From 3e2be04bd16802a231c417d4866036bb6e375fca Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 17 Jun 2011 03:32:14 +0000 Subject: [PATCH] in progress --- .../src/org/forester/application/surfacing.java | 30 +- .../org/forester/application/surfacing_old.java | 2592 -------------------- .../src/org/forester/surfacing/SurfacingUtil.java | 255 +- 3 files changed, 168 insertions(+), 2709 deletions(-) delete mode 100644 forester/java/src/org/forester/application/surfacing_old.java diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 580eea4..ec2ddd9 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -110,20 +110,20 @@ public class surfacing { 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_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 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"; // --- @@ -281,6 +281,8 @@ public class surfacing { 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; + 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"; // final String error = ForesterUtil.isReadableFile( new File( // input_file_properties[ i ][ 0 ] ) ); @@ -2472,7 +2474,7 @@ public class surfacing { System.out.println(); 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" + + " 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 diff --git a/forester/java/src/org/forester/application/surfacing_old.java b/forester/java/src/org/forester/application/surfacing_old.java deleted file mode 100644 index 443191c..0000000 --- a/forester/java/src/org/forester/application/surfacing_old.java +++ /dev/null @@ -1,2592 +0,0 @@ -// $Id: -// -// FORESTER -- software libraries and applications -// for evolutionary biology research and applications. -// -// 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 -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// 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 -// -// Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester - -package org.forester.application; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.io.Writer; -import java.util.ArrayList; -import java.util.Date; -import java.util.HashSet; -import java.util.List; -import java.util.Map; -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; -import org.forester.go.GoUtils; -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.writers.PhylogenyWriter; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -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.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.util.BasicTable; -import org.forester.util.BasicTableParser; -import org.forester.util.CommandLineArguments; -import org.forester.util.DescriptiveStatistics; -import org.forester.util.ForesterConstants; -import org.forester.util.ForesterUtil; - -public class surfacing_old { - - 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"; - // 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"; - // 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 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; - //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 = "1.00"; - final static private String PRG_DATE = "2009.07.06"; - 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 ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT = true; - 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"; - - // 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, - final File outdir ) { - for( int i = 0; i < input_file_properties.length; ++i ) { - for( int j = 0; j < i; ++j ) { - final String species_i = input_file_properties[ i ][ 1 ]; - final String species_j = input_file_properties[ j ][ 1 ]; - String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_" - + species_j + automated_pairwise_comparison_suffix; - switch ( domain_similarity_print_option ) { - case HTML: - if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) { - pairwise_similarities_output_file_str += ".html"; - } - break; - } - final String error = ForesterUtil - .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir - + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, error ); - } - } - } - } - - private static StringBuilder createParametersAsString( final boolean ignore_dufs, - final double e_value_max, - final int max_allowed_overlap, - final boolean no_engulfing_overlaps, - final File cutoff_scores_file, - final BinaryDomainCombination.DomainCombinationType dc_type ) { - final StringBuilder parameters_sb = new StringBuilder(); - parameters_sb.append( "E-value: " + e_value_max ); - if ( cutoff_scores_file != null ) { - parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file ); - } - else { - parameters_sb.append( ", Cutoff-scores-file: not-set" ); - } - if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) { - parameters_sb.append( ", Max-overlap: " + max_allowed_overlap ); - } - else { - parameters_sb.append( ", Max-overlap: not-set" ); - } - if ( no_engulfing_overlaps ) { - parameters_sb.append( ", Engulfing-overlaps: not-allowed" ); - } - else { - parameters_sb.append( ", Engulfing-overlaps: allowed" ); - } - if ( ignore_dufs ) { - parameters_sb.append( ", Ignore-dufs: true" ); - } - else { - parameters_sb.append( ", Ignore-dufs: false" ); - } - parameters_sb.append( ", DC type (if applicable): " + dc_type ); - return parameters_sb; - } - - /** - * Warning: This sideeffects 'all_bin_domain_combinations_encountered'! - * - * - * @param output_file - * @param all_bin_domain_combinations_changed - * @param sum_of_all_domains_encountered - * @param all_bin_domain_combinations_encountered - * @param is_gains_analysis - * @throws IOException - */ - private static void executeFitchGainsAnalysis( final File output_file, - final List all_bin_domain_combinations_changed, - final int sum_of_all_domains_encountered, - final SortedSet all_bin_domain_combinations_encountered, - final boolean is_gains_analysis ) throws IOException { - SurfacingUtil.checkForOutputFileWriteability( output_file ); - final Writer out = ForesterUtil.createBufferedWriter( output_file ); - final SortedMap bdc_to_counts = ForesterUtil - .listToSortedCountsMap( all_bin_domain_combinations_changed ); - final SortedSet all_domains_in_combination_changed_more_than_once = new TreeSet(); - final SortedSet all_domains_in_combination_changed_only_once = new TreeSet(); - int above_one = 0; - int one = 0; - for( final Object bdc_object : bdc_to_counts.keySet() ) { - final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object; - final int count = bdc_to_counts.get( bdc_object ); - if ( count < 1 ) { - ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " ); - } - out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR ); - if ( count > 1 ) { - all_domains_in_combination_changed_more_than_once.add( bdc.getId0() ); - all_domains_in_combination_changed_more_than_once.add( bdc.getId1() ); - above_one++; - } - else if ( count == 1 ) { - all_domains_in_combination_changed_only_once.add( bdc.getId0() ); - all_domains_in_combination_changed_only_once.add( bdc.getId1() ); - one++; - } - } - final int all = all_bin_domain_combinations_encountered.size(); - int never_lost = -1; - if ( !is_gains_analysis ) { - all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed ); - never_lost = all_bin_domain_combinations_encountered.size(); - for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) { - out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR ); - } - } - if ( is_gains_analysis ) { - out.write( "Sum of all distinct domain combinations appearing once : " + one - + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one - + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domains in combinations apppearing only once : " - + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domains in combinations apppearing more than once: " - + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR ); - } - else { - out.write( "Sum of all distinct domain combinations never lost : " + never_lost - + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domain combinations lost once : " + one - + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domain combinations lost more than once : " + above_one - + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domains in combinations lost only once : " - + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); - out.write( "Sum of all distinct domains in combinations lost more than once: " - + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR ); - } - out.write( "All binary combinations : " + all - + ForesterUtil.LINE_SEPARATOR ); - out.write( "All domains : " - + sum_of_all_domains_encountered ); - out.close(); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, - "Wrote fitch domain combination dynamics counts analysis to \"" + output_file - + "\"" ); - } - - private static void executePlusMinusAnalysis( final File output_file, - final List plus_minus_analysis_high_copy_base, - final List plus_minus_analysis_high_copy_target, - final List plus_minus_analysis_low_copy, - final List gwcd_list, - final SortedMap> protein_lists_per_species, - final Map> domain_id_to_go_ids_map, - final Map go_id_to_term_map, - final List plus_minus_analysis_numbers ) { - final Set all_spec = new HashSet(); - for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { - all_spec.add( gwcd.getSpecies().getSpeciesId() ); - } - final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML ); - final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX ); - final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML ); - final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX ); - final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX ); - final File proteins_file_base = new File( output_file + "" ); - final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue(); - final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue(); - try { - DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list, - protein_lists_per_species, - plus_minus_analysis_high_copy_base, - plus_minus_analysis_high_copy_target, - plus_minus_analysis_low_copy, - min_diff, - factor, - plain_out_dom, - html_out_dom, - html_out_dc, - domain_id_to_go_ids_map, - go_id_to_term_map, - all_domains_go_ids_out_dom, - passing_domains_go_ids_out_dom, - proteins_file_base ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() ); - } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \"" - + html_out_dom + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \"" - + plain_out_dom + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \"" - + html_out_dc + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, - "Wrote plus minus domain analysis based passing GO ids to \"" - + passing_domains_go_ids_out_dom + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \"" - + all_domains_go_ids_out_dom + "\"" ); - } - - private static Phylogeny[] getIntrees( final File[] intree_files, - final int number_of_genomes, - final String[][] input_file_properties ) { - final Phylogeny[] intrees = new Phylogeny[ intree_files.length ]; - int i = 0; - for( final File intree_file : intree_files ) { - Phylogeny intree = null; - final String error = ForesterUtil.isReadableFile( intree_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read input tree file [" + intree_file + "]: " - + error ); - } - try { - final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance() - .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) ); - if ( p_array.length < 1 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "file [" + intree_file - + "] does not contain any phylogeny in phyloXML format" ); - } - else if ( p_array.length > 1 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "file [" + intree_file - + "] contains more than one phylogeny in phyloXML format" ); - } - intree = p_array[ 0 ]; - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to read input tree from file [" + intree_file - + "]: " + error ); - } - if ( ( intree == null ) || intree.isEmpty() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is empty" ); - } - if ( !intree.isRooted() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is not rooted" ); - } - if ( intree.getNumberOfExternalNodes() < number_of_genomes ) { - ForesterUtil.fatalError( surfacing_old.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 ); - if ( nodes_lacking_name > 0 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] has " - + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" ); - } - preparePhylogenyForParsimonyAnalyses( intree, input_file_properties ); - if ( !intree.isCompletelyBinary() ) { - ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "input tree [" + intree_file - + "] is not completely binary" ); - } - intrees[ i++ ] = intree; - } - 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; - } - - public static void main( final String args[] ) { - final long start_time = new Date().getTime(); - // final StringBuffer log = new StringBuffer(); - final StringBuilder html_desc = new StringBuilder(); - ForesterUtil.printProgramInformation( surfacing_old.PRG_NAME, - surfacing_old.PRG_VERSION, - surfacing_old.PRG_DATE, - surfacing_old.E_MAIL, - surfacing_old.WWW ); - final String nl = ForesterUtil.LINE_SEPARATOR; - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - CommandLineArguments cla = null; - try { - cla = new CommandLineArguments( args ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); - } - if ( cla.isOptionSet( surfacing_old.HELP_OPTION_1 ) || cla.isOptionSet( surfacing_old.HELP_OPTION_2 ) ) { - surfacing_old.printHelp(); - System.exit( 0 ); - } - if ( ( args.length < 1 ) ) { - surfacing_old.printHelp(); - System.exit( -1 ); - } - final List allowed_options = new ArrayList(); - allowed_options.add( surfacing_old.NOT_IGNORE_DUFS_OPTION ); - allowed_options.add( surfacing_old.MAX_E_VALUE_OPTION ); - allowed_options.add( surfacing_old.DETAILEDNESS_OPTION ); - allowed_options.add( surfacing_old.OUTPUT_FILE_OPTION ); - allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ); - allowed_options.add( surfacing_old.SPECIES_MATRIX_OPTION ); - allowed_options.add( surfacing_old.SCORING_OPTION ); - allowed_options.add( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION ); - allowed_options.add( surfacing_old.NO_ENGULFING_OVERLAP_OPTION ); - allowed_options.add( surfacing_old.DOMAIN_COUNT_SORT_OPTION ); - allowed_options.add( surfacing_old.CUTOFF_SCORE_FILE_OPTION ); - allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ); - allowed_options.add( surfacing_old.OUTPUT_DIR_OPTION ); - allowed_options.add( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION ); - allowed_options.add( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ); - allowed_options.add( surfacing_old.GO_OBO_FILE_USE_OPTION ); - allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ); - allowed_options.add( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ); - allowed_options.add( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); - allowed_options.add( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ); - allowed_options.add( surfacing_old.DISPLAY_M_HISTOGRAMS_OPTION ); - allowed_options.add( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ); - allowed_options.add( JACKNIFE_OPTION ); - allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION ); - allowed_options.add( JACKNIFE_RATIO_OPTION ); - allowed_options.add( INPUT_SPECIES_TREE_OPTION ); - //allowed_options.add( INFER_SPECIES_TREES_OPTION ); - allowed_options.add( FILTER_POSITIVE_OPTION ); - allowed_options.add( FILTER_NEGATIVE_OPTION ); - allowed_options.add( INPUT_FILES_FROM_FILE_OPTION ); - allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ); - allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION ); - allowed_options.add( IGNORE_VIRAL_IDS ); - allowed_options.add( SEQ_EXTRACT_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 ); - allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ); - allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ); - boolean ignore_dufs = surfacing_old.IGNORE_DUFS_DEFAULT; - boolean ignore_combination_with_same = surfacing_old.IGNORE_COMBINATION_WITH_SAME_DEFAULLT; - double e_value_max = surfacing_old.MAX_E_VALUE_DEFAULT; - int max_allowed_overlap = surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT; - final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); - if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown option(s): " + dissallowed_options ); - } - boolean output_binary_domain_combinationsfor_graph_analysis = false; - if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) { - output_binary_domain_combinationsfor_graph_analysis = true; - } - if ( cla.isOptionSet( surfacing_old.MAX_E_VALUE_OPTION ) ) { - try { - e_value_max = cla.getOptionValueAsDouble( surfacing_old.MAX_E_VALUE_OPTION ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no acceptable value for E-value maximum" ); - } - } - if ( cla.isOptionSet( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION ) ) { - try { - max_allowed_overlap = cla.getOptionValueAsInt( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no acceptable value for maximal allowed domain overlap" ); - } - } - boolean no_engulfing_overlaps = false; - if ( cla.isOptionSet( surfacing_old.NO_ENGULFING_OVERLAP_OPTION ) ) { - no_engulfing_overlaps = true; - } - boolean ignore_virus_like_ids = false; - if ( cla.isOptionSet( surfacing_old.IGNORE_VIRAL_IDS ) ) { - ignore_virus_like_ids = true; - } - if ( cla.isOptionSet( surfacing_old.NOT_IGNORE_DUFS_OPTION ) ) { - ignore_dufs = false; - } - if ( cla.isOptionSet( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) { - ignore_combination_with_same = true; - } - boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT; - if ( cla.isOptionSet( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) { - ignore_domains_without_combs_in_all_spec = true; - } - boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT; - if ( cla.isOptionSet( surfacing_old.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) { - ignore_species_specific_domains = true; - } - File output_file = null; - if ( cla.isOptionSet( surfacing_old.OUTPUT_FILE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no value for domain combinations similarities output file: -" - + surfacing_old.OUTPUT_FILE_OPTION + "=" ); - } - output_file = new File( cla.getOptionValue( surfacing_old.OUTPUT_FILE_OPTION ) ); - SurfacingUtil.checkForOutputFileWriteability( output_file ); - } - File cutoff_scores_file = null; - Map individual_domain_score_cutoffs = null; - if ( cla.isOptionSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for individual domain score cutoffs file: -" - + surfacing_old.CUTOFF_SCORE_FILE_OPTION + "=" ); - } - cutoff_scores_file = new File( cla.getOptionValue( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ); - final String error = ForesterUtil.isReadableFile( cutoff_scores_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read individual domain score cutoffs file: " - + error ); - } - try { - final BasicTable scores_table = BasicTableParser.parse( cutoff_scores_file, " " ); - individual_domain_score_cutoffs = scores_table.getColumnsAsMap( 0, 1 ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "cannot read from individual domain score cutoffs file: " + e ); - } - } - BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC; - if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) { - dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED; - } - if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) { - dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT; - } - File out_dir = null; - if ( cla.isOptionSet( surfacing_old.OUTPUT_DIR_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_DIR_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for output directory: -" - + surfacing_old.OUTPUT_DIR_OPTION + "=" ); - } - out_dir = new File( cla.getOptionValue( surfacing_old.OUTPUT_DIR_OPTION ) ); - if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" ); - } - if ( !out_dir.exists() ) { - final boolean success = out_dir.mkdir(); - if ( !success || !out_dir.exists() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to create \"" + out_dir + "\"" ); - } - } - if ( !out_dir.canWrite() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot write to \"" + out_dir + "\"" ); - } - } - File positive_filter_file = null; - File negative_filter_file = null; - File negative_domains_filter_file = null; - if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) - && cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) { - ForesterUtil - .fatalError( surfacing_old.PRG_NAME, "attempt to use both negative and positive protein filter" ); - } - if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) - && ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) || cla - .isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) ) { - ForesterUtil - .fatalError( surfacing_old.PRG_NAME, - "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); - } - if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative filter: -" - + surfacing_old.FILTER_NEGATIVE_OPTION + "=" ); - } - negative_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( negative_filter_file ); - if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_filter_file + "\": " - + msg ); - } - } - else if ( cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for positive filter: -" - + surfacing_old.FILTER_POSITIVE_OPTION + "=" ); - } - positive_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_POSITIVE_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( positive_filter_file ); - if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + positive_filter_file + "\": " - + msg ); - } - } - else if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative domains filter: -" - + surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION + "=" ); - } - negative_domains_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file ); - if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_domains_filter_file - + "\": " + msg ); - } - } - final List plus_minus_analysis_high_copy_base_species = new ArrayList(); - final List plus_minus_analysis_high_copy_target_species = new ArrayList(); - final List plus_minus_analysis_high_low_copy_species = new ArrayList(); - final List plus_minus_analysis_numbers = new ArrayList(); - processPlusMinusAnalysisOption( cla, - plus_minus_analysis_high_copy_base_species, - plus_minus_analysis_high_copy_target_species, - plus_minus_analysis_high_low_copy_species, - plus_minus_analysis_numbers ); - File input_files_file = null; - String[] input_file_names_from_file = null; - if ( cla.isOptionSet( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input files file: -" - + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=" ); - } - input_files_file = new File( cla.getOptionValue( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( input_files_file ); - if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + input_files_file + "\": " - + msg ); - } - try { - input_file_names_from_file = ForesterUtil.file2array( input_files_file ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to read from \"" + input_files_file + "\": " - + e ); - } - } - if ( ( cla.getNumberOfNames() < 1 ) - && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "No hmmpfam output file indicated is input: use comand line directly or " - + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=" ); - } - DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT; - if ( cla.isOptionSet( surfacing_old.SCORING_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.SCORING_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no value for scoring method for domain combinations similarity calculation: -" - + surfacing_old.SCORING_OPTION + "=<" - + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|" - + surfacing_old.SCORING_COMBINATION_BASED + ">\"" ); - } - final String scoring_str = cla.getOptionValue( surfacing_old.SCORING_OPTION ); - if ( scoring_str.equals( surfacing_old.SCORING_DOMAIN_COUNT_BASED ) ) { - scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS; - } - else if ( scoring_str.equals( surfacing_old.SCORING_COMBINATION_BASED ) ) { - scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; - } - else if ( scoring_str.equals( surfacing_old.SCORING_PROTEIN_COUNT_BASED ) ) { - scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS; - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + scoring_str - + "\" for scoring method for domain combinations similarity calculation: \"-" - + surfacing_old.SCORING_OPTION + "=<" + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing_old.SCORING_COMBINATION_BASED - + ">\"" ); - } - } - boolean sort_by_species_count_first = false; - if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) { - sort_by_species_count_first = true; - } - boolean species_matrix = false; - if ( cla.isOptionSet( surfacing_old.SPECIES_MATRIX_OPTION ) ) { - species_matrix = true; - } - boolean output_protein_lists_for_all_domains = false; - if ( cla.isOptionSet( surfacing_old.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) { - output_protein_lists_for_all_domains = true; - } - Detailedness detailedness = DETAILEDNESS_DEFAULT; - if ( cla.isOptionSet( surfacing_old.DETAILEDNESS_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.DETAILEDNESS_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for -" + surfacing_old.DETAILEDNESS_OPTION - + "=<" + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|" - + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" ); - } - final String detness = cla.getOptionValue( surfacing_old.DETAILEDNESS_OPTION ).toLowerCase(); - if ( detness.equals( surfacing_old.DETAILEDNESS_BASIC ) ) { - detailedness = DomainSimilarityCalculator.Detailedness.BASIC; - } - else if ( detness.equals( surfacing_old.DETAILEDNESS_LIST_IDS ) ) { - detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES; - } - else if ( detness.equals( surfacing_old.DETAILEDNESS_PUNCTILIOUS ) ) { - detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + detness - + "\" for detailedness: \"-" + surfacing_old.DETAILEDNESS_OPTION + "=<" - + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|" - + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" ); - } - } - String automated_pairwise_comparison_suffix = null; - boolean perform_pwc = false; - boolean write_pwc_files = false; - if ( cla.isOptionSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) { - perform_pwc = true; - if ( !cla.isOptionValueSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) { - write_pwc_files = false; - } - else { - write_pwc_files = true; - automated_pairwise_comparison_suffix = "_" - + cla.getOptionValue( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ); - } - } - String query_domain_ids = null; - if ( cla.isOptionSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) { - ForesterUtil - .fatalError( surfacing_old.PRG_NAME, - "no domain ids given for sequences with given domains to be extracted : -" - + surfacing_old.SEQ_EXTRACT_OPTION - + "=" ); - } - query_domain_ids = cla.getOptionValue( surfacing_old.SEQ_EXTRACT_OPTION ); - } - DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT; - DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT; - if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no value for domain combinations similarities sorting: -" - + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<" - + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" ); - } - final String sort_str = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase(); - if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MAX ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MIN ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_SD ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; - } - else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE; - domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE; - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort_str - + "\" for domain combinations similarities sorting: \"-" - + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<" - + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX - + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF - + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" - + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" ); - } - } - PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT; - if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for print option: -" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); - } - final String sort = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase(); - if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) { - domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML; - } - else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) { - // domain_similarity_print_option = - // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML; - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "simple HTML output not implemented yet :(" ); - } - else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) { - domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED; - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort + "\" for print option: -" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|" - + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" ); - } - } - GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT; - if ( cla.isOptionSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for sorting of domain counts: -" - + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|" - + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); - } - final String sort = cla.getOptionValue( surfacing_old.DOMAIN_COUNT_SORT_OPTION ).toLowerCase(); - if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_ALPHA ) ) { - dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; - } - else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) { - dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT; - } - else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) { - dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT; - } - else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) { - dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT; - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort - + "\" for sorting of domain counts: \"-" + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<" - + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|" - + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); - } - } - String[][] input_file_properties = null; - if ( input_file_names_from_file != null ) { - input_file_properties = surfacing_old.processInputFileNames( input_file_names_from_file ); - } - else { - input_file_properties = surfacing_old.processInputFileNames( cla.getNames() ); - } - final int number_of_genomes = input_file_properties.length; - if ( number_of_genomes < 2 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot analyze less than two files" ); - } - if ( ( number_of_genomes < 3 ) && perform_pwc ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use : -" - + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "= to turn on pairwise analyses with less than three input files" ); - } - checkWriteabilityForPairwiseComparisons( domain_similarity_print_option, - input_file_properties, - automated_pairwise_comparison_suffix, - out_dir ); - for( int i = 0; i < number_of_genomes; i++ ) { - File dcc_outfile = new File( input_file_properties[ i ][ 0 ] - + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ); - if ( out_dir != null ) { - dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile ); - } - SurfacingUtil.checkForOutputFileWriteability( dcc_outfile ); - } - File pfam_to_go_file = null; - Map> domain_id_to_go_ids_map = null; - int domain_id_to_go_ids_count = 0; - if ( cla.isOptionSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for Pfam to GO mapping file: -" - + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=" ); - } - pfam_to_go_file = new File( cla.getOptionValue( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ); - final String error = ForesterUtil.isReadableFile( pfam_to_go_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read Pfam to GO mapping file: " + error ); - } - try { - final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file ); - final List pfam_to_go_mappings = parser.parse(); - domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings ); - if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) { - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, - "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); - } - domain_id_to_go_ids_count = parser.getMappingCount(); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e ); - } - } - File go_obo_file = null; - List go_terms = null; - if ( cla.isOptionSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO OBO file: -" - + surfacing_old.GO_OBO_FILE_USE_OPTION + "=" ); - } - if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO OBO file (-" - + surfacing_old.GO_OBO_FILE_USE_OPTION + "=) without Pfam to GO mapping file (" - + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=)" ); - } - go_obo_file = new File( cla.getOptionValue( surfacing_old.GO_OBO_FILE_USE_OPTION ) ); - final String error = ForesterUtil.isReadableFile( go_obo_file ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read GO OBO file: " + error ); - } - try { - final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM ); - go_terms = parser.parse(); - if ( parser.getGoTermCount() != go_terms.size() ) { - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, - "parser.getGoTermCount() != go_terms.size()" ); - } - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "cannot read from GO OBO file: " + e.getLocalizedMessage() ); - } - } - Map go_id_to_term_map = null; - if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) ) - && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) { - go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms ); - } - GoNameSpace go_namespace_limit = null; - if ( cla.isOptionSet( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) ) { - if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO namespace limit (-" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=) without Pfam to GO mapping file (" - + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=) and GO OBO file (-" - + surfacing_old.GO_OBO_FILE_USE_OPTION + "=)" ); - } - if ( !cla.isOptionValueSet( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO namespace limit: \"-" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); - } - final String go_namespace_limit_str = cla.getOptionValue( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) - .toLowerCase(); - if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) { - go_namespace_limit = GoNameSpace.createMolecularFunction(); - } - else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) { - go_namespace_limit = GoNameSpace.createBiologicalProcess(); - } - else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) { - go_namespace_limit = GoNameSpace.createCellularComponent(); - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + go_namespace_limit_str - + "\" for GO namespace limit: \"-" + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); - } - } - if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE ) - && ( number_of_genomes > 2 ) ) { - domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE; - } - boolean jacknifed_distances = false; - int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT; - double jacknife_ratio = JACKNIFE_RATIO_DEFAULT; - long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT; - if ( cla.isOptionSet( surfacing_old.JACKNIFE_OPTION ) ) { - if ( ( number_of_genomes < 3 ) || !perform_pwc ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use jacknife resampling analysis (-" - + surfacing_old.JACKNIFE_OPTION + "[=]) without pairwise analyses (" - + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "=)" ); - } - jacknifed_distances = true; - if ( cla.isOptionHasAValue( surfacing_old.JACKNIFE_OPTION ) ) { - try { - jacknife_resamplings = cla.getOptionValueAsInt( surfacing_old.JACKNIFE_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for number of resamplings" ); - } - if ( jacknife_resamplings < 2 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "attempt to use less than 2 resamplings" ); - } - } - if ( cla.isOptionSet( surfacing_old.JACKNIFE_RATIO_OPTION ) - && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RATIO_OPTION ) ) { - try { - jacknife_ratio = cla.getOptionValueAsDouble( surfacing_old.JACKNIFE_RATIO_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for jacknife ratio" ); - } - if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "attempt to use illegal value for jacknife ratio: " + jacknife_ratio ); - } - } - if ( cla.isOptionSet( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION ) - && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION ) ) { - try { - random_seed = cla.getOptionValueAsLong( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for random generator seed" ); - } - } - } - // boolean infer_species_trees = false; - // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) { - // if ( ( output_file == null ) || ( number_of_genomes < 3 ) - // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) { - // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-" - // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses (" - // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - // + "=)" ); - // } - // infer_species_trees = true; - // } - File[] intree_files = null; - Phylogeny[] intrees = null; - if ( cla.isOptionSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) { - // TODO FIXME if jacknife.... maybe not - if ( number_of_genomes < 3 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "cannot infer gains and losses on input species trees (-" - + surfacing_old.INPUT_SPECIES_TREE_OPTION - + " without pairwise analyses (" - + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "=)" ); - } - if ( !cla.isOptionValueSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input tree: -" - + surfacing_old.INPUT_SPECIES_TREE_OPTION + "=" ); - } - final String intrees_str = cla.getOptionValue( surfacing_old.INPUT_SPECIES_TREE_OPTION ); - if ( intrees_str.indexOf( "#" ) > 0 ) { - final String[] intrees_strs = intrees_str.split( "#" ); - intree_files = new File[ intrees_strs.length ]; - int i = 0; - for( final String s : intrees_strs ) { - intree_files[ i++ ] = new File( s.trim() ); - } - } - else { - intree_files = new File[ 1 ]; - intree_files[ 0 ] = new File( intrees_str ); - } - intrees = getIntrees( intree_files, number_of_genomes, input_file_properties ); - } - long random_number_seed_for_fitch_parsimony = 0l; - boolean radomize_fitch_parsimony = false; - if ( cla.isOptionSet( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for random number seed: -" - + surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=" ); - } - try { - random_number_seed_for_fitch_parsimony = cla - .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); - } - radomize_fitch_parsimony = true; - } - SortedSet filter = null; - if ( ( positive_filter_file != null ) || ( negative_filter_file != null ) - || ( negative_domains_filter_file != null ) ) { - filter = new TreeSet(); - if ( positive_filter_file != null ) { - processFilter( positive_filter_file, filter ); - } - else if ( negative_filter_file != null ) { - processFilter( negative_filter_file, filter ); - } - else if ( negative_domains_filter_file != null ) { - processFilter( negative_domains_filter_file, filter ); - } - } - Map>[] domain_id_to_secondary_features_maps = null; - File[] secondary_features_map_files = null; - final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); - if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { - SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); - } - if ( cla.isOptionSet( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { - if ( !cla.isOptionValueSet( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for secondary features map file: -" - + surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=" ); - } - final String[] secondary_features_map_files_strs = cla - .getOptionValue( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" ); - secondary_features_map_files = new File[ secondary_features_map_files_strs.length ]; - domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ]; - int i = 0; - for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) { - secondary_features_map_files[ i ] = new File( secondary_features_map_files_str ); - final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read secondary features map file: " - + error ); - } - try { - domain_id_to_secondary_features_maps[ i ] = SurfacingUtil - .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "cannot read secondary features map file: " + e.getMessage() ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "problem with contents of features map file [" - + secondary_features_map_files[ i ] + "]: " + e.getMessage() ); - } - i++; - } - } - if ( out_dir == null ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no output directory indicated (-" - + surfacing_old.OUTPUT_DIR_OPTION + "=)" ); - } - if ( output_file == null ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no name for (main) output file indicated (-" - + surfacing_old.OUTPUT_FILE_OPTION + "=)" ); - } - if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-" - + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=)" ); - } - if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "no (acceptable) go id to term mapping file provided ('GO OBO file') (-" - + surfacing_old.GO_OBO_FILE_USE_OPTION + "=)" ); - } - boolean display_histograms = false; - if ( cla.isOptionSet( surfacing_old.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 + " [" - + input_file_names_from_file.length + " input files]" ); - html_desc.append( "" + nl ); - } - if ( positive_filter_file != null ) { - final int filter_size = filter.size(); - System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size - + " domain ids]" ); - html_desc.append( "" + nl ); - } - if ( negative_filter_file != null ) { - final int filter_size = filter.size(); - System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size - + " domain ids]" ); - html_desc.append( "" + nl ); - } - if ( negative_domains_filter_file != null ) { - final int filter_size = filter.size(); - System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size - + " domain ids]" ); - html_desc.append( "" + nl ); - } - if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) { - String plus0 = ""; - for( final String s : plus_minus_analysis_high_copy_base_species ) { - plus0 += "+" + s + " "; - } - String plus1 = ""; - for( final String s : plus_minus_analysis_high_copy_target_species ) { - plus1 += "*" + s + " "; - } - String minus = ""; - for( final String s : plus_minus_analysis_high_low_copy_species ) { - minus += "-" + s + " "; - } - System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus ); - html_desc.append( "" + nl ); - } - if ( cutoff_scores_file != null ) { - System.out.println( "Cutoff scores file : " + cutoff_scores_file ); - html_desc.append( "" + nl ); - } - if ( e_value_max >= 0.0 ) { - System.out.println( "E-value maximum (inclusive) : " + e_value_max ); - html_desc.append( "" + nl ); - } - System.out.println( "Ignore DUFs : " + ignore_dufs ); - if ( ignore_virus_like_ids ) { - System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids ); - html_desc.append( "" + nl ); - } - html_desc.append( "" + nl ); - if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) { - System.out.println( "Max allowed domain overlap : " + max_allowed_overlap ); - html_desc.append( "" + nl ); - } - if ( no_engulfing_overlaps ) { - System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps ); - html_desc.append( "" + nl ); - } - System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec ); - html_desc - .append( "" + nl ); - System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains ); - html_desc - .append( "" + nl ); - System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); - html_desc.append( "" + nl ); - ; - System.out.println( "Consider directedness : " - + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) ); - html_desc.append( "" + nl ); - if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) { - System.out.println( "Consider adjacency : " - + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) ); - html_desc.append( "" - + nl ); - } - System.out.print( "Domain counts sort order : " ); - switch ( dc_sort_order ) { - case ALPHABETICAL_KEY_ID: - System.out.println( "alphabetical" ); - break; - case KEY_DOMAIN_COUNT: - System.out.println( "domain count" ); - break; - case KEY_DOMAIN_PROTEINS_COUNT: - System.out.println( "domain proteins count" ); - break; - case COMBINATIONS_COUNT: - System.out.println( "domain combinations count" ); - break; - default: - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for dc sort order" ); - } - if ( domain_id_to_go_ids_map != null ) { - System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count - + " mappings]" ); - html_desc.append( "" + nl ); - } - if ( go_terms != null ) { - System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" ); - html_desc.append( "" + nl ); - } - if ( go_namespace_limit != null ) { - System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() ); - html_desc.append( "" + nl ); - } - if ( perform_pwc ) { - System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix ); - html_desc.append( "" + nl ); - } - if ( out_dir != null ) { - System.out.println( "Output directory : " + out_dir ); - } - if ( query_domain_ids != null ) { - System.out.println( "Query domains (ordered) : " + query_domain_ids ); - html_desc.append( "" + nl ); - } - System.out.println( "Write similarities to : " + output_file ); - System.out.print( " Scoring method : " ); - html_desc.append( "" + nl ); - break; - case DOMAINS: - System.out.println( "domain counts based" ); - html_desc.append( "domain counts based" + "" + nl ); - break; - case PROTEINS: - System.out.println( "domain proteins counts based" ); - html_desc.append( "domain proteins counts based" + "" + nl ); - break; - default: - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for scoring" ); - } - System.out.print( " Sort by : " ); - html_desc.append( "" + nl ); - System.out.print( " Detailedness : " ); - switch ( detailedness ) { - case BASIC: - System.out.println( "basic" ); - break; - case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES: - System.out.println( "list combining domains for each species" ); - break; - case PUNCTILIOUS: - System.out.println( "punctilious" ); - break; - default: - ForesterUtil - .unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for detailedness" ); - } - System.out.print( " Print option : " ); - switch ( domain_similarity_print_option ) { - case HTML: - System.out.println( "HTML" ); - break; - case SIMPLE_TAB_DELIMITED: - System.out.println( "simple tab delimited" ); - break; - default: - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for print option" ); - } - System.out.print( " Species matrix : " + species_matrix ); - System.out.println(); - if ( perform_pwc ) { - System.out.println( "Pairwise comparisons: " ); - html_desc.append( "" ); - System.out.print( " Sort by : " ); - html_desc.append( "" + nl ); - if ( jacknifed_distances ) { - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" ); - System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) ); - System.out.println( " Random number seed : " + random_seed ); - } - // if ( infer_species_trees ) { - // html_desc.append( "" + nl ); - // System.out.println( " Infer species trees : true" ); - // } - if ( ( intrees != null ) && ( intrees.length > 0 ) ) { - for( final File intree_file : intree_files ) { - html_desc.append( "" + nl ); - System.out.println( " Intree for gain/loss pars.: " + intree_file ); - } - } - if ( radomize_fitch_parsimony ) { - html_desc.append( "" + nl ); - System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony ); - } - if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { - for( int i = 0; i < secondary_features_map_files.length; i++ ) { - html_desc.append( "" + nl ); - System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ] - + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" ); - if ( VERBOSE ) { - System.out.println(); - System.out.println( "Domain ids to secondary features map:" ); - for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) { - System.out.print( domain_id.getId() ); - System.out.print( " => " ); - for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) { - System.out.print( sec ); - System.out.print( " " ); - } - System.out.println(); - } - } - } - } - } // if ( perform_pwc ) { - System.out.println(); - html_desc.append( "" + nl ); - System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); - BufferedWriter[] query_domains_writer_ary = null; - List[] query_domain_ids_array = null; - if ( query_domain_ids != null ) { - final String[] query_domain_ids_str_array = query_domain_ids.split( "#" ); - query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ]; - query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ]; - for( int i = 0; i < query_domain_ids_str_array.length; i++ ) { - String query_domain_ids_str = query_domain_ids_str_array[ i ]; - final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" ); - final List query = new ArrayList(); - for( final String element : query_domain_ids_str_ary ) { - query.add( new DomainId( element ) ); - } - query_domain_ids_array[ i ] = query; - query_domain_ids_str = query_domain_ids_str.replace( '~', '_' ); - String protein_names_writer_str = query_domain_ids_str + surfacing_old.SEQ_EXTRACT_SUFFIX; - if ( out_dir != null ) { - protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str; - } - try { - query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "Could not open [" + protein_names_writer_str - + "]: " + e.getLocalizedMessage() ); - } - } - } - SortedMap> protein_lists_per_species = null; //This will only be created if neede. - boolean need_protein_lists_per_species = false; - if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) { - need_protein_lists_per_species = true; - } - if ( need_protein_lists_per_species ) { - protein_lists_per_species = new TreeMap>(); - } - final List gwcd_list = new ArrayList( number_of_genomes ); - final SortedSet all_domains_encountered = new TreeSet(); - final SortedSet all_bin_domain_combinations_encountered = new TreeSet(); - List all_bin_domain_combinations_gained_fitch = null; - List all_bin_domain_combinations_lost_fitch = null; - if ( ( intrees != null ) && ( intrees.length == 1 ) ) { - all_bin_domain_combinations_gained_fitch = new ArrayList(); - all_bin_domain_combinations_lost_fitch = new ArrayList(); - } - final DomainLengthsTable domain_lengths_table = new DomainLengthsTable(); - final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + D_PROMISCUITY_FILE_SUFFIX ); - BufferedWriter per_genome_domain_promiscuity_statistics_writer = null; - try { - per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) ); - per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "N:\t" ); - per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:" - + ForesterUtil.LINE_SEPARATOR ); - } - catch ( final IOException e2 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e2.getMessage() ); - } - for( int i = 0; i < number_of_genomes; ++i ) { - System.out.println(); - System.out.println( ( i + 1 ) + "/" + number_of_genomes ); - System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] ); - HmmPfamOutputParser parser = null; - if ( ( positive_filter_file != null ) || ( negative_filter_file != null ) - || ( negative_domains_filter_file != null ) ) { - HmmPfamOutputParser.FilterType filter_type = HmmPfamOutputParser.FilterType.NONE; - if ( positive_filter_file != null ) { - filter_type = HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN; - } - else if ( negative_filter_file != null ) { - filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN; - } - else if ( negative_domains_filter_file != null ) { - filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN; - } - parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ), - input_file_properties[ i ][ 1 ], - input_file_properties[ i ][ 2 ], - filter, - filter_type ); - } - else { - parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ), - input_file_properties[ i ][ 1 ], - input_file_properties[ i ][ 2 ] ); - } - if ( e_value_max >= 0.0 ) { - parser.setEValueMaximum( e_value_max ); - } - parser.setIgnoreDufs( ignore_dufs ); - parser.setIgnoreVirusLikeIds( ignore_virus_like_ids ); - parser.setIgnoreEngulfedDomains( no_engulfing_overlaps ); - if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) { - parser.setMaxAllowedOverlap( max_allowed_overlap ); - } - parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); - if ( individual_domain_score_cutoffs != null ) { - parser.setIndividualDomainScoreCutoffs( individual_domain_score_cutoffs ); - } - parser.setAllowNonUniqueQuery( ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT ); - parser.setVerbose( VERBOSE_DEFAULT ); - List protein_list = null; - try { - protein_list = parser.parse(); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); - } - catch ( final Exception e ) { - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, e.getMessage(), e ); - } - if ( VERBOSE ) { - System.out.println( "Domains ignored due to negative domain filter: " ); - ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() ); - System.out.println( "Domains ignored due to virus like id: " ); - ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() ); - } - System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() ); - System.out.println( "Number of proteins stored : " + protein_list.size() ); - System.out.println( "Domains encountered : " + parser.getDomainsEncountered() ); - System.out.println( "Domains stored : " + parser.getDomainsStored() ); - System.out.println( "Distinct domains stored : " - + parser.getDomainsStoredSet().size() ); - System.out.println( "Domains ignored due to individual score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff() ); - System.out.println( "Domains ignored due to E-value : " - + parser.getDomainsIgnoredDueToEval() ); - System.out.println( "Domains ignored due to DUF designation : " - + parser.getDomainsIgnoredDueToDuf() ); - if ( ignore_virus_like_ids ) { - System.out.println( "Domains ignored due virus like ids : " - + parser.getDomainsIgnoredDueToVirusLikeIds() ); - } - System.out.println( "Domains ignored due negative domain filter : " - + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); - System.out.println( "Domains ignored due to overlap : " - + parser.getDomainsIgnoredDueToOverlap() ); - if ( negative_filter_file != null ) { - System.out.println( "Proteins ignored due to negative filter : " - + parser.getProteinsIgnoredDueToFilter() ); - } - if ( positive_filter_file != null ) { - System.out.println( "Proteins ignored due to positive filter : " - + parser.getProteinsIgnoredDueToFilter() ); - } - System.out.println( "Time for processing : " + parser.getTime() + "ms" ); - html_desc.append( "" + nl ); - // domain_partner_counts_array[ i ] = - // Methods.getDomainPartnerCounts( protein_domain_collections_array[ - // i ], - // false, input_file_properties[ i ][ 1 ] ); - 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 ) ); - domain_lengths_table.addLengths( protein_list ); - if ( gwcd_list.get( i ).getSize() > 0 ) { - SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties, - out_dir, - per_genome_domain_promiscuity_statistics_writer, - gwcd_list.get( i ), - i, - dc_sort_order ); - if ( output_binary_domain_combinationsfor_graph_analysis ) { - SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties, - out_dir, - gwcd_list.get( i ), - i, - dc_sort_order ); - } - SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered ); - SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ), - all_bin_domain_combinations_encountered ); - } - if ( query_domains_writer_ary != null ) { - for( int j = 0; j < query_domain_ids_array.length; j++ ) { - try { - SurfacingUtil.extractProteinNames( protein_list, - query_domain_ids_array[ j ], - query_domains_writer_ary[ j ], - "\t" ); - query_domains_writer_ary[ j ].flush(); - } - catch ( final IOException e ) { - e.printStackTrace(); - } - } - } - if ( need_protein_lists_per_species ) { - protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list ); - } - System.gc(); - } // for( int i = 0; i < number_of_hmmpfam_files_to_analyze; ++i ) { - try { - per_genome_domain_promiscuity_statistics_writer.flush(); - per_genome_domain_promiscuity_statistics_writer.close(); - } - catch ( final IOException e2 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e2.toString() ); - } - 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 { - query_domains_writer_ary[ j ].close(); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.toString() ); - } - } - } - if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) { - try { - SurfacingUtil.executeDomainLengthAnalysis( input_file_properties, - number_of_genomes, - domain_lengths_table, - domain_lengths_analysis_outfile ); - } - catch ( final IOException e1 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e1.toString() ); - } - System.out.println(); - ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile ); - System.out.println(); - } - final long analysis_start_time = new Date().getTime(); - PairwiseDomainSimilarityCalculator pw_calc = null; - // double[] values_for_all_scores_histogram = null; - final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field, - sort_by_species_count_first, - number_of_genomes == 2 ); - switch ( scoring ) { - case COMBINATIONS: - pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator(); - break; - case DOMAINS: - pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator(); - break; - case PROTEINS: - pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator(); - break; - default: - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for scoring" ); - } - DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE; - if ( domain_id_to_go_ids_map != null ) { - go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL; - } - final SortedSet similarities = calc - .calculateSimilarities( pw_calc, - gwcd_list, - ignore_domains_without_combs_in_all_spec, - ignore_species_specific_domains ); - SurfacingUtil.decoratePrintableDomainSimilarities( similarities, - detailedness, - go_annotation_output, - go_id_to_term_map, - go_namespace_limit ); - DescriptiveStatistics pw_stats = null; - try { - String my_outfile = output_file.toString(); - if ( !my_outfile.endsWith( ".html" ) ) { - my_outfile += ".html"; - } - 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(); - for( int i = 0; i < number_of_genomes; i++ ) { - species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) ); - } - } - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "" + nl ); - html_desc.append( "
Produced by:" + surfacing_old.PRG_NAME + "
Version:" + surfacing_old.PRG_VERSION + "
Release Date:" + surfacing_old.PRG_DATE + "
Contact:" + surfacing_old.E_MAIL + "
WWW:" + surfacing_old.WWW + "
Input files names from:" + input_files_file + " [" - + input_file_names_from_file.length + " input files]
Positive protein filter:" + positive_filter_file + " [" + filter_size - + " domain ids]
Negative protein filter:" + negative_filter_file + " [" + filter_size - + " domain ids]
Negative domain filter:" + negative_domains_filter_file + " [" - + filter_size + " domain ids]
Plus-minus analysis:" + plus1 + "&& " + plus0 + "&& " + minus - + "
Cutoff scores file:" + cutoff_scores_file + "
E-value maximum (inclusive):" + e_value_max + "
Ignore virus, phage, transposition related ids:" - + ignore_virus_like_ids + "
Ignore DUFs:" + ignore_dufs + "
Max allowed domain overlap:" + max_allowed_overlap + "
Ignore (lower confidence) engulfed domains:" + no_engulfing_overlaps - + "
Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_domains_without_combs_in_all_spec + "
Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_species_specific_domains + "
Ignore combination with self for domain combination similarity analyses:" - + ignore_combination_with_same + "
Consider directedness of binary domain combinations:" - + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "
Consider djacency of binary domain combinations:" - + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "
Pfam to GO mappings from:" + pfam_to_go_file + " [" - + domain_id_to_go_ids_count + " mappings]" + "
GO terms from:" + go_obo_file + " [" + go_terms.size() + " terms]" - + "
Limit GO terms to" + go_namespace_limit + "
Suffix for PWC files" + automated_pairwise_comparison_suffix - + "
" + query_domain_ids + "
Scoring method:" ); - switch ( scoring ) { - case COMBINATIONS: - System.out.println( "domain combinations based" ); - html_desc.append( "domain combinations based" + "
Sort by:" ); - switch ( domain_similarity_sort_field ) { - case MIN: - System.out.print( "score minimum" ); - html_desc.append( "score minimum" ); - break; - case MAX: - System.out.print( "score maximum" ); - html_desc.append( "score maximum" ); - break; - case MEAN: - System.out.print( "score mean" ); - html_desc.append( "score mean" ); - break; - case SD: - System.out.print( "score standard deviation" ); - html_desc.append( "score standard deviation" ); - break; - case SPECIES_COUNT: - System.out.print( "species number" ); - html_desc.append( "species number" ); - break; - case DOMAIN_ID: - System.out.print( "alphabetical domain identifier" ); - html_desc.append( "alphabetical domain identifier" ); - break; - case MAX_DIFFERENCE: - System.out.print( "(maximal) difference" ); - html_desc.append( "(maximal) difference" ); - break; - case ABS_MAX_COUNTS_DIFFERENCE: - System.out.print( "absolute (maximal) counts difference" ); - html_desc.append( "absolute (maximal) counts difference" ); - break; - case MAX_COUNTS_DIFFERENCE: - System.out.print( "(maximal) counts difference" ); - html_desc.append( "(maximal) counts difference" ); - break; - default: - ForesterUtil - .unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for similarities" ); - } - if ( sort_by_species_count_first ) { - System.out.println( " (sort by species count first)" ); - html_desc.append( " (sort by species count first)" ); - } - else { - System.out.println(); - } - html_desc.append( "
Pairwise comparisons:
Sort by:" ); - switch ( domain_similarity_sort_field_for_automated_pwc ) { - case MEAN: - System.out.print( "score mean" ); - html_desc.append( "score mean" ); - break; - case DOMAIN_ID: - System.out.print( "alphabetical domain identifier" ); - html_desc.append( "alphabetical domain identifier" ); - break; - case MAX_DIFFERENCE: - System.out.print( "difference" ); - html_desc.append( "difference" ); - break; - case ABS_MAX_COUNTS_DIFFERENCE: - System.out.print( "absolute counts difference" ); - html_desc.append( "absolute counts difference" ); - break; - case MAX_COUNTS_DIFFERENCE: - System.out.print( "counts difference" ); - html_desc.append( "counts difference" ); - break; - default: - ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, - "unknown value for sorting for similarities" ); - } - System.out.println(); - html_desc.append( "
Jacknife:" + jacknife_resamplings + " resamplings
Jacknife ratio:" + ForesterUtil.round( jacknife_ratio, 2 ) - + "
Jacknife random number seed:" + random_seed + "
Infer species trees:true
Intree for gain/loss parsimony analysis:" + intree_file - + "
Random number seed for Fitch parsimony analysis:" - + random_number_seed_for_fitch_parsimony + "
Secondary features map file:" - + secondary_features_map_files[ i ] + "
Command line:" + cla.getCommandLineArgsAsString() + "
" + input_file_properties[ i ][ 0 ] + " [species: " - + input_file_properties[ i ][ 1 ] + "]" + ":domains analyzed: " - + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: " - + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf() - + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds() - + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter() - + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" ); - if ( negative_filter_file != null ) { - html_desc.append( "; proteins ignored due to negative filter: " - + parser.getProteinsIgnoredDueToFilter() ); - } - if ( positive_filter_file != null ) { - html_desc.append( "; proteins ignored due to positive filter: " - + parser.getProteinsIgnoredDueToFilter() ); - } - html_desc.append( "
Sum of all distinct binary combinations:" - + all_bin_domain_combinations_encountered.size() + "
Sum of all distinct domains:" + all_domains_encountered.size() - + "
Analysis date/time:" - + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) - + "
" + nl ); - pw_stats = SurfacingUtil - .writeDomainSimilaritiesToFile( html_desc, - new StringBuilder( number_of_genomes + " genomes" ), - writer, - similarities, - number_of_genomes == 2, - species_order, - domain_similarity_print_option, - domain_similarity_sort_field, - scoring, - true ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, - "Wrote main output (includes domain similarities) to: \"" - + ( out_dir == null ? my_outfile : out_dir - + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "Failed to write similarites to: \"" + output_file - + "\" [" + e.getMessage() + "]" ); - } - System.out.println(); - // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray(); - final Species[] species = new Species[ number_of_genomes ]; - for( int i = 0; i < number_of_genomes; ++i ) { - species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] ); - } - List inferred_trees = null; - if ( ( number_of_genomes > 2 ) && perform_pwc ) { - final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator(); - pwgc.performPairwiseComparisons( html_desc, - sort_by_species_count_first, - detailedness, - ignore_domains_without_combs_in_all_spec, - ignore_species_specific_domains, - domain_similarity_sort_field_for_automated_pwc, - domain_similarity_print_option, - scoring, - domain_id_to_go_ids_map, - go_id_to_term_map, - go_namespace_limit, - species, - number_of_genomes, - gwcd_list, - pw_calc, - automated_pairwise_comparison_suffix, - true, - surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_PREFIX, - surfacing_old.PRG_NAME, - display_histograms, - out_dir, - write_pwc_files ); - String matrix_output_file = new String( output_file.toString() ); - if ( matrix_output_file.indexOf( '.' ) > 1 ) { - matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) ); - } - if ( out_dir != null ) { - 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_old.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getDomainDistanceScoresMeans() ); - SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + surfacing_old.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedBinaryCombinationsBasedDistances() ); - SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + surfacing_old.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedDomainsBasedDistances() ); - final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing_old.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getDomainDistanceScoresMeans().get( 0 ) ); - final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing_old.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); - final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing_old.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances().get( 0 ) ); - inferred_trees = new ArrayList(); - 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, - gwcd_list, - true, - jacknife_resamplings, - jacknife_ratio, - random_seed ); - SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + "_" - + ForesterUtil.round( jacknife_ratio, 2 ) - + "_" - + jacknife_resamplings - + surfacing_old.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_old.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 - // .getSharedBinaryCombinationsBasedDistances() ); - // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings - // + 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 ); - } - writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list ); - if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) { - final StringBuilder parameters_sb = createParametersAsString( ignore_dufs, - e_value_max, - max_allowed_overlap, - no_engulfing_overlaps, - cutoff_scores_file, - dc_type ); - String s = "_"; - if ( radomize_fitch_parsimony ) { - s += random_number_seed_for_fitch_parsimony + "_"; - } - int i = 0; - for( final Phylogeny intree : intrees ) { - final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s - + ForesterUtil.removeSuffix( intree_files[ i ].toString() ); - final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree, - gwcd_list ); - SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony, - radomize_fitch_parsimony, - outfile_name, - domain_parsimony, - intree, - domain_id_to_go_ids_map, - go_id_to_term_map, - go_namespace_limit, - parameters_sb.toString(), - domain_id_to_secondary_features_maps, - positive_filter_file == null ? null : filter, - output_binary_domain_combinationsfor_graph_analysis, - all_bin_domain_combinations_gained_fitch, - all_bin_domain_combinations_lost_fitch, - dc_type ); - // 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 ) ) { - int j = 0; - for( final Map> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) { - final Map mapping_results_map = new TreeMap(); - final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator - .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map ); - SurfacingUtil - .executeParsimonyAnalysisForSecondaryFeatures( outfile_name - + "_" - + secondary_features_map_files[ j++ ], - secondary_features_parsimony, - intree, - parameters_sb.toString(), - mapping_results_map ); - if ( i == 0 ) { - System.out.println(); - System.out.println( "Mapping to secondary features:" ); - for( final Species spec : mapping_results_map.keySet() ) { - final MappingResults mapping_results = mapping_results_map.get( spec ); - final int total_domains = mapping_results.getSumOfFailures() - + mapping_results.getSumOfSuccesses(); - System.out.print( spec + ":" ); - System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() ); - System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() ); - if ( total_domains > 0 ) { - System.out.println( ", mapped ratio = " - + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" ); - } - else { - System.out.println( ", mapped ratio = n/a (total domains = 0 )" ); - } - } - } - } - } - i++; - } // for( final Phylogeny intree : intrees ) { - } - if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) { - executePlusMinusAnalysis( output_file, - plus_minus_analysis_high_copy_base_species, - plus_minus_analysis_high_copy_target_species, - plus_minus_analysis_high_low_copy_species, - gwcd_list, - protein_lists_per_species, - domain_id_to_go_ids_map, - go_id_to_term_map, - 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++; - // } - // } - if ( all_bin_domain_combinations_gained_fitch != null ) { - try { - executeFitchGainsAnalysis( new File( output_file - + surfacing_old.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_gained_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - true ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); - } - } - if ( all_bin_domain_combinations_lost_fitch != null ) { - try { - executeFitchGainsAnalysis( new File( output_file - + surfacing_old.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_lost_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - false ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); - } - } - 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_old.WWW ); - System.out.println(); - ForesterUtil.programMessage( PRG_NAME, "OK" ); - System.out.println(); - } - - private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree, - final String[][] input_file_properties ) { - final String[] genomes = new String[ input_file_properties.length ]; - for( int i = 0; i < input_file_properties.length; ++i ) { - if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ] - + "] is not unique in input tree " + intree.getName() ); - } - genomes[ i ] = input_file_properties[ i ][ 1 ]; - } - PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree ); - for( int i = 0; i < input_file_properties.length; ++i ) { - try { - intree.getNode( input_file_properties[ i ][ 1 ] ); - } - catch ( final IllegalArgumentException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ] - + "] not present/not unique in input tree" ); - } - } - } - - // 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:" ); - System.out.println(); - System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." - + surfacing_old.PRG_NAME - + " [options] [external node name 1] [name 2] ... [name n]" ); - System.out.println(); - System.out.println( " Note: This software might need a significant amount of memory (heap space);" ); - System.out - .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); - System.out.println(); - System.out.println( " Options: " ); - System.out.println( surfacing_old.DETAILEDNESS_OPTION - + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" ); - System.out.println( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION - + ": to ignore combinations with self (default: not to ignore)" ); - System.out - .println( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION - + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); - System.out - .println( surfacing_old.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION - + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); - System.out.println( surfacing_old.NOT_IGNORE_DUFS_OPTION - + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); - System.out - .println( surfacing_old.IGNORE_VIRAL_IDS - + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); - System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: " - + DOMAIN_SORT_FILD_DEFAULT + ")" ); - System.out.println( surfacing_old.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" ); - System.out.println( surfacing_old.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" ); - System.out.println( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" ); - System.out - .println( surfacing_old.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" ); - System.out.println( surfacing_old.SPECIES_MATRIX_OPTION + ": species matrix" ); - System.out.println( surfacing_old.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" ); - System.out.println( surfacing_old.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:" - + DOMAINS_SORT_ORDER_DEFAULT + ")" ); - System.out.println( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:" - + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" ); - System.out.println( surfacing_old.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" ); - System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION - + ": sort by species count first" ); - System.out.println( surfacing_old.OUTPUT_DIR_OPTION + ": output directory" ); - System.out.println( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" ); - System.out.println( surfacing_old.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" ); - System.out.println( surfacing_old.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" ); - System.out.println( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "[=]: to perform pairwise comparison based analyses" ); - System.out.println( surfacing_old.INPUT_SPECIES_TREE_OPTION - + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); - System.out.println( surfacing_old.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 + "]" ); - System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: " - + JACKNIFE_RATIO_DEFAULT + "]" ); - System.out.println( JACKNIFE_RANDOM_SEED_OPTION - + ": seed for random number generator for jacknife resampling [default: " - + JACKNIFE_RANDOM_SEED_DEFAULT + "]" ); - // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION - // + ": to infer NJ species trees based on shared domains/binary domain combinations" ); - System.out - .println( surfacing_old.INPUT_SPECIES_TREE_OPTION - + "=: to infer domain/binary domain combination gains/losses on given species trees" ); - System.out.println( surfacing_old.FILTER_POSITIVE_OPTION - + "=: to filter out proteins not containing at least one domain listed in " ); - System.out.println( surfacing_old.FILTER_NEGATIVE_OPTION - + "=: to filter out proteins containing at least one domain listed in " ); - System.out.println( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION - + "=: to filter out (ignore) domains listed in " ); - System.out.println( surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=: to read input files from " ); - System.out - .println( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION - + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); - System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS - + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); - System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY - + ": to consider directedness and adjacency in binary combinations" ); - System.out - .println( surfacing_old.SEQ_EXTRACT_OPTION - + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); - System.out.println( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE - + "=: to perfom parsimony analysis on secondary features" ); - System.out.println( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); - System.out.println( surfacing_old.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - + ": to output binary domain combinations for (downstream) graph analysis" ); - System.out.println( surfacing_old.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" ); - System.out.println(); - 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" - + " -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" ); - System.out.println(); - } - - private static void processFilter( final File filter_file, final SortedSet filter ) { - SortedSet filter_str = null; - try { - filter_str = ForesterUtil.file2set( filter_file ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); - } - if ( filter_str != null ) { - for( final String string : filter_str ) { - filter.add( new DomainId( string ) ); - } - } - if ( VERBOSE ) { - System.out.println( "Filter:" ); - for( final DomainId domainId : filter ) { - System.out.println( domainId.getId() ); - } - } - } - - private static String[][] processInputFileNames( final String[] names ) { - final String[][] input_file_properties = new String[ names.length ][]; - for( int i = 0; i < names.length; ++i ) { - if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) { - input_file_properties[ i ] = new String[ 3 ]; - input_file_properties[ i ][ 0 ] = names[ i ]; - input_file_properties[ i ][ 1 ] = names[ i ]; - input_file_properties[ i ][ 2 ] = DEFAULT_SEARCH_PARAMETER; - } - else { - input_file_properties[ i ] = names[ i ].split( surfacing_old.SEPARATOR_FOR_INPUT_VALUES + "" ); - if ( input_file_properties[ i ].length != 3 ) { - ForesterUtil - .fatalError( surfacing_old.PRG_NAME, - "properties for the input files (hmmpfam output) are expected " - + "to be in the following format \"##\" (or just one word, which is both the filename and the species id), instead received \"" - + names[ i ] + "\"" ); - } - } - final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) ); - if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, error ); - } - } - return input_file_properties; - } - - private static void processPlusMinusAnalysisOption( final CommandLineArguments cla, - final List high_copy_base, - final List high_copy_target, - final List low_copy, - final List numbers ) { - if ( cla.isOptionSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) { - if ( !cla.isOptionValueSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for 'plus-minus' file: -" - + surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=" ); - } - final File plus_minus_file = new File( cla.getOptionValue( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ); - final String msg = ForesterUtil.isReadableFile( plus_minus_file ); - if ( !ForesterUtil.isEmpty( msg ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " - + msg ); - } - processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers ); - } - } - - // First numbers is minimal difference, second is factor. - private static void processPlusMinusFile( final File plus_minus_file, - final List high_copy_base, - final List high_copy_target, - final List low_copy, - final List numbers ) { - Set species_set = null; - int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT; - double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT; - try { - species_set = ForesterUtil.file2set( plus_minus_file ); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); - } - if ( species_set != null ) { - for( final String species : species_set ) { - final String species_trimmed = species.substring( 1 ); - if ( species.startsWith( "+" ) ) { - if ( low_copy.contains( species_trimmed ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \"" - + species_trimmed + "\"" ); - } - high_copy_base.add( species_trimmed ); - } - else if ( species.startsWith( "*" ) ) { - if ( low_copy.contains( species_trimmed ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \"" - + species_trimmed + "\"" ); - } - high_copy_target.add( species_trimmed ); - } - else if ( species.startsWith( "-" ) ) { - if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \"" - + species_trimmed + "\"" ); - } - low_copy.add( species_trimmed ); - } - else if ( species.startsWith( "$D" ) ) { - try { - min_diff = Integer.parseInt( species.substring( 3 ) ); - } - catch ( final NumberFormatException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "could not parse integer value for minimal difference from: \"" - + species.substring( 3 ) + "\"" ); - } - } - else if ( species.startsWith( "$F" ) ) { - try { - factor = Double.parseDouble( species.substring( 3 ) ); - } - catch ( final NumberFormatException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, - "could not parse double value for factor from: \"" - + species.substring( 3 ) + "\"" ); - } - } - else if ( species.startsWith( "#" ) ) { - // Comment, ignore. - } - else { - ForesterUtil - .fatalError( surfacing_old.PRG_NAME, - "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=' minimal Difference (default is 1), '$F=' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \"" - + species + "\"" ); - } - numbers.add( new Integer( min_diff + "" ) ); - numbers.add( new Double( factor + "" ) ); - } - } - else { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, "'plus minus' file [" + plus_minus_file - + "] appears empty" ); - } - } - - private static void writePresentToNexus( final File output_file, - final File positive_filter_file, - final SortedSet filter, - final List gwcd_list ) { - try { - SurfacingUtil - .writeMatrixToFile( DomainParsimonyCalculator - .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null - : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY ); - SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator - .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file - + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY ); - } - catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() ); - } - } - - private static void writeProteinListsForAllSpecies( final File output_dir, - final SortedMap> protein_lists_per_species, - final List gwcd_list ) { - final SortedSet all_domains = new TreeSet(); - for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { - all_domains.addAll( gwcd.getAllDomainIds() ); - } - for( final DomainId domain : all_domains ) { - final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX ); - 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" ); - proteins_file_writer.close(); - } - catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() ); - } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote proteins list to \"" + out + "\"" ); - } - } -} diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 8b1ffe7..6e58f58 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -48,7 +48,7 @@ import java.util.TreeSet; import java.util.regex.Matcher; import java.util.regex.Pattern; -import org.forester.application.surfacing_old; +import org.forester.application.surfacing; import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -174,7 +174,7 @@ public final class SurfacingUtil { public static void checkForOutputFileWriteability( final File outfile ) { final String error = ForesterUtil.isWritableFile( outfile ); if ( !ForesterUtil.isEmpty( error ) ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, error ); + ForesterUtil.fatalError( surfacing.PRG_NAME, error ); } } @@ -437,24 +437,23 @@ public final class SurfacingUtil { domain_parsimony.executeDolloParsimonyOnDomainPresence(); } SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.GAIN, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_D, + outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); + SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), + CharacterStateMatrix.GainLossStates.LOSS, + outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D, sep, ForesterUtil.LINE_SEPARATOR, null ); - SurfacingUtil - .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.LOSS, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_D, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null ); + + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null ); //HTML: writeBinaryStatesMatrixToList( domain_id_to_go_ids_map, go_id_to_term_map, @@ -462,7 +461,7 @@ public final class SurfacingUtil { false, domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.GAIN, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D, + outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D, sep, ForesterUtil.LINE_SEPARATOR, "Dollo Parsimony | Gains | Domains", @@ -477,7 +476,7 @@ public final class SurfacingUtil { false, domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.LOSS, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D, + outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D, sep, ForesterUtil.LINE_SEPARATOR, "Dollo Parsimony | Losses | Domains", @@ -492,7 +491,7 @@ public final class SurfacingUtil { false, domain_parsimony.getGainLossMatrix(), null, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D, + outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D, sep, ForesterUtil.LINE_SEPARATOR, "Dollo Parsimony | Present | Domains", @@ -508,14 +507,14 @@ public final class SurfacingUtil { "dollo_on_domains_" + outfile_name, parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name - + surfacing_old.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); + + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); try { writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" ); writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" ); } catch ( final IOException e ) { e.printStackTrace(); - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() ); } if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) { // FITCH DOMAIN COMBINATIONS @@ -530,25 +529,25 @@ public final class SurfacingUtil { domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false ); } SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); - SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.GAIN, - outfile_name - + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_BC, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); SurfacingUtil .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.LOSS, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_BC, + CharacterStateMatrix.GainLossStates.GAIN, + outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); + SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), + CharacterStateMatrix.GainLossStates.LOSS, + outfile_name + + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); + + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); if ( all_binary_domains_combination_gained_fitch != null ) { collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), dc_type, @@ -567,7 +566,7 @@ public final class SurfacingUtil { .getGainLossMatrix(), null, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS, + + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS, sep, ForesterUtil.LINE_SEPARATOR, BinaryDomainCombination.OutputFormat.DOT ); @@ -579,7 +578,7 @@ public final class SurfacingUtil { true, domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.GAIN, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC, + outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC, sep, ForesterUtil.LINE_SEPARATOR, "Fitch Parsimony | Gains | Domain Combinations", @@ -594,7 +593,7 @@ public final class SurfacingUtil { true, domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.LOSS, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC, + outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC, sep, ForesterUtil.LINE_SEPARATOR, "Fitch Parsimony | Losses | Domain Combinations", @@ -609,7 +608,7 @@ public final class SurfacingUtil { true, domain_parsimony.getGainLossMatrix(), null, - outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC, + outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC, sep, ForesterUtil.LINE_SEPARATOR, "Fitch Parsimony | Present | Domain Combinations", @@ -622,13 +621,11 @@ public final class SurfacingUtil { go_id_to_term_map, outfile_name, all_pfams_encountered ); - writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, - all_pfams_gained_as_domains ); - writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains ); - writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DC_SUFFIX, + writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains ); + writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains ); + writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX, all_pfams_gained_as_dom_combinations ); - writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DC_SUFFIX, - all_pfams_lost_as_dom_combinations ); + writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations ); preparePhylogeny( local_phylogeny_l, domain_parsimony, date_time, @@ -637,8 +634,63 @@ public final class SurfacingUtil { "fitch_on_binary_domain_combinations_" + outfile_name, parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name - + surfacing_old.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH ); + + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH ); + calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX ); + } + } + + private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l, + final String outfilename_for_counts, + final String outfilename_for_dc ) { + try { + final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) ); + final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) ); + final SortedMap dc_gain_counts = new TreeMap(); + for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + final Set gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters(); + for( final String dc : gained_dc ) { + if ( dc_gain_counts.containsKey( dc ) ) { + dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 ); + } + else { + dc_gain_counts.put( dc, 1 ); + } + } + } + final SortedMap histogram = new TreeMap(); + final SortedMap domain_lists = new TreeMap(); + final Set dcs = dc_gain_counts.keySet(); + for( final String dc : dcs ) { + final int count = dc_gain_counts.get( dc ); + if ( histogram.containsKey( count ) ) { + histogram.put( count, histogram.get( count ) + 1 ); + domain_lists.put( count, domain_lists.get( count ).append( ", " + dc ) ); + } + else { + histogram.put( count, 1 ); + domain_lists.put( count, new StringBuilder( dc ) ); + } + } + final Set histogram_keys = histogram.keySet(); + for( final Integer histogram_key : histogram_keys ) { + final int count = histogram.get( histogram_key ); + final StringBuilder dc = domain_lists.get( histogram_key ); + out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR ); + out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR ); + } + out_counts.close(); + out_dc.close(); + } + catch ( final IOException e ) { + ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e ); } + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to [" + + outfilename_for_counts + "]" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to [" + + outfilename_for_dc + "]" ); } public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name, @@ -649,20 +701,20 @@ public final class SurfacingUtil { final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR; final String date_time = ForesterUtil.getCurrentDateTime(); System.out.println(); - writeToNexus( outfile_name + surfacing_old.NEXUS_SECONDARY_FEATURES, + writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES, secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ), phylogeny ); final Phylogeny local_phylogeny_copy = phylogeny.copy(); secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map ); SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); SurfacingUtil .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.GAIN, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES, + + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES, sep, ForesterUtil.LINE_SEPARATOR, null ); @@ -670,7 +722,7 @@ public final class SurfacingUtil { .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.LOSS, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES, + + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES, sep, ForesterUtil.LINE_SEPARATOR, null ); @@ -678,7 +730,7 @@ public final class SurfacingUtil { .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), null, outfile_name - + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES, + + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES, sep, ForesterUtil.LINE_SEPARATOR, null ); @@ -689,7 +741,7 @@ public final class SurfacingUtil { "dollo_on_secondary_features_" + outfile_name, parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name - + surfacing_old.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); + + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); } public static void extractProteinNames( final List proteins, @@ -921,7 +973,7 @@ public final class SurfacingUtil { if ( !get_gains ) { state = CharacterStateMatrix.GainLossStates.LOSS; } - final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES, + final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES, false, state, outdir ); @@ -946,11 +998,10 @@ public final class SurfacingUtil { final Map go_id_to_term_map, final String outfile_name, final SortedSet all_pfams_encountered ) { - final File all_pfams_encountered_file = new File( outfile_name + surfacing_old.ALL_PFAMS_ENCOUNTERED_SUFFIX ); + final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX ); final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name - + surfacing_old.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX ); - final File encountered_pfams_summary_file = new File( outfile_name - + surfacing_old.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX ); + + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX ); + final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX ); int biological_process_counter = 0; int cellular_component_counter = 0; int molecular_function_counter = 0; @@ -1017,41 +1068,41 @@ public final class SurfacingUtil { } all_pfams_encountered_writer.close(); all_pfams_encountered_with_go_annotation_writer.close(); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + all_pfams_encountered.size() + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size() + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote summary (including all [" + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all [" + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \"" + encountered_pfams_summary_file + "\"" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Sum of Pfams encountered : " + ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered : " + all_pfams_encountered.size() ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without a mapping : " + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : " + pfams_without_mappings_counter + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without mapping to proc. or func. : " + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : " + pfams_without_mappings_to_bp_or_mf_counter + " [" + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : " + pfams_with_mappings_counter + " [" + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping to proc. or func. : " + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : " + pfams_with_mappings_to_bp_or_mf_counter + " [" + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: " + biological_process_counter + " [" + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: " + molecular_function_counter + " [" + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" ); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, + ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: " + cellular_component_counter + " [" + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) @@ -1085,7 +1136,7 @@ public final class SurfacingUtil { summary_writer.close(); } catch ( final IOException e ) { - ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e ); + ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e ); } } @@ -1095,7 +1146,7 @@ public final class SurfacingUtil { final int i, final GenomeWideCombinableDomainsSortOrder dc_sort_order ) { File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ] - + surfacing_old.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS ); + + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS ); if ( output_dir != null ) { dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot ); } @@ -1111,9 +1162,9 @@ public final class SurfacingUtil { out_dot.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote binary domain combination for \"" + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \"" + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", " + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" ); } @@ -1245,9 +1296,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" ); } public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix matrix, @@ -1279,7 +1330,7 @@ public final class SurfacingUtil { bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) ); } catch ( final Exception e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() ); } out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() ); out.write( character_separator ); @@ -1290,9 +1341,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" ); } public static void writeBinaryStatesMatrixToList( final Map> domain_id_to_go_ids_map, @@ -1327,7 +1378,7 @@ public final class SurfacingUtil { } try { final Writer out = new BufferedWriter( new FileWriter( outfile ) ); - final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES, + final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES, domain_combinations, state, filename ); @@ -1470,10 +1521,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename - + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" ); } public static void writeBinaryStatesMatrixToListORIGIG( final Map> domain_id_to_go_ids_map, @@ -1508,7 +1558,7 @@ public final class SurfacingUtil { } try { final Writer out = new BufferedWriter( new FileWriter( outfile ) ); - final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES, + final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES, domain_combinations, state, filename ); @@ -1646,10 +1696,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename - + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" ); } public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties, @@ -1659,7 +1708,7 @@ public final class SurfacingUtil { final int i, final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) { File dc_outfile = new File( input_file_properties[ i ][ 0 ] - + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ); + + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ); if ( output_dir != null ) { dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile ); } @@ -1670,7 +1719,7 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics(); try { @@ -1694,15 +1743,15 @@ public final class SurfacingUtil { per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } if ( input_file_properties[ i ].length == 3 ) { - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \"" + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \"" + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", " + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" ); } else { - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \"" + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \"" + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \"" + dc_outfile + "\"" ); } @@ -2273,9 +2322,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote matrix: \"" + filename + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" ); } public static void writeMatrixToFile( final File matrix_outfile, final List matrices ) { @@ -2290,9 +2339,9 @@ public final class SurfacingUtil { out.close(); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" ); } private static void writePfamsToFile( final String outfile_name, final SortedSet pfams ) { @@ -2303,11 +2352,11 @@ public final class SurfacingUtil { writer.write( ForesterUtil.LINE_SEPARATOR ); } writer.close(); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name + "]" ); } catch ( final IOException e ) { - ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e ); + ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e ); } } @@ -2317,10 +2366,10 @@ public final class SurfacingUtil { writer.toPhyloXML( new File( filename ), phylogeny, 1 ); } catch ( final IOException e ) { - ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "failed to write phylogeny to \"" + filename - + "\": " + e ); + ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": " + + e ); } - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" ); } public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException { @@ -2381,10 +2430,10 @@ public final class SurfacingUtil { my_matrix.writeNexusBinaryChractersBlock( w ); w.flush(); w.close(); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } } @@ -2407,27 +2456,27 @@ public final class SurfacingUtil { PhylogenyWriter.writeNexusTreesBlock( w, phylogenies ); w.flush(); w.close(); - ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" ); } catch ( final IOException e ) { - ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() ); + ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() ); } } private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony ) { - writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, + writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS, domain_parsimony.createMatrixOfDomainPresenceOrAbsence() ); - writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, + writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence() ); } private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony, final Phylogeny phylogeny ) { - writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, + writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS, domain_parsimony.createMatrixOfDomainPresenceOrAbsence(), phylogeny ); - writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, + writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(), phylogeny ); } -- 1.7.10.2