From: cmzmasek@gmail.com Date: Thu, 15 Nov 2012 07:29:02 +0000 (+0000) Subject: "rio" work X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=602ada25840da8498d57d160ade3fc12483cc43e;p=jalview.git "rio" work --- diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java index 58a48ff..219f859 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -238,7 +238,8 @@ public final class ParserUtils { if ( s.length > 1 ) { final String str = s[ 1 ]; // if ( str.length() < 6 ) { - if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) { + if ( ( str.length() < 5 ) + && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) || str.startsWith( "CAP" ) ) ) { return str.substring( 0, 3 ); } final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( str ); diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index 6678e70..5f0dd30 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -1612,15 +1612,37 @@ public class PhylogenyMethods { */ public static int taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference, final Phylogeny to_be_stripped ) { final Set ref_ext_taxo = new HashSet(); - final ArrayList nodes_to_delete = new ArrayList(); for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) { - ref_ext_taxo.add( getSpecies( it.next() ) ); + final PhylogenyNode n = it.next(); + if ( !n.getNodeData().isHasTaxonomy() ) { + throw new IllegalArgumentException( "no taxonomic data in node: " + n ); + } + // ref_ext_taxo.add( getSpecies( n ) ); + if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() ); + } + if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + } } + System.out.println( " ref_ext_tax:" ); + for( final String string : ref_ext_taxo ) { + System.out.println( string ); + } + final ArrayList nodes_to_delete = new ArrayList(); for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) { final PhylogenyNode n = it.next(); - if ( !ref_ext_taxo.contains( getSpecies( n ) ) ) { + if ( !n.getNodeData().isHasTaxonomy() ) { nodes_to_delete.add( n ); } + else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) ) + && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + nodes_to_delete.add( n ); + } + } + System.out.println( " to delete:" ); + for( final PhylogenyNode string : nodes_to_delete ) { + System.out.println( string.getNodeData().getTaxonomy().getTaxonomyCode() ); } for( final PhylogenyNode phylogenyNode : nodes_to_delete ) { to_be_stripped.deleteSubtree( phylogenyNode, true ); diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java index 028881c..4388808 100644 --- a/forester/java/src/org/forester/sdi/RIO.java +++ b/forester/java/src/org/forester/sdi/RIO.java @@ -33,12 +33,15 @@ 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; 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; @@ -62,7 +65,7 @@ public final class RIO { private HashMap> _sn_hash_maps; // HashMap of HashMaps private DistanceMatrix _m; private HashMap _l; - private String[] _seq_names; + private List _seq_names; private int _bootstraps; private int _ext_nodes_; private long _time; @@ -239,34 +242,47 @@ public final class RIO { 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>(); _so_hash_maps = new HashMap>(); _up_hash_maps = new HashMap>(); _sn_hash_maps = new HashMap>(); - _o_hash_maps.put( query, new HashMap( _seq_names.length ) ); - _so_hash_maps.put( query, new HashMap( _seq_names.length ) ); - _up_hash_maps.put( query, new HashMap( _seq_names.length ) ); - _sn_hash_maps.put( query, new HashMap( _seq_names.length ) ); + _o_hash_maps.put( query, new HashMap( _seq_names.size() ) ); + _so_hash_maps.put( query, new HashMap( _seq_names.size() ) ); + _up_hash_maps.put( query, new HashMap( _seq_names.size() ) ); + _sn_hash_maps.put( query, new HashMap( _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. @@ -280,6 +296,20 @@ public final class RIO { } } + public List getNodesViaSequenceName( final Phylogeny phy, final String seq_name ) { + final List nodes = new ArrayList(); + 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 ) @@ -299,7 +329,7 @@ public final class RIO { 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" ); } @@ -348,9 +378,9 @@ public final class RIO { 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; } @@ -434,7 +464,7 @@ public final class RIO { value1 = 0.0, value2 = 0.0, value3 = 0.0, value4 = 0.0, d = 0.0; final ArrayList nv = new ArrayList(); 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; @@ -458,12 +488,12 @@ public final class RIO { 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; } @@ -570,7 +600,7 @@ public final class RIO { // Helper method for inferredOrthologTableToFile. // Returns individual rows for the table as String. private String inferredOrthologsToTableHelper( final String name2, - final String[] names, + final List names, final int j, final boolean super_orthologs ) { HashMap hashmap = null; @@ -585,8 +615,8 @@ public final class RIO { 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; } @@ -630,19 +660,16 @@ public final class RIO { 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"; } @@ -713,9 +740,9 @@ public final class RIO { 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; } @@ -825,7 +852,14 @@ public final class RIO { 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 ); } @@ -989,14 +1023,19 @@ public final class RIO { 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 getAllExternalSequenceNames( final Phylogeny phy ) { + final List names = new ArrayList(); 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; }