import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
private HashMap<String, HashMap<String, Integer>> _sn_hash_maps; // HashMap of HashMaps
private DistanceMatrix _m;
private HashMap<String, Double> _l;
- private String[] _seq_names;
+ private List<String> _seq_names;
private int _bootstraps;
private int _ext_nodes_;
private long _time;
if ( RIO.TIME ) {
_time = System.currentTimeMillis();
}
- if ( !gene_trees_file.exists() ) {
- throw new IllegalArgumentException( gene_trees_file.getAbsolutePath() + " does not exist." );
- }
- else if ( !gene_trees_file.isFile() ) {
- throw new IllegalArgumentException( gene_trees_file.getAbsolutePath() + " is not a file." );
- }
// Read in first tree to get its sequence names
// and strip species_tree.
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny gene_tree = factory.create( gene_trees_file, new PhyloXmlParser() )[ 0 ];
+ 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( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+ }
+ final Phylogeny gene_tree = factory.create( gene_trees_file, p )[ 0 ];
+ 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.length < 1 ) ) {
- return;
+ if ( ( _seq_names == null ) || ( _seq_names.size() < 1 ) ) {
+ throw new IOException( "could not get sequence names" );
}
_o_hash_maps = new HashMap<String, HashMap<String, Integer>>();
_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.length ) );
- _so_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.length ) );
- _up_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.length ) );
- _sn_hash_maps.put( query, new HashMap<String, Integer>( _seq_names.length ) );
+ _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, new PhyloXmlParser() );
+ 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.
}
}
+ public 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;
+ }
+
// 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 String query )
true,
1 )[ 0 ];
setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
- nodes = assigned_tree.getNodesViaSequenceName( query );
+ nodes = getNodesViaSequenceName( assigned_tree, query );
if ( nodes.size() > 1 ) {
throw new IllegalArgumentException( "node named [" + query + "] not unique" );
}
if ( o_hashmap == null ) {
throw new RuntimeException( "Orthologs for " + seq_name + " were not established." );
}
- if ( _seq_names.length > 0 ) {
- I: for( int i = 0; i < _seq_names.length; ++i ) {
- name = _seq_names[ i ];
+ if ( _seq_names.size() > 0 ) {
+ I: for( int i = 0; i < _seq_names.size(); ++i ) {
+ name = _seq_names.get( i );
if ( name.equals( seq_name ) ) {
continue I;
}
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 ) ) {
- throw new RuntimeException( "Orthologs have not been calculated (successfully)" );
+ //TODO ~~~ 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 ) ) {
- throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
+ //TODO ~~~ throw new RuntimeException( "Orthologs for " + query_name + " were not established" );
}
final StringBuffer orthologs = new StringBuffer();
- if ( _seq_names.length > 0 ) {
- I: for( int i = 0; i < _seq_names.length; ++i ) {
- name = _seq_names[ i ];
+ 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;
}
// Helper method for inferredOrthologTableToFile.
// Returns individual rows for the table as String.
private String inferredOrthologsToTableHelper( final String name2,
- final String[] names,
+ final List<String> names,
final int j,
final boolean super_orthologs ) {
HashMap<String, Integer> hashmap = null;
if ( hashmap == null ) {
throw new RuntimeException( "Unexpected failure in method inferredOrthologsToTableHelper" );
}
- for( int i = 0; i < names.length; ++i ) {
- name = names[ i ];
+ for( int i = 0; i < names.size(); ++i ) {
+ name = names.get( i );
if ( !hashmap.containsKey( name ) ) {
value = 0;
}
if ( _seq_names == null ) {
throw new RuntimeException( "inferredOrthologTableToFile: seq_names_ is null." );
}
- Arrays.sort( _seq_names );
+ Collections.sort( _seq_names );
out = new PrintWriter( new FileWriter( outfile ), true );
- if ( out == null ) {
- throw new RuntimeException( "inferredOrthologTableToFile: failure to create PrintWriter." );
- }
line = "\t\t\t\t";
- for( int i = 0; i < _seq_names.length; ++i ) {
+ for( int i = 0; i < _seq_names.size(); ++i ) {
line += ( i + ")\t" );
}
line += "\n";
out.println( line );
- for( int i = 0; i < _seq_names.length; ++i ) {
- name = _seq_names[ i ];
+ 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";
}
if ( sp_hashmap == null ) {
throw new RuntimeException( "Ultra paralogs for " + query_name + " were not established" );
}
- if ( _seq_names.length > 0 ) {
- I: for( int i = 0; i < _seq_names.length; ++i ) {
- name = _seq_names[ i ];
+ 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;
}
throw new RuntimeException( "Unexpected failure in method updateHash." );
}
for( int j = 0; j < nodes.size(); ++j ) {
- final String seq_name = ( nodes.get( j ) ).getNodeData().getSequence().getName();
+ 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 );
}
return s;
}
- private static String[] getAllExternalSequenceNames( final Phylogeny phy ) {
- if ( phy.isEmpty() ) {
- return null;
- }
- int i = 0;
- final String[] names = new String[ phy.getNumberOfExternalNodes() ];
+ private static List<String> getAllExternalSequenceNames( final Phylogeny phy ) {
+ final List<String> names = new ArrayList<String>();
for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- names[ i++ ] = iter.next().getNodeData().getSequence().getName();
+ 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 IllegalArgumentException( "node has no (sequence) name: " + n );
+ }
}
return names;
}
git://source.jalview.org / jalview.git / commitdiff