import java.util.ArrayList;
import java.util.Date;
import java.util.List;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.sdi.GSDI;
import org.forester.sdi.SDI;
import org.forester.sdi.SDI.TaxonomyComparisonBase;
+import org.forester.sdi.SDIException;
import org.forester.sdi.SDIse;
-import org.forester.sdi.SdiException;
import org.forester.util.CommandLineArguments;
import org.forester.util.EasyWriter;
import org.forester.util.ForesterConstants;
final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
switch ( comp_base ) {
case SCIENTIFIC_NAME:
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1,
- true );
+ try {
+ PhylogenyMethods
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to scientific name, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
case CODE:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
- true );
+ try {
+ PhylogenyMethods
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to taxonomy code, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
case ID:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
- true );
+ try {
+ PhylogenyMethods.transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to taxonomy id, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
default:
ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
}
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: "
+ + e.getMessage() );
}
gene_tree.setRooted( true );
species_tree.setRooted( true );
ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
}
}
- // For timing.
- // gene_tree = Helper.createBalancedTree( 10 );
- // species_tree = Helper.createBalancedTree( 13 );
- // species_tree = Helper.createUnbalancedTree( 1024 );
- // gene_tree = Helper.createUnbalancedTree( 8192 );
- // species_tree = gene_tree.copyTree();
- // gene_tree = species_tree.copyTree();
- // Helper.numberSpeciesInOrder( species_tree );
- // Helper.numberSpeciesInOrder( gene_tree );
- // Helper.randomizeSpecies( 1, 8192, gene_tree );
- // Helper.intervalNumberSpecies( gene_tree, 4096 );
- // Helper.numberSpeciesInDescOrder( gene_tree );
log_writer.println( PRG_NAME + " - " + PRG_DESC );
log_writer.println( " version : " + PRG_VERSION );
log_writer.println( " date : " + PRG_DATE );
log_writer.println( " forester version: " + ForesterConstants.FORESTER_VERSION );
- log_writer.println( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
- log_writer.println( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
- log_writer.println( "Gene tree name: "
+ log_writer.println();
+ log_writer.println( "Start time : "
+ + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ System.out.println( "Start time : "
+ + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ log_writer.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
+ System.out.println( "Gene tree file : " + gene_tree_file.getCanonicalPath() );
+ log_writer.println( "Gene tree name : "
+ + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ System.out.println( "Gene tree name : "
+ ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
- log_writer.println( "Species tree file: " + species_tree_file.getCanonicalPath() );
- log_writer.println( "Species tree name: "
+ log_writer.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
+ System.out.println( "Species tree file : " + species_tree_file.getCanonicalPath() );
+ log_writer.println( "Species tree name : "
+ + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
+ System.out.println( "Species tree name : "
+ ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
- System.out.println();
SDI sdi = null;
final long start_time = new Date().getTime();
try {
if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
- System.out.println();
- System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
- System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
- log_writer.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
- log_writer.write( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
+ System.out.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
+ System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
+ log_writer.println( "Use most parsimonous duplication model : " + most_parsimonous_duplication_model );
+ log_writer.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
log_writer.flush();
sdi = new GSDI( gene_tree,
species_tree,
sdi = new SDIse( gene_tree, species_tree );
}
}
- catch ( final SdiException e ) {
+ catch ( final SDIException e ) {
log_writer.println( "User Error: " + e.getLocalizedMessage() );
log_writer.close();
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
e.printStackTrace();
System.exit( -1 );
}
- System.out.println();
- System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
- log_writer.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
+ System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
+ + "ms" );
+ log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time )
+ + "ms" );
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) sdi;
+ System.out.println( "Mapping based on : " + gsdi.getTaxCompBase() );
+ log_writer.println( "Mapping based on : " + gsdi.getTaxCompBase() );
+ }
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( out_file, gene_tree, 0 );
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
}
- System.out.println();
- System.out.println( "Wrote resulting gene tree to: " + out_file );
- System.out.println();
- log_writer.println( "Wrote resulting gene tree to: " + out_file );
+ System.out.println( "Wrote resulting gene tree to : " + out_file );
+ log_writer.println( "Wrote resulting gene tree to : " + out_file );
if ( base_algorithm == BASE_ALGORITHM.SDI ) {
sdi.computeMappingCostL();
- System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
- log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
+ System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
+ log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
}
- System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
final GSDI gsdi = ( GSDI ) sdi;
final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
try {
ForesterUtil.fatalError( PRG_NAME,
"Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
}
- System.out.println();
- System.out.println( "Wrote used species tree to: " + species_tree_used_file );
- System.out.println();
- log_writer.println( "Wrote used species tree to: " + species_tree_used_file );
+ System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file );
+ log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file );
+ }
+ System.out.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
+ log_writer.println( "Number of external nodes in gene tree : " + gene_tree.getNumberOfExternalNodes() );
+ System.out.println( "Number of external nodes in species tree : "
+ + sdi.getSpeciesTree().getNumberOfExternalNodes() );
+ log_writer.println( "Number of external nodes in species tree : "
+ + sdi.getSpeciesTree().getNumberOfExternalNodes() );
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) sdi;
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
+ System.out.println( "Number of polytomies in species tree : " + poly );
+ log_writer.println( "Number of polytomies in species tree : " + poly );
+ System.out.println( "External nodes stripped from gene tree : "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() );
+ log_writer.println( "External nodes stripped from gene tree : "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() );
+ System.out.println( "External nodes stripped from species tree: "
+ + gsdi.getStrippedSpeciesTreeNodes().size() );
+ log_writer.println( "External nodes stripped from species tree: "
+ + gsdi.getStrippedSpeciesTreeNodes().size() );
+ }
+ System.out.println();
+ System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
+ log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() );
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) sdi;
if ( !most_parsimonous_duplication_model ) {
- final int duplications = gsdi.getSpeciationOrDuplicationEventsSum();
- System.out.println( "Number of potential duplications: " + duplications );
- log_writer.println( "Number of potential duplications: " + duplications );
- }
- final int spec = gsdi.getSpeciationsSum();
- System.out.println( "Number of speciations : " + spec );
- log_writer.println( "Number of speciations : " + spec );
- for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
- System.out.println( n.toString() );
+ final int u = gsdi.getSpeciationOrDuplicationEventsSum();
+ System.out.println( "Number of potential duplications : " + u );
+ log_writer.println( "Number of potential duplications : " + u );
}
+ System.out.println( "Number of speciations : " + gsdi.getSpeciationsSum() );
+ log_writer.println( "Number of speciations : " + gsdi.getSpeciationsSum() );
+ log_writer.println();
+ printMappedNodesToLog( log_writer, gsdi );
+ log_writer.println();
+ printStrippedGeneTreeNodesToLog( log_writer, gsdi );
+ log_writer.println();
+ printStrippedSpeciesTreeNodesToLog( log_writer, gsdi );
}
System.out.println();
+ System.out.println( "Wrote log to : " + log_file );
+ System.out.println();
log_writer.close();
- // some stat on gene tree:
- // filename, name
- // number of external nodes, strppided nodes
- // some stats on sepcies tree, external nodes,
- // filename, name
- // internal nodes
- // how many of which are polytomies
- //wrote log file to
- // if ( allow_stripping_of_gene_tree ) {
- // stripped x nodes, y external nodes remain
- // }
+ }
+
+ private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
+ final SortedSet<String> ss = new TreeSet<String>();
+ for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
+ ss.add( n.toString() );
+ }
+ log_writer.println( "The following " + ss.size() + " species were used: " );
+ for( final String s : ss ) {
+ log_writer.println( " " + s );
+ }
+ }
+
+ private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
+ throws IOException {
+ final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
+ for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
+ final String s = n.toString();
+ if ( sm.containsKey( s ) ) {
+ sm.put( s, sm.get( s ) + 1 );
+ }
+ else {
+ sm.put( s, 1 );
+ }
+ }
+ log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
+ for( final String s : sm.keySet() ) {
+ final int count = sm.get( s );
+ if ( count == 1 ) {
+ log_writer.println( " " + s );
+ }
+ else {
+ log_writer.println( " " + s + " [" + count + "]" );
+ }
+ }
+ }
+
+ private static void printStrippedSpeciesTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
+ throws IOException {
+ final SortedSet<String> ss = new TreeSet<String>();
+ for( final PhylogenyNode n : gsdi.getStrippedSpeciesTreeNodes() ) {
+ ss.add( n.toString() );
+ }
+ log_writer.println( "The following " + ss.size() + " nodes were stripped from the species tree: " );
+ for( final String n : ss ) {
+ log_writer.println( " " + n );
+ }
}
private static void print_help() {
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