import org.forester.datastructures.IntMatrix;
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.util.ParserUtils;
private Phylogeny[] _analyzed_gene_trees;
private List<PhylogenyNode> _removed_gene_tree_nodes;
private int _ext_nodes;
+ private int _int_nodes;
private TaxonomyComparisonBase _gsdir_tax_comp_base;
private final StringBuilder _log;
private final BasicDescriptiveStatistics _duplications_stats;
_verbose = verbose;
_rerooting = rerooting;
_ext_nodes = -1;
+ _int_nodes = -1;
_log = new StringBuilder();
_gsdir_tax_comp_base = null;
_analyzed_gene_trees = null;
return _ext_nodes;
}
+ /**
+ * 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() {
+ return _int_nodes;
+ }
+
public final TaxonomyComparisonBase getGSDIRtaxCompBase() {
return _gsdir_tax_comp_base;
}
}
if ( i == 0 ) {
_ext_nodes = assigned_tree.getNumberOfExternalNodes();
+ _int_nodes = assigned_tree.getNumberOfInternalNodes();
}
else if ( _ext_nodes != assigned_tree.getNumberOfExternalNodes() ) {
throw new RIOException( "after stripping gene tree #" + ( i + 1 )
final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
log( "Gene trees analyzed : " + _duplications_stats.getN() );
log( "Mean number of duplications : " + df.format( _duplications_stats.arithmeticMean() )
- + " (sd: " + df.format( _duplications_stats.sampleStandardDeviation() ) + ")" );
+ + " (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() ) );
- }
- log( "Minimum duplications : " + ( int ) _duplications_stats.getMin() );
- log( "Maximum duplications : " + ( int ) _duplications_stats.getMax() );
+ 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() );
}
private final void preLog( final Phylogeny[] gene_trees,
final String outgroup,
final int first,
final int last ) {
- log( "Number of gene tree (total) : " + gene_trees.length );
+ log( "Number of gene trees (total) : " + gene_trees.length );
log( "Algorithm : " + algorithm );
log( "Species tree external nodes (prior to stripping): " + species_tree.getNumberOfExternalNodes() );
log( "Species tree polytomies (prior to stripping) : "
final int last,
final boolean produce_log,
final boolean verbose ) throws IOException, SDIException, RIOException {
- 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( NHXParser.TAXONOMY_EXTRACTION.YES );
- }
- final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
+ 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 String outgroup,
final boolean produce_log,
final boolean verbose ) throws IOException, SDIException, RIOException {
- 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( NHXParser.TAXONOMY_EXTRACTION.YES );
- }
- final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
- return new RIO( gene_trees,
+ return new RIO( parseGeneTrees( gene_trees_file ),
species_tree,
algorithm,
rerooting,
final int last,
final boolean produce_log,
final boolean verbose ) throws IOException, SDIException, RIOException {
- 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( NHXParser.TAXONOMY_EXTRACTION.YES );
- }
- final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
- if ( gene_trees.length < 1 ) {
- throw new RIOException( "\"" + gene_trees_file + "\" is devoid of appropriate gene trees" );
- }
- return new RIO( gene_trees, species_tree, algorithm, rerooting, outgroup, first, last, produce_log, verbose );
+ return new RIO( parseGeneTrees( gene_trees_file ),
+ species_tree,
+ algorithm,
+ rerooting,
+ outgroup,
+ first,
+ last,
+ produce_log,
+ verbose );
}
public final static RIO executeAnalysis( final Phylogeny[] gene_trees, final Phylogeny species_tree )
}
}
+ 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( NHXParser.TAXONOMY_EXTRACTION.YES );
+ }
+ else if ( p instanceof NexusPhylogeniesParser ) {
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
+ nex.setReplaceUnderscores( false );
+ nex.setIgnoreQuotes( true );
+ nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+ }
+ return factory.create( gene_trees_file, p );
+ }
+
private final static void removeSingleDescendentsNodes( final Phylogeny species_tree, final boolean verbose ) {
final int o = PhylogenyMethods.countNumberOfOneDescendantNodes( species_tree );
if ( o > 0 ) {