X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgsdi.java;h=eab52df09d22bdf1d1ea05a4ec5df41ee039438a;hb=6005bacbd8aecc0d320b70568a24d321a30bc85c;hp=0395e649c540f212573f946f3c08a9d9c3971e7c;hpb=01e346a4821c5e59d76db8e3a07a6ac95f4fe726;p=jalview.git diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 0395e64..eab52df 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -48,6 +48,7 @@ import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.sdi.GSDI; +import org.forester.sdi.GSDIR; import org.forester.sdi.SDI; import org.forester.sdi.SDI.TaxonomyComparisonBase; import org.forester.sdi.SDIException; @@ -60,11 +61,12 @@ import org.forester.util.ForesterUtil; public final class gsdi { private enum BASE_ALGORITHM { - GSDI, SDI + GSDIR, GSDI, SDI } final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true; final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; final static private String SDISE_OPTION = "b"; + final static private String GSDIR_OPTION = "r"; final static private String MOST_PARSIMONIOUS_OPTION = "m"; final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; final static private String HELP_OPTION_1 = "help"; @@ -109,6 +111,7 @@ public final class gsdi { } final List allowed_options = new ArrayList(); allowed_options.add( gsdi.SDISE_OPTION ); + allowed_options.add( gsdi.GSDIR_OPTION ); allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ); allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION ); allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); @@ -127,18 +130,21 @@ public final class gsdi { BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI; boolean most_parsimonous_duplication_model = false; boolean allow_stripping_of_gene_tree = false; - if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) { + if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) { + base_algorithm = BASE_ALGORITHM.GSDIR; + } + else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) { base_algorithm = BASE_ALGORITHM.SDI; } if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { - if ( base_algorithm != BASE_ALGORITHM.GSDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" ); + if ( base_algorithm == BASE_ALGORITHM.SDI ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); } most_parsimonous_duplication_model = true; } if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { - if ( base_algorithm != BASE_ALGORITHM.GSDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" ); + if ( base_algorithm == BASE_ALGORITHM.SDI ) { + ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); } allow_stripping_of_gene_tree = true; } @@ -248,9 +254,11 @@ public final class gsdi { if ( !gene_tree.isCompletelyBinary() ) { fatalError( "user error", "gene tree is not completely binary", log_writer ); } - if ( base_algorithm != BASE_ALGORITHM.GSDI ) { + if ( base_algorithm == BASE_ALGORITHM.SDI ) { if ( !species_tree.isCompletelyBinary() ) { - fatalError( "user error", "species tree is not completely binary, use GSDI instead", log_writer ); + fatalError( "user error", + "species tree is not completely binary, use GSDI or GSDIR instead", + log_writer ); } } log_writer.println( PRG_NAME + " - " + PRG_DESC ); @@ -277,22 +285,35 @@ public final class gsdi { SDI sdi = null; final long start_time = new Date().getTime(); try { - if ( base_algorithm == BASE_ALGORITHM.GSDI ) { + if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { + if ( base_algorithm == BASE_ALGORITHM.GSDI ) { + System.out.println( "Algorithm : GSDI" ); + log_writer.println( "Algorithm : GSDI" ); + } + else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + System.out.println( "Algorithm : GSDIR" ); + log_writer.println( "Algorithm : GSDIR" ); + } 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, - most_parsimonous_duplication_model, - allow_stripping_of_gene_tree, - true ); + if ( base_algorithm == BASE_ALGORITHM.GSDI ) { + sdi = new GSDI( gene_tree, + species_tree, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + true ); + } + else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 ); + } } else { System.out.println(); - System.out.println( "Using SDIse algorithm" ); - log_writer.println( "Using SDIse algorithm" ); + System.out.println( "Algorithm : SDI" ); + log_writer.println( "Algorithm : SDI" ); log_writer.flush(); sdi = new SDIse( gene_tree, species_tree ); } @@ -316,9 +337,26 @@ public final class gsdi { System.out.println( "Mapping based on : " + gsdi.getTaxCompBase() ); log_writer.println( "Mapping based on : " + gsdi.getTaxCompBase() ); } + if ( ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { + final GSDIR gsdir = ( GSDIR ) sdi; + System.out.println( "Mapping based on : " + gsdir.getTaxCompBase() ); + log_writer.println( "Mapping based on : " + gsdir.getTaxCompBase() ); + System.out.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() ); + log_writer.println( "Minimal duplications sum : " + gsdir.getMinDuplicationsSum() ); + System.out.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); + log_writer.println( "Duplications sum statistics : " + gsdir.getMinDuplicationsSum() ); + } try { final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( out_file, gene_tree, 0 ); + if ( base_algorithm == BASE_ALGORITHM.GSDIR ) { + writer.toPhyloXML( out_file, + ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(), + 0, + ForesterUtil.LINE_SEPARATOR ); + } + else { + writer.toPhyloXML( out_file, gene_tree, 0 ); + } } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, @@ -331,7 +369,7 @@ public final class gsdi { System.out.println( "Mapping cost : " + sdi.computeMappingCostL() ); log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() ); } - else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) { + else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) { final GSDI gsdi = ( GSDI ) sdi; final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + SUFFIX_FOR_SPECIES_TREE_USED ); @@ -476,6 +514,8 @@ public final class gsdi { + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); System.out.println( " -" + gsdi.SDISE_OPTION + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" ); + System.out.println( " -" + gsdi.GSDIR_OPTION + + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); System.out.println(); System.out.println( "Gene tree:" ); System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" ); @@ -484,7 +524,7 @@ public final class gsdi { System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION - + " gene_tree.xml tree_of_life.xml out.xml" ); + + " gene_tree.xml tree_of_life.xml out.xml" ); System.out.println(); } }