X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing_hmmpfam.java;h=4104a34ee12d9af85c2008596eeefd5e9dd495c1;hb=94fc8a7809432b86c41a2ae5f3ab4977cd5d5599;hp=91857253c67d948ef385d001249908aad718be13;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing_hmmpfam.java b/forester/java/src/org/forester/application/surfacing_hmmpfam.java index 9185725..4104a34 100644 --- a/forester/java/src/org/forester/application/surfacing_hmmpfam.java +++ b/forester/java/src/org/forester/application/surfacing_hmmpfam.java @@ -6,7 +6,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either @@ -16,7 +16,7 @@ // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. -// +// // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -52,6 +52,7 @@ import org.forester.go.OBOparser; import org.forester.go.PfamToGoMapping; import org.forester.go.PfamToGoParser; import org.forester.io.parsers.HmmPfamOutputParser; +import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; @@ -67,21 +68,21 @@ import org.forester.surfacing.DomainId; import org.forester.surfacing.DomainLengthsTable; import org.forester.surfacing.DomainParsimonyCalculator; import org.forester.surfacing.DomainSimilarity; +import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring; +import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField; import org.forester.surfacing.DomainSimilarityCalculator; +import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; import org.forester.surfacing.GenomeWideCombinableDomains; +import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder; import org.forester.surfacing.MappingResults; import org.forester.surfacing.PairwiseDomainSimilarityCalculator; import org.forester.surfacing.PairwiseGenomeComparator; import org.forester.surfacing.PrintableDomainSimilarity; +import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; import org.forester.surfacing.Protein; import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator; import org.forester.surfacing.Species; import org.forester.surfacing.SurfacingUtil; -import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring; -import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField; -import org.forester.surfacing.DomainSimilarityCalculator.Detailedness; -import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder; -import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; import org.forester.util.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; @@ -495,7 +496,7 @@ public class surfacing_hmmpfam { } try { final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance() - .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) ); + .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) ); if ( p_array.length < 1 ) { ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file + "] does not contain any phylogeny in phyloXML format" ); @@ -517,9 +518,11 @@ public class surfacing_hmmpfam { ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] is not rooted" ); } if ( intree.getNumberOfExternalNodes() < number_of_genomes ) { - ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "number of external nodes [" - + intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file - + "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" ); + ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, + "number of external nodes [" + intree.getNumberOfExternalNodes() + + "] of input tree [" + intree_file + + "] is smaller than the number of genomes the be analyzed [" + + number_of_genomes + "]" ); } final StringBuilder parent_names = new StringBuilder(); final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names ); @@ -777,8 +780,7 @@ public class surfacing_hmmpfam { ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for negative domains filter: -" + surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION + "=" ); } - negative_domains_filter_file = new File( cla - .getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ); + negative_domains_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ); final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" @@ -1119,8 +1121,8 @@ public class surfacing_hmmpfam { } } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read from GO OBO file: " - + e.getLocalizedMessage() ); + ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, + "cannot read from GO OBO file: " + e.getLocalizedMessage() ); } } Map go_id_to_term_map = null; @@ -2016,7 +2018,6 @@ public class surfacing_hmmpfam { true, surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, surfacing_hmmpfam.PRG_NAME, - display_histograms, out_dir, write_pwc_files ); String matrix_output_file = new String( output_file.toString() ); @@ -2027,15 +2028,18 @@ public class surfacing_hmmpfam { matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file; output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); } - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing_hmmpfam.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getDomainDistanceScoresMeans() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + surfacing_hmmpfam.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getDomainDistanceScoresMeans() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file + surfacing_hmmpfam.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc .getDomainDistanceScoresMeans().get( 0 ) ); @@ -2067,14 +2071,22 @@ public class surfacing_hmmpfam { jacknife_resamplings, jacknife_ratio, random_seed ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings - + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings - + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + "_" + + ForesterUtil.round( jacknife_ratio, 2 ) + + "_" + + jacknife_resamplings + + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + "_" + + ForesterUtil.round( jacknife_ratio, 2 ) + + "_" + + jacknife_resamplings + + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); // if ( infer_species_trees ) { // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc