package org.forester.sdi;
import java.io.File;
-import java.io.FileWriter;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
import java.util.HashMap;
import java.util.List;
if ( _o_hash_maps == null ) {
return null;
}
- for( String key : _o_hash_maps.keySet() ) {
- System.out.println( key + " -> " + _o_hash_maps.get( key ) );
- }
- System.out.println( "seq_name: " + seq_name );
return _o_hash_maps.get( seq_name );
}
System.out.println( "species " + species_tree.toString() );
// Removes from species_tree all species not found in gene_tree.
PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( gene_tree, species_tree );
- // System.out.println( "gene " + gene_tree.toString() );
- // System.out.println( "species " + species_tree.toString() );
- // Removes from gene_tree all species not found in species_tree.
- // Archaeopteryx.createApplication( gene_tree );
- // Archaeopteryx.createApplication( species_tree );
- // try {
- // Thread.sleep( 40000 );
- // }
- // catch ( InterruptedException e ) {
- // // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
_seq_names = getAllExternalSequenceNames( gene_tree );
if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
_so_hash_maps = new HashMap<String, HashMap<String, Integer>>();
_up_hash_maps = new HashMap<String, HashMap<String, Integer>>();
_sn_hash_maps = new HashMap<String, HashMap<String, Integer>>();
+ _o_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
+ _so_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
+ _up_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
+ _sn_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.size() ) );
// Go through all gene trees in the file.
final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
for( final Phylogeny gt : gene_trees ) {
bs++;
// Removes from gene_tree all species not found in species_tree.
PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gt );
- inferOrthologsHelper( gt, species_tree, _seq_names );
+ inferOrthologsHelper( gt, species_tree, query );
// System.out.println( bs );
}
setBootstraps( bs );
// Helper method which performs the actual ortholog inference for
// the external node with seqname query.
- private void inferOrthologsHelper( final Phylogeny gene_tree,
- final Phylogeny species_tree,
- final List<String> seq_names ) throws SDIException {
+ private void inferOrthologsHelper( final Phylogeny gene_tree, final Phylogeny species_tree, final String query )
+ throws SDIException {
Phylogeny assigned_tree = null;
List<PhylogenyNode> nodes = null;
final SDIR sdiunrooted = new SDIR();
true,
1 )[ 0 ];
setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
- for( String seq_name : seq_names ) {
- _o_hash_maps.put( seq_name, new HashMap<String, Integer>() );
- _so_hash_maps.put( seq_name, new HashMap<String, Integer>() );
- _up_hash_maps.put( seq_name, new HashMap<String, Integer>() );
- _sn_hash_maps.put( seq_name, new HashMap<String, Integer>() );
- nodes = getNodesViaSequenceName( assigned_tree, seq_name );
- if ( nodes.size() > 1 ) {
- throw new IllegalArgumentException( "node named [" + seq_name + "] not unique" );
- }
- else if ( nodes.isEmpty() ) {
- throw new IllegalArgumentException( "no node containing a sequence named [" + seq_name + "] found" );
- }
- final PhylogenyNode query_node = nodes.get( 0 );
- final PhylogenyMethods methods = PhylogenyMethods.getInstance();
- orthologs = methods.getOrthologousNodes( assigned_tree, query_node );
- updateHash( _o_hash_maps, seq_name, orthologs );
- super_orthologs = PhylogenyMethods.getSuperOrthologousNodes( query_node );
- updateHash( _so_hash_maps, seq_name, super_orthologs );
- subtree_neighbors = getSubtreeNeighbors( query_node, 2 );
- updateHash( _sn_hash_maps, seq_name, subtree_neighbors );
- ultra_paralogs = PhylogenyMethods.getUltraParalogousNodes( query_node );
- updateHash( _up_hash_maps, seq_name, ultra_paralogs );
- }
+ nodes = getNodesViaSequenceName( assigned_tree, query );
+ if ( nodes.size() > 1 ) {
+ throw new IllegalArgumentException( "node named [" + query + "] not unique" );
+ }
+ else if ( nodes.isEmpty() ) {
+ throw new IllegalArgumentException( "no node containing a sequence named [" + query + "] found" );
+ }
+ final PhylogenyNode query_node = nodes.get( 0 );
+ final PhylogenyMethods methods = PhylogenyMethods.getInstance();
+ orthologs = methods.getOrthologousNodes( assigned_tree, query_node );
+ updateHash( _o_hash_maps, query, orthologs );
+ super_orthologs = PhylogenyMethods.getSuperOrthologousNodes( query_node );
+ updateHash( _so_hash_maps, query, super_orthologs );
+ subtree_neighbors = getSubtreeNeighbors( query_node, 2 );
+ updateHash( _sn_hash_maps, query, subtree_neighbors );
+ ultra_paralogs = PhylogenyMethods.getUltraParalogousNodes( query_node );
+ updateHash( _up_hash_maps, query, ultra_paralogs );
}
/**
value1 = 0.0, value2 = 0.0, value3 = 0.0, value4 = 0.0, d = 0.0;
final ArrayList<Tuplet> nv = new ArrayList<Tuplet>();
if ( ( _o_hash_maps == null ) || ( _so_hash_maps == null ) || ( _sn_hash_maps == null ) ) {
- //TODO ~~~ throw new RuntimeException( "Orthologs have not been calculated (successfully)" );
+ throw new RuntimeException( "Orthologs have not been calculated (successfully)" );
}
if ( ( sort < 0 ) || ( sort > 17 ) ) {
sort = 12;
s_hashmap = getInferredSuperOrthologs( query_name );
n_hashmap = getInferredSubtreeNeighbors( query_name );
if ( ( o_hashmap == null ) || ( s_hashmap == null ) || ( n_hashmap == null ) ) {
- //TODO ~~~ throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
+ throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
}
final StringBuffer orthologs = new StringBuffer();
if ( _seq_names.size() > 0 ) {
return orthologs;
} // inferredOrthologsToString( String, int, double )
- // Helper method for inferredOrthologTableToFile.
- // Returns individual rows for the table as String.
- private String inferredOrthologsToTableHelper( final String name2,
- final List<String> names,
- final int j,
- final boolean super_orthologs ) {
- HashMap<String, Integer> hashmap = null;
- String name = null, orthologs = new String( "" );
- int value = 0;
- if ( super_orthologs ) {
- hashmap = getInferredSuperOrthologs( name2 );
- }
- else {
- hashmap = getInferredOrthologs( name2 );
- }
- if ( hashmap == null ) {
- throw new RuntimeException( "Unexpected failure in method inferredOrthologsToTableHelper" );
- }
- for( int i = 0; i < names.size(); ++i ) {
- name = names.get( i );
- if ( !hashmap.containsKey( name ) ) {
- value = 0;
- }
- else {
- value = hashmap.get( name );
- }
- if ( i == j ) {
- // Sanity check.
- if ( value != 0 ) {
- throw new RuntimeException( "Failed sanity check in method inferredOrthologsToTableHelper: value not 0." );
- }
- orthologs += ( " " + "\t" );
- }
- else {
- orthologs += ( value + "\t" );
- }
- }
- return orthologs;
- }
-
- /**
- * Writes the orthologs for each external node of the gene trees to outfile
- * in the form of a table. Orthologs are to be inferred by method
- * "inferOrthologs". Overwrites without asking! (Last modified: 12/07/00)
- *
- * @param outfile
- * the File to write to
- */
- public void inferredOrthologTableToFile( final File outfile ) throws IOException {
- if ( _o_hash_maps == null ) {
- return;
- }
- inferredOrthologTableToFile( outfile, false );
- }
-
- private void inferredOrthologTableToFile( final File outfile, final boolean super_orthologs ) throws IOException {
- String name = "", line = "";
- PrintWriter out = null;
- if ( _seq_names == null ) {
- throw new RuntimeException( "inferredOrthologTableToFile: _seq_names is null" );
- }
- Collections.sort( _seq_names );
- out = new PrintWriter( new FileWriter( outfile ), true );
- line = "\t\t\t\t";
- for( int i = 0; i < _seq_names.size(); ++i ) {
- line += ( i + ")\t" );
- }
- line += "\n";
- out.println( line );
- for( int i = 0; i < _seq_names.size(); ++i ) {
- name = _seq_names.get( i );
- if ( name.length() < 8 ) {
- line = i + ")\t" + name + "\t\t\t";
- }
- else if ( name.length() < 16 ) {
- line = i + ")\t" + name + "\t\t";
- }
- else {
- line = i + ")\t" + name + "\t";
- }
- line += inferredOrthologsToTableHelper( name, _seq_names, i, super_orthologs );
- out.println( line );
- }
- out.close();
- }
-
- /**
- * Writes the "super orthologs" for each external nodes of the gene trees to
- * outfile in the form of a table. Super orthologs are to be inferred by
- * method "inferOrthologs". Overwrites without asking!
- *
- * @param outfile
- * the File to write to
- */
- public void inferredSuperOrthologTableToFile( final File outfile ) throws IOException {
- if ( _so_hash_maps == null ) {
- return;
- }
- inferredOrthologTableToFile( outfile, true );
- }
-
/**
* Returns a String containg the names of orthologs of the PhylogenyNode
* with seq name query_name. The String also contains how many times a
git://source.jalview.org / jalview.git / commitdiff