == _duplications_stats.getMin() ) { + new_dist = PhylogenyMethods.calculateMaxDistanceToRoot( assigned_tree ); + if ( new_dist < PhylogenyMethods.calculateMaxDistanceToRoot( _min_dub_gene_tree ) ) { + _min_dub_gene_tree = assigned_tree; + } + } + if ( _dup_to_tree_map == null ) { + _dup_to_tree_map = new HashMap(); + } + if ( !_dup_to_tree_map.containsKey( dups ) ) { + _dup_to_tree_map.put( dups, assigned_tree ); + } + else { + if ( new_dist == -1 ) { + new_dist = PhylogenyMethods.calculateMaxDistanceToRoot( assigned_tree ); + } + if ( new_dist < PhylogenyMethods.calculateMaxDistanceToRoot( _dup_to_tree_map.get( dups ) ) ) { + _dup_to_tree_map.put( dups, assigned_tree ); + } + } _duplications_stats.addValue( dups ); return assigned_tree; } + final public Map getDuplicationsToTreeMap() { + return _dup_to_tree_map; + } + private final Phylogeny performOrthologInferenceBySDI( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException { final SDIR sdir = new SDIR(); - return sdir.infer( gene_tree, species_tree, false, true, true, true, 1 )[ 0 ]; + final Phylogeny r = sdir.infer( gene_tree, species_tree, false, true, true, true, 1 )[ 0 ]; + r.setRerootable( false ); + final int dups = sdir.getMinimalDuplications(); + _duplications_stats.addValue( dups ); + return r; } private final void postLog( final Phylogeny species_tree, final int first, final int last ) { - log( "" ); + final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.##" ); + final int min = ( int ) getDuplicationsStatistics().getMin(); + final int max = ( int ) getDuplicationsStatistics().getMax(); + final int median = ( int ) getDuplicationsStatistics().median(); + int min_count = 0; + int max_count = 0; + int median_count = 0; + for( double d : getDuplicationsStatistics().getData() ) { + if ( ( ( int ) d ) == min ) { + ++min_count; + } + if ( ( ( int ) d ) == max ) { + ++max_count; + } + if ( ( ( int ) d ) == median ) { + ++median_count; + } + } + final double min_count_percentage = ( 100.0 * min_count ) / getDuplicationsStatistics().getN(); + final double max_count_percentage = ( 100.0 * max_count ) / getDuplicationsStatistics().getN(); + final double median_count_percentage = ( 100.0 * median_count ) / getDuplicationsStatistics().getN(); if ( ( getRemovedGeneTreeNodes() != null ) && ( getRemovedGeneTreeNodes().size() > 0 ) ) { logRemovedGeneTreeNodes(); } - log( "Species tree external nodes (after stripping) : " + species_tree.getNumberOfExternalNodes() ); - log( "Species tree polytomies (after stripping) : " - + PhylogenyMethods.countNumberOfPolytomies( species_tree ) ); - log( "Taxonomy linking based on : " + getGSDIRtaxCompBase() ); - final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" ); + log( "Gene trees analyzed :\t" + getDuplicationsStatistics().getN() ); if ( ( first >= 0 ) && ( last >= 0 ) ) { - log( "Gene trees analyzed range : " + first + "-" + last ); - } - log( "Gene trees analyzed : " + _duplications_stats.getN() ); - log( "Mean number of duplications : " + df.format( _duplications_stats.arithmeticMean() ) - + " (sd: " + df.format( _duplications_stats.sampleStandardDeviation() ) + ")" + " (" - + df.format( ( 100.0 * _duplications_stats.arithmeticMean() ) / getIntNodesOfAnalyzedGeneTrees() ) - + "%)" ); - if ( _duplications_stats.getN() > 3 ) { - log( "Median number of duplications : " + df.format( _duplications_stats.median() ) - + " (" + df.format( ( 100.0 * _duplications_stats.median() ) / getIntNodesOfAnalyzedGeneTrees() ) - + "%)" ); - } - log( "Minimum duplications : " + ( int ) _duplications_stats.getMin() + " (" - + df.format( ( 100.0 * _duplications_stats.getMin() ) / getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); - log( "Maximum duplications : " + ( int ) _duplications_stats.getMax() + " (" - + df.format( ( 100.0 * _duplications_stats.getMax() ) / getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); - log( "Gene tree internal nodes : " + getIntNodesOfAnalyzedGeneTrees() ); - log( "Gene tree external nodes : " + getExtNodesOfAnalyzedGeneTrees() ); + log( "Gene trees analyzed range :\t" + first + "-" + last ); + } + log( "Gene tree internal nodes :\t" + getIntNodesOfAnalyzedGeneTrees() ); + log( "Gene tree external nodes :\t" + getExtNodesOfAnalyzedGeneTrees() ); + log( "Removed ext gene tree nodes :\t" + getRemovedGeneTreeNodes().size() ); + log( "Spec tree ext nodes (after strip) :\t" + species_tree.getNumberOfExternalNodes() ); + log( "Spec tree polytomies (after strip) :\t" + PhylogenyMethods.countNumberOfPolytomies( species_tree ) ); + log( "Taxonomy linking based on :\t" + getGSDIRtaxCompBase() ); + log( "Mean number of duplications :\t" + df.format( getDuplicationsStatistics().arithmeticMean() ) + + "\t" + + df.format( ( 100.0 * getDuplicationsStatistics().arithmeticMean() ) + / getIntNodesOfAnalyzedGeneTrees() ) + + "%\t(sd: " + df.format( getDuplicationsStatistics().sampleStandardDeviation() ) + ")" ); + if ( getDuplicationsStatistics().getN() > 3 ) { + log( "Median number of duplications :\t" + df.format( median ) + "\t" + + df.format( ( 100.0 * median ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" ); + } + log( "Minimum duplications :\t" + min + "\t" + + df.format( ( 100.0 * min ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" ); + log( "Maximum duplications :\t" + ( int ) max + "\t" + + df.format( ( 100.0 * max ) / getIntNodesOfAnalyzedGeneTrees() ) + "%" ); + log( "Gene trees with median duplications :\t" + median_count + "\t" + df.format( median_count_percentage ) + + "%" ); + log( "Gene trees with minimum duplications:\t" + min_count + "\t" + df.format( min_count_percentage ) + "%" ); + log( "Gene trees with maximum duplications:\t" + max_count + "\t" + df.format( max_count_percentage ) + "%" ); } private final void preLog( final int gene_trees, @@ -521,12 +584,11 @@ public final class RIO { final ALGORITHM algorithm, final String outgroup ) { if ( gene_trees > 0 ) { - log( "Number of gene trees (total) : " + gene_trees ); + log( "Number of gene trees (total) :\t" + gene_trees ); } - log( "Algorithm : " + algorithm ); - log( "Species tree external nodes (prior to stripping): " + species_tree.getNumberOfExternalNodes() ); - log( "Species tree polytomies (prior to stripping) : " - + PhylogenyMethods.countNumberOfPolytomies( species_tree ) ); + log( "Algorithm :\t" + algorithm ); + log( "Spec tree ext nodes (prior strip) :\t" + species_tree.getNumberOfExternalNodes() ); + log( "Spec tree polytomies (prior strip) :\t" + PhylogenyMethods.countNumberOfPolytomies( species_tree ) ); String rs = ""; switch ( _rerooting ) { case BY_ALGORITHM: { @@ -546,7 +608,7 @@ public final class RIO { break; } } - log( "Re-rooting : " + rs ); + log( "Re-rooting :\t" + rs ); } public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees, final boolean sort ) @@ -579,17 +641,14 @@ public final class RIO { final int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { final Phylogeny[] gene_trees = parseGeneTrees( gene_trees_file ); if ( gene_trees.length < 1 ) { throw new RIOException( "\"" + gene_trees_file + "\" is devoid of appropriate gene trees" ); } - final Phylogeny species_tree = SDIutil.parseSpeciesTree( gene_trees[ 0 ], - species_tree_file, - false, - true, - TAXONOMY_EXTRACTION.NO ); + final Phylogeny species_tree = SDIutil + .parseSpeciesTree( gene_trees[ 0 ], species_tree_file, false, true, TAXONOMY_EXTRACTION.NO ); return new RIO( gene_trees, species_tree, algorithm, @@ -609,8 +668,8 @@ public final class RIO { final String outgroup, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( parseGeneTrees( gene_trees_file ), species_tree, algorithm, @@ -632,8 +691,8 @@ public final class RIO { final int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( parseGeneTrees( gene_trees_file ), species_tree, algorithm, @@ -655,17 +714,14 @@ public final class RIO { final int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { final Phylogeny g0 = p.next(); if ( ( g0 == null ) || g0.isEmpty() || ( g0.getNumberOfExternalNodes() < 2 ) ) { throw new RIOException( "input file does not seem to contain any gene trees" ); } - final Phylogeny species_tree = SDIutil.parseSpeciesTree( g0, - species_tree_file, - false, - true, - TAXONOMY_EXTRACTION.NO ); + final Phylogeny species_tree = SDIutil + .parseSpeciesTree( g0, species_tree_file, false, true, TAXONOMY_EXTRACTION.NO ); p.reset(); return new RIO( p, species_tree, @@ -686,8 +742,8 @@ public final class RIO { final String outgroup, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( p, species_tree, algorithm, @@ -709,8 +765,8 @@ public final class RIO { final int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( p, species_tree, algorithm, @@ -744,8 +800,8 @@ public final class RIO { final String outgroup, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( gene_trees, species_tree, algorithm, @@ -767,8 +823,8 @@ public final class RIO { final int last, final boolean produce_log, final boolean verbose, - final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + final boolean transfer_taxonomy ) + throws IOException, SDIException, RIOException { return new RIO( gene_trees, species_tree, algorithm, @@ -804,7 +860,8 @@ public final class RIO { final REROOTING rerooting, final String outgroup, final int first, - final int last ) throws RIOException, IOException { + final int last ) + throws RIOException, IOException { final Phylogeny g0 = p.next(); if ( ( g0 == null ) || g0.isEmpty() ) { throw new RIOException( "input file does not seem to contain any gene trees" ); @@ -844,7 +901,8 @@ public final class RIO { final REROOTING rerooting, final String outgroup, final int first, - final int last ) throws RIOException { + final int last ) + throws RIOException { if ( !species_tree.isRooted() ) { throw new RIOException( "species tree is not rooted" ); } @@ -878,9 +936,14 @@ public final class RIO { if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { label = n.getNodeData().getSequence().getName(); } - else if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { + else if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { label = n.getNodeData().getSequence().getSymbol(); } + else if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { + label = n.getNodeData().getSequence().getGeneName(); + } else if ( !ForesterUtil.isEmpty( n.getName() ) ) { label = n.getName(); } @@ -893,21 +956,21 @@ public final class RIO { return label; } - private final static Phylogeny[] parseGeneTrees( final File gene_trees_file ) throws FileNotFoundException, - IOException { + private final static Phylogeny[] parseGeneTrees( final File gene_trees_file ) + throws FileNotFoundException, IOException { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true ); if ( p instanceof NHXParser ) { 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 ); } return factory.create( gene_trees_file, p ); } @@ -949,6 +1012,9 @@ public final class RIO { } public enum REROOTING { - NONE, BY_ALGORITHM, MIDPOINT, OUTGROUP; + NONE, + BY_ALGORITHM, + MIDPOINT, + OUTGROUP; } }