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;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.sdi.GSDIR;
import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
+import org.forester.sdi.SDIutil;
import org.forester.sdi.SDIutil.ALGORITHM;
import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
import org.forester.util.BasicDescriptiveStatistics;
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;
else if ( ( first == DEFAULT_RANGE ) && ( last >= 0 ) ) {
first = 0;
}
- checkPreconditions( gene_trees, rerooting, outgroup, first, last );
+ removeSingleDescendentsNodes( species_tree, verbose );
+ checkPreconditions( gene_trees, species_tree, rerooting, outgroup, first, last );
_produce_log = produce_log;
_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;
}
}
final Phylogeny[] my_gene_trees;
if ( ( first >= 0 ) && ( last >= first ) && ( last < gene_trees.length ) ) {
- my_gene_trees = new Phylogeny[ 1 + last - first ];
+ my_gene_trees = new Phylogeny[ ( 1 + last ) - first ];
int c = 0;
for( int i = first; i <= last; ++i ) {
my_gene_trees[ c++ ] = gene_trees[ i ];
}
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) : "
}
public final static RIO executeAnalysis( final File gene_trees_file,
+ final File species_tree_file,
+ final ALGORITHM algorithm,
+ final REROOTING rerooting,
+ final String outgroup,
+ final int first,
+ final int last,
+ final boolean produce_log,
+ final boolean verbose ) 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 );
+ return new RIO( gene_trees, species_tree, algorithm, rerooting, outgroup, first, last, produce_log, verbose );
+ }
+
+ public final static RIO executeAnalysis( final File gene_trees_file,
final Phylogeny species_tree,
final ALGORITHM algorithm,
final REROOTING rerooting,
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 );
- 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 void checkPreconditions( final Phylogeny[] gene_trees,
+ final Phylogeny species_tree,
final REROOTING rerooting,
final String outgroup,
final int first,
final int last ) throws RIOException {
+ if ( !species_tree.isRooted() ) {
+ throw new RIOException( "species tree is not rooted" );
+ }
if ( !( ( last == DEFAULT_RANGE ) && ( first == DEFAULT_RANGE ) )
&& ( ( last < first ) || ( last >= gene_trees.length ) || ( last < 0 ) || ( first < 0 ) ) ) {
throw new RIOException( "attempt to set range (0-based) of gene to analyze to: from " + first + " to "
}
}
+ 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 ) {
+ if ( verbose ) {
+ System.out.println( "warning: species tree has " + o
+ + " internal nodes with only one descendent which are therefore going to be removed" );
+ }
+ PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree );
+ }
+ }
+
public enum REROOTING {
NONE, BY_ALGORITHM, MIDPOINT, OUTGROUP;
}
git://source.jalview.org / jalview.git / blobdiff