X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=4c17f0e0c3ac33ee348108f10782eef9769fb60d;hb=0ee466206ea1e3ac3025df1110538e3815c160b4;hp=4c5d0cd84bdd40d503c3a7b9f5bee9bcab3c577b;hpb=a1faf8469197d44197c70d2eeb529f22e8e396b4;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 4c5d0cd..4c17f0e 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -31,6 +31,10 @@ import java.text.SimpleDateFormat; 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; @@ -46,8 +50,8 @@ import org.forester.phylogeny.factories.PhylogenyFactory; 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; @@ -264,39 +268,35 @@ public final class gsdi { 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() ) ); - log_writer.println( "Species tree file: " + species_tree_file.getCanonicalPath() ); - log_writer.println( "Species tree name: " + System.out.println( "Gene tree name : " + + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) ); + 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, @@ -312,7 +312,7 @@ public final class gsdi { 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() ); @@ -328,9 +328,15 @@ public final class gsdi { 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 ); @@ -338,18 +344,14 @@ public final class gsdi { 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 { @@ -360,35 +362,99 @@ public final class gsdi { 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 ss = new TreeSet(); + 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 sm = new TreeMap(); + 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 ss = new TreeSet(); + 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() {