X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=99e946cfab2541c9f18ae453abdf5bb938658ec3;hb=e0914db6b0fa3516bc77186eec4d36dd9a753a24;hp=4f1073c641064406ee3db9b2907ec711a4da3e69;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 4f1073c..99e946c 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.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 @@ -33,18 +33,18 @@ import java.io.IOException; import java.io.Writer; import java.util.ArrayList; import java.util.Date; +import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.Set; import java.util.SortedMap; import java.util.SortedSet; import java.util.TreeMap; import java.util.TreeSet; -import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format; -import org.forester.evoinference.matrix.distance.DistanceMatrix; import org.forester.go.GoId; import org.forester.go.GoNameSpace; import org.forester.go.GoTerm; @@ -54,38 +54,40 @@ import org.forester.go.PfamToGoMapping; import org.forester.go.PfamToGoParser; import org.forester.io.parsers.HmmscanPerDomainTableParser; import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF; -import org.forester.io.writers.PhylogenyWriter; +import org.forester.io.parsers.util.ParserUtils; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.protein.BinaryDomainCombination; +import org.forester.protein.Domain; +import org.forester.protein.DomainId; +import org.forester.protein.Protein; +import org.forester.species.BasicSpecies; +import org.forester.species.Species; import org.forester.surfacing.BasicDomainSimilarityCalculator; import org.forester.surfacing.BasicGenomeWideCombinableDomains; -import org.forester.surfacing.BasicSpecies; -import org.forester.surfacing.BinaryDomainCombination; import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator; import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator; import org.forester.surfacing.DomainCountsDifferenceUtil; -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.Protein; +import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION; 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.BasicDescriptiveStatistics; import org.forester.util.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; @@ -95,198 +97,193 @@ import org.forester.util.ForesterUtil; public class surfacing { - public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; - public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; - public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; + private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; + public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; + public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; + public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; // gain/loss: - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; // gain/loss counts: - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; // tables: - // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; - // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; - // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; - // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; - // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; - // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; - // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; - // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d"; - // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; - // public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; - //public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; - // public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d"; - //public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; - public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; - public final static String BDC_PRESENT_NEXUS = "_dc.nex"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; + public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; + public final static String BDC_PRESENT_NEXUS = "_dc.nex"; // --- - public final static String PRG_NAME = "surfacing"; - public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex"; - public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex"; - public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex"; - public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features"; - public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features"; - public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d"; - public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d"; - public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d"; - public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d"; - public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc"; - public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc"; - public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc"; - public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String OUTPUT_DIR_OPTION = "out_dir"; - final static private String SCORING_OPTION = "scoring"; - private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; - final static private String SCORING_DOMAIN_COUNT_BASED = "domains"; - final static private String SCORING_PROTEIN_COUNT_BASED = "proteins"; - final static private String SCORING_COMBINATION_BASED = "combinations"; - final static private String DETAILEDNESS_OPTION = "detail"; - private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; - final static private String SPECIES_MATRIX_OPTION = "smatrix"; - final static private String DETAILEDNESS_BASIC = "basic"; - final static private String DETAILEDNESS_LIST_IDS = "list_ids"; - final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious"; - final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort"; - private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - final static private String DOMAIN_SIMILARITY_SORT_MIN = "min"; - final static private String DOMAIN_SIMILARITY_SORT_MAX = "max"; - final static private String DOMAIN_SIMILARITY_SORT_SD = "sd"; - final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean"; - final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff"; - final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff"; - final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff"; - final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species"; - final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha"; - final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first"; - final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort"; - private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; - final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha"; - final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom"; - final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot"; - final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb"; - final static private String CUTOFF_SCORE_FILE_OPTION = "cos"; - final static private String NOT_IGNORE_DUFS_OPTION = "dufs"; - final static private String MAX_E_VALUE_OPTION = "e"; - final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo"; - final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo"; - final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb"; - final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; - final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc"; - final static private String OUTPUT_FILE_OPTION = "o"; - final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g"; - final static private String GO_OBO_FILE_USE_OPTION = "obo"; - final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace"; - final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function"; - final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process"; - final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component"; - final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output"; - private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML; - final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains"; - final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids"; - final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false; - final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains"; - final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false; - final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd"; - final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd"; - final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd"; - final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; - final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; - final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; - final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto"; - // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false; - final static private String JACKNIFE_OPTION = "jack"; - final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed"; - final static private String JACKNIFE_RATIO_OPTION = "jack_ratio"; - private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100; - final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19; - final static private double JACKNIFE_RATIO_DEFAULT = 0.5; + public final static String PRG_NAME = "surfacing"; + public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex"; + public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex"; + public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex"; + public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features"; + public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features"; + public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d"; + public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String OUTPUT_DIR_OPTION = "out_dir"; + final static private String SCORING_OPTION = "scoring"; + private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; + final static private String SCORING_DOMAIN_COUNT_BASED = "domains"; + final static private String SCORING_PROTEIN_COUNT_BASED = "proteins"; + final static private String SCORING_COMBINATION_BASED = "combinations"; + final static private String DETAILEDNESS_OPTION = "detail"; + private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; + final static private String SPECIES_MATRIX_OPTION = "smatrix"; + final static private String DETAILEDNESS_BASIC = "basic"; + final static private String DETAILEDNESS_LIST_IDS = "list_ids"; + final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious"; + final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort"; + private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; + final static private String DOMAIN_SIMILARITY_SORT_MIN = "min"; + final static private String DOMAIN_SIMILARITY_SORT_MAX = "max"; + final static private String DOMAIN_SIMILARITY_SORT_SD = "sd"; + final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean"; + final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff"; + final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff"; + final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff"; + final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species"; + final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha"; + final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first"; + final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort"; + private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; + final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha"; + final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom"; + final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot"; + final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb"; + final static private String CUTOFF_SCORE_FILE_OPTION = "cos"; + final static private String NOT_IGNORE_DUFS_OPTION = "dufs"; + final static private String MAX_E_VALUE_OPTION = "e"; + final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo"; + final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo"; + final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb"; + final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; + final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc"; + final static private String OUTPUT_FILE_OPTION = "o"; + final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g"; + final static private String GO_OBO_FILE_USE_OPTION = "obo"; + final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace"; + final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function"; + final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process"; + final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component"; + final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output"; + private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML; + final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains"; + final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids"; + final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false; + final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains"; + final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false; + final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd"; + final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd"; + final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd"; + final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ" + + ForesterConstants.PHYLO_XML_SUFFIX; + final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ" + + ForesterConstants.PHYLO_XML_SUFFIX; + final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ" + + ForesterConstants.PHYLO_XML_SUFFIX; + final static private String JACKNIFE_OPTION = "jack"; + final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed"; + final static private String JACKNIFE_RATIO_OPTION = "jack_ratio"; + private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100; + final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19; + final static private double JACKNIFE_RATIO_DEFAULT = 0.5; //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference"; - final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh"; - final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh"; - final static private String FILTER_POSITIVE_OPTION = "pos_filter"; - final static private String FILTER_NEGATIVE_OPTION = "neg_filter"; - final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter"; - final static private String INPUT_FILES_FROM_FILE_OPTION = "input"; - final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; - final static private String SEQ_EXTRACT_OPTION = "prot_extract"; - final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; - final static private String PRG_VERSION = "2.003"; - final static private String PRG_DATE = "2010.12.03"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; - final static private boolean IGNORE_DUFS_DEFAULT = true; - final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false; - final static private double MAX_E_VALUE_DEFAULT = -1; - final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1; - final static private String DEFAULT_SEARCH_PARAMETER = "ls"; - final private static boolean VERBOSE_DEFAULT = true; - private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj"; - private static final String SEQ_EXTRACT_SUFFIX = ".prot"; - private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus"; - private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt"; - private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html"; - private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html"; - private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0; - private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0; - private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; - private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; - private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; - private static final boolean VERBOSE = false; - private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; - private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; - private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis"; - private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true; - public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams"; - public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation"; - public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary"; - public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains"; - public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains"; - public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc"; - public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc"; - public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS"; - public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS"; - public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities"; - private static final String LOG_FILE_SUFFIX = "_log.txt"; - private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; - private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; - private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; + final static private String FILTER_POSITIVE_OPTION = "pos_filter"; + final static private String FILTER_NEGATIVE_OPTION = "neg_filter"; + final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter"; + final static private String INPUT_FILES_FROM_FILE_OPTION = "input"; + final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; + final static private String SEQ_EXTRACT_OPTION = "prot_extract"; + final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; + final static private String PRG_VERSION = "2.252"; + final static private String PRG_DATE = "2012.08.01"; + final static private String E_MAIL = "czmasek@burnham.org"; + final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; + final static private boolean IGNORE_DUFS_DEFAULT = true; + final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false; + final static private double MAX_E_VALUE_DEFAULT = -1; + final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1; + private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed"; + private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction"; + private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj"; + private static final String SEQ_EXTRACT_SUFFIX = ".prot"; + private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus"; + private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt"; + private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html"; + private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html"; + private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0; + private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0; + private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; + private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; + private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; + final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e"; + private static final boolean VERBOSE = false; + private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; + private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; + private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis"; + private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true; + public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams"; + public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation"; + public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary"; + public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains"; + public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains"; + public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc"; + public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc"; + public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS"; + public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS"; + public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities"; + private static final String LOG_FILE_SUFFIX = "_log.txt"; + private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; + private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; + private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change? + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; + public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default). + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt"; + private static final boolean PERFORM_DC_REGAIN_PROTEINS_STATS = true; - // final String error = ForesterUtil.isReadableFile( new File( - // input_file_properties[ i ][ 0 ] ) ); - // if ( !ForesterUtil.isEmpty( error ) ) { - // ForesterUtil.fatalError( surfacing.PRG_NAME, error ); - // } private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option, final String[][] input_file_properties, final String automated_pairwise_comparison_suffix, @@ -351,7 +348,7 @@ public class surfacing { } /** - * Warning: This sideeffects 'all_bin_domain_combinations_encountered'! + * Warning: This side-effects 'all_bin_domain_combinations_encountered'! * * * @param output_file @@ -359,6 +356,7 @@ public class surfacing { * @param sum_of_all_domains_encountered * @param all_bin_domain_combinations_encountered * @param is_gains_analysis + * @param protein_length_stats_by_dc * @throws IOException */ private static void executeFitchGainsAnalysis( final File output_file, @@ -500,7 +498,7 @@ public class surfacing { } 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.PRG_NAME, "file [" + intree_file + "] does not contain any phylogeny in phyloXML format" ); @@ -522,9 +520,11 @@ public class surfacing { ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" ); } if ( intree.getNumberOfExternalNodes() < number_of_genomes ) { - ForesterUtil.fatalError( surfacing.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.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 ); @@ -542,19 +542,6 @@ public class surfacing { return intrees; } - private static List inferSpeciesTrees( final File outfile, final List distances_list ) { - final NeighborJoining nj = NeighborJoining.createInstance(); - final List phylogenies = nj.execute( distances_list ); - final PhylogenyWriter w = new PhylogenyWriter(); - try { - w.toNewHampshire( phylogenies, true, true, outfile, ";" ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() ); - } - return phylogenies; - } - private static void log( final String msg, final Writer w ) { try { w.write( msg ); @@ -617,7 +604,6 @@ public class surfacing { allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION ); allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ); - allowed_options.add( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ); allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ); allowed_options.add( JACKNIFE_OPTION ); allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION ); @@ -631,6 +617,7 @@ public class surfacing { allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION ); allowed_options.add( IGNORE_VIRAL_IDS ); allowed_options.add( SEQ_EXTRACT_OPTION ); + allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE ); allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION ); allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ); @@ -863,8 +850,20 @@ public class surfacing { species_matrix = true; } boolean output_protein_lists_for_all_domains = false; + double output_list_of_all_proteins_per_domain_e_value_max = -1; if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) { output_protein_lists_for_all_domains = true; + // + if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) { + try { + output_list_of_all_proteins_per_domain_e_value_max = cla + .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" ); + } + } + // } Detailedness detailedness = DETAILEDNESS_DEFAULT; if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) { @@ -1304,8 +1303,8 @@ public class surfacing { .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " - + e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, + "cannot read secondary features map file: " + e.getMessage() ); } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file [" @@ -1332,10 +1331,6 @@ public class surfacing { "no (acceptable) go id to term mapping file provided ('GO OBO file') (-" + surfacing.GO_OBO_FILE_USE_OPTION + "=)" ); } - boolean display_histograms = false; - if ( cla.isOptionSet( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ) ) { - display_histograms = true; - } System.out.println( "Output directory : " + out_dir ); if ( input_file_names_from_file != null ) { System.out.println( "Input files names from : " + input_files_file + " [" @@ -1389,6 +1384,11 @@ public class surfacing { System.out.println( "E-value maximum (inclusive) : " + e_value_max ); html_desc.append( "E-value maximum (inclusive):" + e_value_max + "" + nl ); } + if ( output_protein_lists_for_all_domains ) { + System.out.println( "Domain E-value max : " + output_list_of_all_proteins_per_domain_e_value_max ); + html_desc.append( "Protein lists: E-value maximum per domain (inclusive):" + + output_list_of_all_proteins_per_domain_e_value_max + "" + nl ); + } System.out.println( "Ignore DUFs : " + ignore_dufs ); if ( ignore_virus_like_ids ) { System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids ); @@ -1416,7 +1416,6 @@ public class surfacing { System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); html_desc.append( "Ignore combination with self for domain combination similarity analyses:" + ignore_combination_with_same + "" + nl ); - ; System.out.println( "Consider directedness : " + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) ); html_desc.append( "Consider directedness of binary domain combinations:" @@ -1652,7 +1651,7 @@ public class surfacing { } } // if ( perform_pwc ) { System.out.println(); - html_desc.append( "Command line:" + cla.getCommandLineArgsAsString() + "" + nl ); + html_desc.append( "Command line:\n" + cla.getCommandLineArgsAsString() + "\n" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = null; List[] query_domain_ids_array = null; @@ -1735,6 +1734,42 @@ public class surfacing { catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() ); } + final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics(); + final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics(); + final SortedMap all_genomes_domains_per_potein_histo = new TreeMap(); + final SortedSet domains_which_are_always_single = new TreeSet(); + final SortedSet domains_which_are_sometimes_single_sometimes_not = new TreeSet(); + final SortedSet domains_which_never_single = new TreeSet(); + BufferedWriter domains_per_potein_stats_writer = null; + try { + domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + + output_file + "__domains_per_potein_stats.txt" ) ); + domains_per_potein_stats_writer.write( "Genome" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "Mean" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "SD" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "Median" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "N" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "Min" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( "Max" ); + domains_per_potein_stats_writer.write( "\n" ); + } + catch ( final IOException e3 ) { + e3.printStackTrace(); + } + Map protein_length_stats_by_dc = null; + Map domain_number_stats_by_dc = null; + final Map domain_length_stats_by_domain = new HashMap(); + if ( PERFORM_DC_REGAIN_PROTEINS_STATS ) { + protein_length_stats_by_dc = new HashMap(); + domain_number_stats_by_dc = new HashMap(); + } + // Main loop: for( int i = 0; i < number_of_genomes; ++i ) { System.out.println(); System.out.println( ( i + 1 ) + "/" + number_of_genomes ); @@ -1762,12 +1797,14 @@ public class surfacing { input_file_properties[ i ][ 1 ], filter, filter_type, - ind_score_cutoff ); + ind_score_cutoff, + true ); } else { parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ), input_file_properties[ i ][ 1 ], - ind_score_cutoff ); + ind_score_cutoff, + true ); } if ( e_value_max >= 0.0 ) { parser.setEValueMaximum( e_value_max ); @@ -1778,8 +1815,7 @@ public class surfacing { if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) { parser.setMaxAllowedOverlap( max_allowed_overlap ); } - parser - .setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); + parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); if ( individual_score_cutoffs != null ) { parser.setIndividualScoreCutoffs( individual_score_cutoffs ); } @@ -1799,10 +1835,16 @@ public class surfacing { System.out.println( "Domains ignored due to virus like id: " ); ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() ); } + final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered(); + protein_coverage_stats.addValue( coverage ); System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() ); log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer ); System.out.println( "Number of proteins stored : " + protein_list.size() ); log( "Number of proteins stored : " + protein_list.size(), log_writer ); + System.out.println( "Coverage : " + + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" ); + log( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage ) + + "%", log_writer ); System.out.println( "Domains encountered : " + parser.getDomainsEncountered() ); log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer ); System.out.println( "Domains stored : " + parser.getDomainsStored() ); @@ -1813,7 +1855,8 @@ public class surfacing { System.out.println( "Domains ignored due to individual score cutoffs: " + parser.getDomainsIgnoredDueToIndividualScoreCutoff() ); log( "Domains ignored due to individual score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer ); + + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), + log_writer ); System.out.println( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval() ); log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer ); @@ -1829,7 +1872,8 @@ public class surfacing { System.out.println( "Domains ignored due negative domain filter : " + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); log( "Domains ignored due negative domain filter : " - + parser.getDomainsIgnoredDueToNegativeDomainFilter(), log_writer ); + + parser.getDomainsIgnoredDueToNegativeDomainFilter(), + log_writer ); System.out.println( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap() ); log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(), @@ -1875,17 +1919,34 @@ public class surfacing { dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ) .toString() ); ++count; + for( final Domain d : protein.getProteinDomains() ) { + final String d_str = d.getDomainId().toString(); + if ( !domain_length_stats_by_domain.containsKey( d_str ) ) { + domain_length_stats_by_domain.put( d_str, new BasicDescriptiveStatistics() ); + } + domain_length_stats_by_domain.get( d_str ).addValue( d.getLength() ); + } } } catch ( final IOException e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() ); } + SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ], + protein_list, + all_genomes_domains_per_potein_stats, + all_genomes_domains_per_potein_histo, + domains_which_are_always_single, + domains_which_are_sometimes_single_sometimes_not, + domains_which_never_single, + domains_per_potein_stats_writer ); gwcd_list.add( BasicGenomeWideCombinableDomains .createInstance( protein_list, ignore_combination_with_same, new BasicSpecies( input_file_properties[ i ][ 1 ] ), domain_id_to_go_ids_map, - dc_type ) ); + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc ) ); domain_lengths_table.addLengths( protein_list ); if ( gwcd_list.get( i ).getSize() > 0 ) { SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties, @@ -1911,7 +1972,8 @@ public class surfacing { SurfacingUtil.extractProteinNames( protein_list, query_domain_ids_array[ j ], query_domains_writer_ary[ j ], - "\t" ); + "\t", + LIMIT_SPEC_FOR_PROT_EX ); query_domains_writer_ary[ j ].flush(); } catch ( final IOException e ) { @@ -1930,19 +1992,48 @@ public class surfacing { } System.gc(); } // for( int i = 0; i < number_of_genomes; ++i ) { + ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: " + + per_genome_domain_promiscuity_statistics_file ); + // try { - per_genome_domain_promiscuity_statistics_writer.flush(); - per_genome_domain_promiscuity_statistics_writer.close(); - dc_data_writer.flush(); - dc_data_writer.close(); - log_writer.flush(); - log_writer.close(); + domains_per_potein_stats_writer.write( "ALL" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" ); + domains_per_potein_stats_writer.write( "\t" ); + domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" ); + domains_per_potein_stats_writer.write( "\n" ); + domains_per_potein_stats_writer.close(); + printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer ); + ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); + ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); + ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); + ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + + "__domains_always_combined.txt" ), domains_which_never_single, "\n" ); + ForesterUtil.programMessage( PRG_NAME, + "Average of proteins with a least one domain assigned: " + + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" ); + ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " + 100 + * protein_coverage_stats.getMin() + "%-" + 100 * protein_coverage_stats.getMax() + "%" ); + log( "Average of prot with a least one dom assigned : " + ( 100 * protein_coverage_stats.arithmeticMean() ) + + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer ); + log( "Range of prot with a least one dom assigned : " + 100 * protein_coverage_stats.getMin() + "%-" + + 100 * protein_coverage_stats.getMax() + "%", log_writer ); } catch ( final IOException e2 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); } - ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: " - + per_genome_domain_promiscuity_statistics_file ); if ( query_domains_writer_ary != null ) { for( int j = 0; j < query_domain_ids_array.length; j++ ) { try { @@ -1953,6 +2044,14 @@ public class surfacing { } } } + try { + per_genome_domain_promiscuity_statistics_writer.close(); + dc_data_writer.close(); + log_writer.close(); + } + catch ( final IOException e2 ) { + ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() ); + } if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { try { SurfacingUtil.executeDomainLengthAnalysis( input_file_properties, @@ -2003,11 +2102,19 @@ public class surfacing { DescriptiveStatistics pw_stats = null; try { String my_outfile = output_file.toString(); - if ( !my_outfile.endsWith( ".html" ) ) { + Map split_writers = null; + Writer writer = null; + if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) { + if ( my_outfile.endsWith( ".html" ) ) { + my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 ); + } + split_writers = new HashMap(); + createSplitWriters( out_dir, my_outfile, split_writers ); + } + else if ( !my_outfile.endsWith( ".html" ) ) { my_outfile += ".html"; + writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) ); } - final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir - + ForesterUtil.FILE_SEPARATOR + my_outfile ) ); List species_order = null; if ( species_matrix ) { species_order = new ArrayList(); @@ -2027,6 +2134,7 @@ public class surfacing { .writeDomainSimilaritiesToFile( html_desc, new StringBuilder( number_of_genomes + " genomes" ), writer, + split_writers, similarities, number_of_genomes == 2, species_order, @@ -2069,7 +2177,6 @@ public class surfacing { true, surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, surfacing.PRG_NAME, - display_histograms, out_dir, write_pwc_files ); String matrix_output_file = new String( output_file.toString() ); @@ -2082,12 +2189,13 @@ public class surfacing { } SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() .get( 0 ) ); @@ -2101,16 +2209,6 @@ public class surfacing { inferred_trees.add( nj_gd ); inferred_trees.add( nj_bc ); inferred_trees.add( nj_d ); - // final List histogram_datas = pwgc.getHistogramDatas(); - // if ( infer_species_trees ) { - // inferred_trees = new ArrayList(); - // final List inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc - // .getSharedBinaryCombinationsBasedDistances() ); - // final List inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc - // .getSharedDomainsBasedDistances() ); - // inferred_trees.addAll( inferred_trees_bc ); - // inferred_trees.addAll( inferred_trees_d ); - // } if ( jacknifed_distances ) { pwgc.performPairwiseComparisonsJacknifed( species, number_of_genomes, @@ -2119,14 +2217,19 @@ public class surfacing { jacknife_resamplings, jacknife_ratio, random_seed ); - SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings - + surfacing.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.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances() ); + SurfacingUtil + .writeMatrixToFile( new File( matrix_output_file + + "_" + + ForesterUtil.round( jacknife_ratio, 2 ) + + "_" + + jacknife_resamplings + + surfacing.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.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 @@ -2135,17 +2238,6 @@ public class surfacing { // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() ); // } } - if ( display_histograms ) { - // final List histogram_datas_all = new ArrayList(); - // histogram_datas_all.add( new HistogramData( "all", - // values_for_all_scores_histogram, - // null, - // 20 ) ); - // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all ); - // final HistogramsFrame hf = new HistogramsFrame( histogram_datas ); - // hf_all.setVisible( true ); - // hf.setVisible( true ); - } } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) ) if ( ( out_dir != null ) && ( !perform_pwc ) ) { output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); @@ -2182,7 +2274,10 @@ public class surfacing { output_binary_domain_combinationsfor_graph_analysis, all_bin_domain_combinations_gained_fitch, all_bin_domain_combinations_lost_fitch, - dc_type ); + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc, + domain_length_stats_by_domain ); // Listing of all domain combinations gained is only done if only one input tree is used. if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { @@ -2235,39 +2330,11 @@ public class surfacing { plus_minus_analysis_numbers ); } if ( output_protein_lists_for_all_domains ) { - writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list ); - } - // if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) { - // final StringBuilder parameters_sb = createParametersAsString( ignore_dufs, - // e_value_max, - // max_allowed_overlap, - // no_engulfing_overlaps, - // cutoff_scores_file ); - // String s = "_"; - // if ( radomize_fitch_parsimony ) { - // s += random_number_seed_for_fitch_parsimony + "_"; - // } - // int i = 0; - // for( final Phylogeny inferred_tree : inferred_trees ) { - // if ( !inferred_tree.isRooted() ) { - // intrees[ 0 ].getRoot().getName(); - // inferred_tree.r - // } - // final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s; - // final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator - // .createInstance( inferred_tree, gwcd_list ); - // SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony, - // radomize_fitch_parsimony, - // outfile_name, - // domain_parsimony, - // inferred_tree, - // domain_id_to_go_ids_map, - // go_id_to_term_map, - // go_namespace_limit, - // parameters_sb.toString() ); - // i++; - // } - // } + writeProteinListsForAllSpecies( out_dir, + protein_lists_per_species, + gwcd_list, + output_list_of_all_proteins_per_domain_e_value_max ); + } if ( all_bin_domain_combinations_gained_fitch != null ) { try { executeFitchGainsAnalysis( new File( output_file @@ -2297,18 +2364,87 @@ public class surfacing { final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; - System.out.println(); - System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" ); - System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); - System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" ); - System.out.println(); - System.out.println( "If this application is useful to you, please cite:" ); - System.out.println( surfacing.WWW ); - System.out.println(); + ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + + "ms" ); + ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); + ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " + + total_memory + "MB" ); + ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" ); + ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); ForesterUtil.programMessage( PRG_NAME, "OK" ); System.out.println(); } + private static void createSplitWriters( final File out_dir, + final String my_outfile, + final Map split_writers ) throws IOException { + split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_A.html" ) ) ); + split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_B.html" ) ) ); + split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_C.html" ) ) ); + split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_D.html" ) ) ); + split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_E.html" ) ) ); + split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_F.html" ) ) ); + split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_G.html" ) ) ); + split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_H.html" ) ) ); + split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_I.html" ) ) ); + split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_J.html" ) ) ); + split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_K.html" ) ) ); + split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_L.html" ) ) ); + split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_M.html" ) ) ); + split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_N.html" ) ) ); + split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_O.html" ) ) ); + split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_P.html" ) ) ); + split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Q.html" ) ) ); + split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_R.html" ) ) ); + split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_S.html" ) ) ); + split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_T.html" ) ) ); + split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_U.html" ) ) ); + split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_V.html" ) ) ); + split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_W.html" ) ) ); + split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_X.html" ) ) ); + split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Y.html" ) ) ); + split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_Z.html" ) ) ); + split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile + + "_domains_0.html" ) ) ); + } + + private static void printOutPercentageOfMultidomainProteins( final SortedMap all_genomes_domains_per_potein_histo, + final Writer log_writer ) { + int sum = 0; + for( final Entry entry : all_genomes_domains_per_potein_histo.entrySet() ) { + sum += entry.getValue(); + } + final double percentage = 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) / sum; + ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" ); + log( "Percentage of multidomain proteins: : " + percentage + "%", log_writer ); + } + private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree, final String[][] input_file_properties ) { final String[] genomes = new String[ input_file_properties.length ]; @@ -2325,12 +2461,21 @@ public class surfacing { final PhylogenyNode n = it.next(); if ( ForesterUtil.isEmpty( n.getName() ) ) { if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + } + else if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { n.setName( n.getNodeData().getTaxonomy().getScientificName() ); } + else if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { + n.setName( n.getNodeData().getTaxonomy().getCommonName() ); + } else { - ForesterUtil.fatalError( surfacing.PRG_NAME, - "node without both name and scientific taxonomy name found" ); + ForesterUtil + .fatalError( surfacing.PRG_NAME, + "node with no name, scientific name, common name, or taxonomy code present" ); } } } @@ -2354,23 +2499,6 @@ public class surfacing { } } - // public static StringBuffer stringCombinableDomainsMapToStringBuffer( - // final SortedMap map ) { - // final StringBuffer sb = new StringBuffer(); - // for( final Iterator iter = map.keySet().iterator(); - // iter.hasNext(); ) { - // final Object key = iter.next(); - // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ', - // false ) ); - // final CombinableDomains domain_combination = map.get( key ); - // sb.append( ForesterUtil.pad( new StringBuffer( "" + - // domain_combination.getNumberOfCombiningDomains() ), 8, - // ' ', false ) ); - // sb.append( domain_combination.toStringBuffer() ); - // sb.append( ForesterUtil.getLineSeparator() ); - // } - // return sb; - // } private static void printHelp() { System.out.println(); System.out.println( "Usage:" ); @@ -2422,8 +2550,6 @@ public class surfacing { System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); System.out - .println( surfacing.DISPLAY_M_HISTOGRAMS_OPTION + ": to display multiple histograms (using fluorite)" ); - System.out .println( JACKNIFE_OPTION + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: " + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" ); @@ -2460,14 +2586,19 @@ public class surfacing { System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS + ": to output binary domain combinations for (downstream) graph analysis" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" ); + System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION + + ": e value max per domain for output of all proteins per domain" ); System.out.println(); + System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar" + + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1" + + " -no_eo -mo=0 -input=genomes_limited.txt -out_dir=out -o=o " + + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" ); System.out.println(); - System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar" - + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST" + System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar" + + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST" + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo " + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo " - + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION - + "=50 human mouse brafl strpu" ); + + "-ds_output=detailed_html -scoring=domains -sort=alpha human mouse brafl strpu" ); System.out.println(); } @@ -2636,7 +2767,8 @@ public class surfacing { private static void writeProteinListsForAllSpecies( final File output_dir, final SortedMap> protein_lists_per_species, - final List gwcd_list ) { + final List gwcd_list, + final double domain_e_cutoff ) { final SortedSet all_domains = new TreeSet(); for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { all_domains.addAll( gwcd.getAllDomainIds() ); @@ -2646,7 +2778,12 @@ public class surfacing { SurfacingUtil.checkForOutputFileWriteability( out ); try { final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) ); - SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" ); + SurfacingUtil.extractProteinNames( protein_lists_per_species, + domain, + proteins_file_writer, + "\t", + LIMIT_SPEC_FOR_PROT_EX, + domain_e_cutoff ); proteins_file_writer.close(); } catch ( final IOException e ) {