import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDI.ALGORITHM;
+import org.forester.sdi.SDI.TaxonomyComparisonBase;
import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
+import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.ForesterUtil;
public final class RIO {
- private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
- private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
- private Phylogeny[] _analyzed_gene_trees;
- private HashMap<String, HashMap<String, Integer>> _o_maps;
- private HashMap<String, HashMap<String, Integer>> _so_maps;
- private HashMap<String, HashMap<String, Integer>> _up_maps;
- private List<String> _seq_names;
- private List<PhylogenyNode> _removed_gene_tree_nodes;
- private int _samples;
- private int _ext_nodes;
-
- /**
- * Default constructor.
- * @throws SDIException
- * @throws IOException
- * @throws RIOException
- */
- public RIO( final File gene_trees_file, final Phylogeny species_tree, final String query ) throws IOException,
- SDIException, RIOException {
- if ( ForesterUtil.isEmpty( query ) ) {
- throw new IllegalArgumentException( "query is empty" );
- }
- init();
- inferOrthologs( gene_trees_file, species_tree, query );
+ private final static boolean ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
+ private final static boolean ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
+ private Phylogeny[] _analyzed_gene_trees;
+ private List<PhylogenyNode> _removed_gene_tree_nodes;
+ private int _samples;
+ private int _ext_nodes;
+ private TaxonomyComparisonBase _gsdir_tax_comp_base;
+ private StringBuilder _log;
+ private boolean _produce_log;
+
+ public RIO( final File gene_trees_file,
+ final Phylogeny species_tree,
+ final ALGORITHM algorithm,
+ final boolean produce_log ) throws IOException, SDIException, RIOException {
+ init( produce_log );
+ inferOrthologs( gene_trees_file, species_tree, algorithm );
}
- public RIO( final File gene_trees_file, final Phylogeny species_tree ) throws IOException, SDIException,
- RIOException {
- init();
- inferOrthologs( gene_trees_file, species_tree, null );
+ private final void init( final boolean produce_log ) {
+ _produce_log = produce_log;
+ _samples = -1;
+ _ext_nodes = -1;
+ _log = null;
+ _gsdir_tax_comp_base = null;
+ _analyzed_gene_trees = null;
+ _removed_gene_tree_nodes = null;
}
public final Phylogeny[] getAnalyzedGeneTrees() {
return _ext_nodes;
}
- /**
- * Returns a HashMap containing the inferred "ultra paralogs" of the
- * external gene tree node with the sequence name seq_name. Sequence names
- * are the keys (String), numbers of observations are the values (Int).
- * "ultra paralogs" are to be inferred by method "inferOrthologs". Throws an
- * exception if seq_name is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred ultra paralogs
- * (name(String)->value(Int))
- */
- public final HashMap<String, Integer> getInferredUltraParalogs( final String seq_name ) {
- if ( _up_maps == null ) {
- return null;
- }
- return _up_maps.get( seq_name );
- }
-
public final int getNumberOfSamples() {
return _samples;
}
- /**
- * Returns a String containg the names of orthologs of the PhylogenyNode
- * with seq name query_name. The String also contains how many times a
- * particular ortholog has been observed.
- * <p>
- * <ul>
- * The output order is (per line): Name, Ortholog, Subtree neighbor, Super
- * ortholog, Distance
- * </ul>
- * <p>
- * The sort priority of this is determined by sort in the following manner:
- * <ul>
- * <li>0 : Ortholog
- * <li>1 : Ortholog, Super ortholog
- * <li>2 : Super ortholog, Ortholog
- * </ul>
- * <p>
- * Returns "-" if no putative orthologs have been found (given
- * threshold_orthologs).
- * <p>
- * Orthologs are to be inferred by method "inferOrthologs".
- * <p>
- * (Last modified: 05/08/01)
- *
- * @param query_name
- * sequence name of a external node of the gene trees
- * @param sort
- * order and sort priority
- * @param threshold_orthologs
- * the minimal number of observations for a a sequence to be
- * reported as orthologous, in percents (0.0-100.0%)
- * @param threshold_subtreeneighborings
- * the minimal number of observations for a a sequence to be
- * reported as orthologous, in percents (0.0-100.0%)
- * @return String containing the inferred orthologs, String containing "-"
- * if no orthologs have been found null in case of error
- */
- public final StringBuffer inferredOrthologsToString( final String query_name, int sort, double threshold_orthologs ) {
- HashMap<String, Integer> o_hashmap = null;
- HashMap<String, Integer> s_hashmap = null;
- String name = "";
- double o = 0.0; // Orthologs.
- double s = 0.0; // Super orthologs.
- double value1 = 0.0;
- double value2 = 0.0;
- final ArrayList<ResultLine> nv = new ArrayList<ResultLine>();
- if ( ( _o_maps == null ) || ( _so_maps == null ) ) {
- throw new RuntimeException( "orthologs have not been calculated (successfully)" );
- }
- if ( ( sort < 0 ) || ( sort > 2 ) ) {
- sort = 1;
- }
- if ( threshold_orthologs < 0.0 ) {
- threshold_orthologs = 0.0;
- }
- else if ( threshold_orthologs > 100.0 ) {
- threshold_orthologs = 100.0;
- }
- o_hashmap = getInferredOrthologs( query_name );
- s_hashmap = getInferredSuperOrthologs( query_name );
- if ( ( o_hashmap == null ) || ( s_hashmap == null ) ) {
- throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
- }
- final StringBuffer orthologs = new StringBuffer();
- if ( _seq_names.size() > 0 ) {
- I: for( int i = 0; i < _seq_names.size(); ++i ) {
- name = _seq_names.get( i );
- if ( name.equals( query_name ) ) {
- continue I;
- }
- o = getBootstrapValueFromHash( o_hashmap, name );
- if ( o < threshold_orthologs ) {
- continue I;
- }
- s = getBootstrapValueFromHash( s_hashmap, name );
- switch ( sort ) {
- case 0:
- nv.add( new ResultLine( name, o, 5 ) );
- break;
- case 1:
- nv.add( new ResultLine( name, o, s, 5 ) );
- break;
- case 2:
- nv.add( new ResultLine( name, s, o, 5 ) );
- break;
- default:
- nv.add( new ResultLine( name, o, 5 ) );
- }
- } // End of I for loop.
- if ( ( nv != null ) && ( nv.size() > 0 ) ) {
- orthologs.append( "seq name\t\tortho\ts-ortho" + ForesterUtil.LINE_SEPARATOR );
- final ResultLine[] nv_array = new ResultLine[ nv.size() ];
- for( int j = 0; j < nv.size(); ++j ) {
- nv_array[ j ] = nv.get( j );
- }
- Arrays.sort( nv_array );
- for( final ResultLine element : nv_array ) {
- name = element.getKey();
- value1 = element.getValue1();
- value2 = element.getValue2();
- orthologs.append( addNameAndValues( name, value1, value2, sort ) );
- }
- }
- }
- // No orthologs found.
- if ( ( orthologs == null ) || ( orthologs.length() < 1 ) ) {
- orthologs.append( "-" );
- }
- return orthologs;
- }
-
- /**
- * Returns a String containg the names of orthologs of the PhylogenyNode
- * with seq name query_name. The String also contains how many times a
- * particular ortholog has been observed. Returns "-" if no putative
- * orthologs have been found (given threshold_orthologs).
- * <p>
- * Orthologs are to be inferred by method "inferOrthologs".
- *
- * @param query_name
- * sequence name of a external node of the gene trees
- * @param return_dists
- * @param threshold_ultra_paralogs
- * between 1 and 100
- * @return String containing the inferred orthologs, String containing "-"
- * if no orthologs have been found null in case of error
- */
- public final String inferredUltraParalogsToString( final String query_name, double threshold_ultra_paralogs ) {
- HashMap<String, Integer> sp_hashmap = null;
- String name = "", ultra_paralogs = "";
- int sort = 0;
- double sp = 0.0;
- double value1 = 0.0;
- double value2 = 0.0;
- final List<ResultLine> nv = new ArrayList<ResultLine>();
- if ( threshold_ultra_paralogs < 1.0 ) {
- threshold_ultra_paralogs = 1.0;
- }
- else if ( threshold_ultra_paralogs > 100.0 ) {
- threshold_ultra_paralogs = 100.0;
- }
- if ( _up_maps == null ) {
- throw new RuntimeException( "Ultra paralogs have not been calculated (successfully)." );
- }
- sp_hashmap = getInferredUltraParalogs( query_name );
- if ( sp_hashmap == null ) {
- throw new RuntimeException( "Ultra paralogs for " + query_name + " were not established" );
- }
- if ( _seq_names.size() > 0 ) {
- I: for( int i = 0; i < _seq_names.size(); ++i ) {
- name = _seq_names.get( i );
- if ( name.equals( query_name ) ) {
- continue I;
- }
- sp = getBootstrapValueFromHash( sp_hashmap, name );
- if ( sp < threshold_ultra_paralogs ) {
- continue I;
- }
- nv.add( new ResultLine( name, sp, 5 ) );
- } // End of I for loop.
- if ( ( nv != null ) && ( nv.size() > 0 ) ) {
- final ResultLine[] nv_array = new ResultLine[ nv.size() ];
- for( int j = 0; j < nv.size(); ++j ) {
- nv_array[ j ] = nv.get( j );
- }
- Arrays.sort( nv_array );
- sort = 90;
- for( final ResultLine element : nv_array ) {
- name = element.getKey();
- value1 = element.getValue1();
- value2 = element.getValue2();
- ultra_paralogs += addNameAndValues( name, value1, value2, sort );
- }
- }
- }
- // No ultra paralogs found.
- if ( ( ultra_paralogs == null ) || ( ultra_paralogs.length() < 1 ) ) {
- ultra_paralogs = "-";
- }
- return ultra_paralogs;
- }
-
- // Helper method for inferredOrthologsToString.
- // inferredOrthologsToArrayList,
- // and inferredUltraParalogsToString.
- private final double getBootstrapValueFromHash( final HashMap<String, Integer> h, final String name ) {
- if ( !h.containsKey( name ) ) {
- return 0.0;
- }
- final int i = h.get( name );
- return ( ( i * 100.0 ) / getNumberOfSamples() );
- }
-
- /**
- * Returns a HashMap containing the inferred orthologs of the external gene
- * tree node with the sequence name seq_name. Sequence names are the keys
- * (String), numbers of observations are the values (Int). Orthologs are to
- * be inferred by method "inferOrthologs". Throws an exception if seq_name
- * is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred orthologs
- * (name(String)->value(Int))
- */
- private final HashMap<String, Integer> getInferredOrthologs( final String seq_name ) {
- if ( _o_maps == null ) {
- return null;
- }
- return _o_maps.get( seq_name );
- }
-
- /**
- * Returns a HashMap containing the inferred "super orthologs" of the
- * external gene tree node with the sequence name seq_name. Sequence names
- * are the keys (String), numbers of observations are the values (Int).
- * Super orthologs are to be inferred by method "inferOrthologs". Throws an
- * exception if seq_name is not found.
- *
- * @param seq_name
- * sequence name of a external node of the gene trees
- * @return HashMap containing the inferred super orthologs
- * (name(String)->value(Int))
- */
- private final HashMap<String, Integer> getInferredSuperOrthologs( final String seq_name ) {
- if ( _so_maps == null ) {
- return null;
- }
- return _so_maps.get( seq_name );
+ public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
+ return _removed_gene_tree_nodes;
}
- /**
- * Infers the orthologs (as well the "super orthologs", the "subtree
- * neighbors", and the "ultra paralogs") for each external node of the gene
- * Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR,
- * for example). Tallies how many times each sequence is (super-)
- * orthologous towards the query. Tallies how many times each sequence is
- * ultra paralogous towards the query. Tallies how many times each sequence
- * is a subtree neighbor of the query. Gene duplications are inferred using
- * SDI. Modifies its argument species_tree. Is a little faster than
- * "inferOrthologs(File,Phylogeny)" since orthologs are only inferred for
- * query.
- * <p>
- * To obtain the results use the methods listed below.
- *
- * @param gene_trees_file
- * a File containing gene Trees in NH format, which is the result
- * of performing a bootstrap analysis in PHYLIP
- * @param species_tree
- * a species Phylogeny, which has species names in its species
- * fields
- * @param query
- * the sequence name of the squence whose orthologs are to be
- * inferred
- * @throws SDIException
- * @throws RIOException
- * @throws IOException
- * @throws FileNotFoundException
- */
- private final void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
- throws SDIException, RIOException, FileNotFoundException, IOException {
+ private final void inferOrthologs( final File gene_trees_file,
+ final Phylogeny species_tree,
+ final ALGORITHM algorithm ) throws SDIException, RIOException,
+ FileNotFoundException, IOException {
// Read in first tree to get its sequence names
// and strip species_tree.
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
}
final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
- // Removes from species_tree all species not found in gene_tree.
- final List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
- .taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
- if ( species_tree.isEmpty() ) {
- throw new RIOException( "failed to establish species based mapping between gene and species trees" );
- }
- if ( !ForesterUtil.isEmpty( query ) ) {
- PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_trees[ 0 ] );
- if ( gene_trees[ 0 ].isEmpty() ) {
+ if ( algorithm == ALGORITHM.SDIR ) {
+ // Removes from species_tree all species not found in gene_tree.
+ PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
+ if ( species_tree.isEmpty() ) {
throw new RIOException( "failed to establish species based mapping between gene and species trees" );
}
- _seq_names = getAllExternalSequenceNames( gene_trees[ 0 ] );
- if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
- throw new RIOException( "could not get sequence names" );
- }
- _o_maps = new HashMap<String, HashMap<String, Integer>>();
- _so_maps = new HashMap<String, HashMap<String, Integer>>();
- _up_maps = new HashMap<String, HashMap<String, Integer>>();
- _o_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
- _so_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
- _up_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
+ }
+ if ( _produce_log ) {
+ _log = new StringBuilder();
}
_analyzed_gene_trees = new Phylogeny[ gene_trees.length ];
- int c = 0;
+ int i = 0;
int gene_tree_ext_nodes = 0;
+ if ( _produce_log ) {
+ _log.append( "#" );
+ _log.append( "\t" );
+ _log.append( "with minimal number of duplications" );
+ _log.append( "/" );
+ _log.append( "root placements" );
+ _log.append( "\t[" );
+ _log.append( "min" );
+ _log.append( "-" );
+ _log.append( "max" );
+ _log.append( "]" );
+ _log.append( ForesterUtil.LINE_SEPARATOR );
+ }
for( final Phylogeny gt : gene_trees ) {
- // Removes from gene_tree all species not found in species_tree.
- PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
- if ( gt.isEmpty() ) {
- throw new RIOException( "failed to establish species based mapping between gene and species trees" );
- }
- if ( c == 0 ) {
- gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
- }
- else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
- throw new RIOException( "(cleaned up) gene tree #" + ( c + 1 )
- + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
- + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
+ if ( algorithm == ALGORITHM.SDIR ) {
+ // Removes from gene_tree all species not found in species_tree.
+ PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
+ if ( gt.isEmpty() ) {
+ throw new RIOException( "failed to establish species based mapping between gene and species trees" );
+ }
+ if ( i == 0 ) {
+ gene_tree_ext_nodes = gt.getNumberOfExternalNodes();
+ }
+ else if ( gene_tree_ext_nodes != gt.getNumberOfExternalNodes() ) {
+ throw new RIOException( "(cleaned up) gene tree #" + ( i + 1 )
+ + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
+ + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
+ }
}
- _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query );
+ _analyzed_gene_trees[ i ] = performOrthologInference( gt, species_tree, algorithm, i );
+ ++i;
}
setNumberOfSamples( gene_trees.length );
}
private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
final Phylogeny species_tree,
- final String query ) throws SDIException, RIOException {
- final SDIR sdiunrooted = new SDIR();
- final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
- species_tree,
- false,
- RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
- RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
- true,
- 1 )[ 0 ];
- setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
- if ( !ForesterUtil.isEmpty( query ) ) {
- final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );
- if ( nodes.size() > 1 ) {
- throw new RIOException( "node named [" + query + "] not unique" );
+ final ALGORITHM algorithm,
+ final int i ) throws SDIException, RIOException {
+ final Phylogeny assigned_tree;
+ switch ( algorithm ) {
+ case SDIR: {
+ final SDIR sdir = new SDIR();
+ assigned_tree = sdir.infer( gene_tree,
+ species_tree,
+ false,
+ RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
+ RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
+ true,
+ 1 )[ 0 ];
+ break;
}
- else if ( nodes.isEmpty() ) {
- throw new RIOException( "no node containing a sequence named [" + query + "] found" );
+ case GSDIR: {
+ // System.out.println( "gene/species tree size before: " + gene_tree.getNumberOfExternalNodes() + "/"
+ // + species_tree.getNumberOfExternalNodes() );
+ final GSDIR gsdir = new GSDIR( gene_tree, species_tree, true, i == 0 );
+ // System.out.println( "gene/species tree size before: " + gene_tree.getNumberOfExternalNodes() + "/"
+ // + species_tree.getNumberOfExternalNodes() );
+ assigned_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 0 );
+ if ( i == 0 ) {
+ _removed_gene_tree_nodes = gsdir.getStrippedExternalGeneTreeNodes();
+ }
+ if ( _produce_log ) {
+ final BasicDescriptiveStatistics stats = gsdir.getDuplicationsSumStats();
+ _log.append( i );
+ _log.append( "\t" );
+ _log.append( gsdir.getMinDuplicationsSumGeneTrees().size() );
+ _log.append( "/" );
+ _log.append( stats.getN() );
+ _log.append( "\t[" );
+ _log.append( ( int ) stats.getMin() );
+ _log.append( "-" );
+ _log.append( ( int ) stats.getMax() );
+ _log.append( "]" );
+ _log.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ _gsdir_tax_comp_base = gsdir.getTaxCompBase();
+ break;
+ }
+ default: {
+ throw new IllegalArgumentException( "illegal algorithm: " + algorithm );
}
- final PhylogenyNode query_node = nodes.get( 0 );
- updateCounts( _o_maps, query, PhylogenyMethods.getOrthologousNodes( assigned_tree, query_node ) );
- updateCounts( _so_maps, query, PhylogenyMethods.getSuperOrthologousNodes( query_node ) );
- updateCounts( _up_maps, query, PhylogenyMethods.getUltraParalogousNodes( query_node ) );
}
+ setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
return assigned_tree;
}
- private final void init() {
- _o_maps = null;
- _so_maps = null;
- _up_maps = null;
- _seq_names = null;
- _samples = 1;
- _ext_nodes = 0;
- }
-
private final void setExtNodesOfAnalyzedGeneTrees( final int i ) {
_ext_nodes = i;
}
- private final void setNumberOfSamples( int i ) {
- if ( i < 1 ) {
- i = 1;
- }
+ private final void setNumberOfSamples( final int i ) {
_samples = i;
}
- // Helper for doInferOrthologs( Phylogeny, Phylogeny, String )
- // and doInferOrthologs( Phylogeny, Phylogeny ).
- private final void updateCounts( final HashMap<String, HashMap<String, Integer>> counter_map,
- final String query_seq_name,
- final List<PhylogenyNode> nodes ) {
- final HashMap<String, Integer> hash_map = counter_map.get( query_seq_name );
- if ( hash_map == null ) {
- throw new RuntimeException( "unexpected error in updateCounts" );
- }
- for( int j = 0; j < nodes.size(); ++j ) {
- String seq_name;
- if ( ( nodes.get( j ) ).getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( ( nodes.get( j ) ).getNodeData().getSequence().getName() ) ) {
- seq_name = ( nodes.get( j ) ).getNodeData().getSequence().getName();
- }
- else {
- seq_name = ( nodes.get( j ) ).getName();
- }
- if ( hash_map.containsKey( seq_name ) ) {
- hash_map.put( seq_name, hash_map.get( seq_name ) + 1 );
- }
- else {
- hash_map.put( seq_name, 1 );
- }
- }
- }
-
- public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees ) throws RIOException {
+ public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees, final boolean sort )
+ throws RIOException {
final List<String> labels = new ArrayList<String>();
final Set<String> labels_set = new HashSet<String>();
String label;
labels_set.add( label );
labels.add( label );
}
+ if ( sort ) {
+ Collections.sort( labels );
+ }
final IntMatrix m = new IntMatrix( labels );
int counter = 0;
for( final Phylogeny gt : analyzed_gene_trees ) {
return m;
}
- /**
- * Returns the order in which ortholog (o), "super ortholog" (s) and
- * distance (d) are returned and sorted (priority of sort always goes from
- * left to right), given sort. For the meaning of sort
- *
- * @see #inferredOrthologsToString(String,int,double,double)
- *
- * @param sort
- * determines order and sort priority
- * @return String indicating the order
- */
- public final static String getOrder( final int sort ) {
- String order = "";
- switch ( sort ) {
- case 0:
- order = "orthologies";
- break;
- case 1:
- order = "orthologies > super orthologies";
- break;
- case 2:
- order = "super orthologies > orthologies";
- break;
- default:
- order = "orthologies";
- break;
- }
- return order;
- }
-
- public final static StringBuffer getOrderHelp() {
- final StringBuffer sb = new StringBuffer();
- sb.append( " 0: orthologies" + ForesterUtil.LINE_SEPARATOR );
- sb.append( " 1: orthologies > super orthologies" + ForesterUtil.LINE_SEPARATOR );
- sb.append( " 2: super orthologies > orthologies" + ForesterUtil.LINE_SEPARATOR );
- return sb;
- }
-
- // Helper method for inferredOrthologsToString
- // and inferredUltraParalogsToString.
- private final static String addNameAndValues( final String name,
- final double value1,
- final double value2,
- final int sort ) {
- final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#####" );
- df.setDecimalSeparatorAlwaysShown( false );
- String line = "";
- if ( name.length() < 8 ) {
- line += ( name + "\t\t\t" );
- }
- else if ( name.length() < 16 ) {
- line += ( name + "\t\t" );
- }
- else {
- line += ( name + "\t" );
- }
- switch ( sort ) {
- case 0:
- line += addToLine( value1, df );
- line += "-\t";
- break;
- case 1:
- line += addToLine( value1, df );
- line += addToLine( value2, df );
- break;
- case 2:
- line += addToLine( value2, df );
- line += addToLine( value1, df );
- break;
- case 90:
- line += addToLine( value1, df );
- line += "-\t";
- break;
- case 91:
- line += addToLine( value1, df );
- line += addToLine( value2, df );
- break;
- }
- line += ForesterUtil.LINE_SEPARATOR;
- return line;
+ public final TaxonomyComparisonBase getGSDIRtaxCompBase() {
+ return _gsdir_tax_comp_base;
}
- // Helper for addNameAndValues.
- private final static String addToLine( final double value, final java.text.DecimalFormat df ) {
- String s = "";
- if ( value != ResultLine.DEFAULT ) {
- s = df.format( value ) + "\t";
- }
- else {
- s = "-\t";
- }
- return s;
+ public final StringBuilder getLog() {
+ return _log;
}
-
- private final static List<String> getAllExternalSequenceNames( final Phylogeny phy ) throws RIOException {
- final List<String> names = new ArrayList<String>();
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- names.add( n.getNodeData().getSequence().getName() );
- }
- else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- names.add( n.getName() );
- }
- else {
- throw new RIOException( "node has no (sequence) name: " + n );
- }
- }
- return names;
- }
-
- private final static List<PhylogenyNode> getNodesViaSequenceName( final Phylogeny phy, final String seq_name ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
- nodes.add( n );
- }
- if ( !n.getNodeData().isHasSequence() && n.getName().equals( seq_name ) ) {
- nodes.add( n );
- }
- }
- return nodes;
- }
-
- public final List<PhylogenyNode> getRemovedGeneTreeNodes() {
- return _removed_gene_tree_nodes;
- }
-
- private final class ResultLine implements Comparable<ResultLine> {
-
- public static final int DEFAULT = -999;
- private final String _key;
- private final double _value1;
- private final double _value2;
- private int[] _p;
-
- ResultLine( final String name, final double value1, final double value2, final int c ) {
- setSigns();
- _key = name;
- _value1 = value1;
- _value2 = value2;
- if ( ( c >= 0 ) && ( c <= 2 ) ) {
- _p[ c ] = -1;
- }
- }
-
- ResultLine( final String name, final double value1, final int c ) {
- setSigns();
- _key = name;
- _value1 = value1;
- _value2 = ResultLine.DEFAULT;
- if ( c == 0 ) {
- _p[ 0 ] = -1;
- }
- }
-
- @Override
- public int compareTo( final ResultLine n ) {
- if ( ( getValue1() != ResultLine.DEFAULT ) && ( n.getValue1() != ResultLine.DEFAULT ) ) {
- if ( getValue1() < n.getValue1() ) {
- return _p[ 0 ];
- }
- if ( getValue1() > n.getValue1() ) {
- return ( -_p[ 0 ] );
- }
- }
- if ( ( getValue2() != ResultLine.DEFAULT ) && ( n.getValue2() != ResultLine.DEFAULT ) ) {
- if ( getValue2() < n.getValue2() ) {
- return _p[ 1 ];
- }
- if ( getValue2() > n.getValue2() ) {
- return ( -_p[ 1 ] );
- }
- }
- return ( getKey().compareTo( n.getKey() ) );
- }
-
- String getKey() {
- return _key;
- }
-
- double getValue1() {
- return _value1;
- }
-
- double getValue2() {
- return _value2;
- }
-
- private void setSigns() {
- _p = new int[ 2 ];
- _p[ 0 ] = _p[ 1 ] = +1;
- }
- } // ResultLine
}
git://source.jalview.org / jalview.git / blobdiff