forester/java/src/org/forester/application/surfacing.java

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.application;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.util.ArrayList;
  35 import java.util.Date;
  36 import java.util.HashMap;
  37 import java.util.HashSet;
  38 import java.util.List;
  39 import java.util.Map;
  40 import java.util.Map.Entry;
  41 import java.util.Set;
  42 import java.util.SortedMap;
  43 import java.util.SortedSet;
  44 import java.util.TreeMap;
  45 import java.util.TreeSet;
  46
  47 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  48 import org.forester.go.GoId;
  49 import org.forester.go.GoNameSpace;
  50 import org.forester.go.GoTerm;
  51 import org.forester.go.GoUtils;
  52 import org.forester.go.OBOparser;
  53 import org.forester.go.PfamToGoMapping;
  54 import org.forester.go.PfamToGoParser;
  55 import org.forester.io.parsers.HmmscanPerDomainTableParser;
  56 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
  57 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  58 import org.forester.io.parsers.util.ParserUtils;
  59 import org.forester.phylogeny.Phylogeny;
  60 import org.forester.phylogeny.PhylogenyMethods;
  61 import org.forester.phylogeny.PhylogenyNode;
  62 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  63 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  64 import org.forester.protein.BinaryDomainCombination;
  65 import org.forester.protein.Domain;
  66 import org.forester.protein.Protein;
  67 import org.forester.species.BasicSpecies;
  68 import org.forester.species.Species;
  69 import org.forester.surfacing.BasicDomainSimilarityCalculator;
  70 import org.forester.surfacing.BasicGenomeWideCombinableDomains;
  71 import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
  72 import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
  73 import org.forester.surfacing.DomainCountsDifferenceUtil;
  74 import org.forester.surfacing.DomainLengthsTable;
  75 import org.forester.surfacing.DomainParsimonyCalculator;
  76 import org.forester.surfacing.DomainSimilarity;
  77 import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
  78 import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
  79 import org.forester.surfacing.DomainSimilarityCalculator;
  80 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  81 import org.forester.surfacing.GenomeWideCombinableDomains;
  82 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  83 import org.forester.surfacing.MappingResults;
  84 import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
  85 import org.forester.surfacing.PairwiseGenomeComparator;
  86 import org.forester.surfacing.PrintableDomainSimilarity;
  87 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  88 import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
  89 import org.forester.surfacing.SurfacingUtil;
  90 import org.forester.util.BasicDescriptiveStatistics;
  91 import org.forester.util.BasicTable;
  92 import org.forester.util.BasicTableParser;
  93 import org.forester.util.CommandLineArguments;
  94 import org.forester.util.DescriptiveStatistics;
  95 import org.forester.util.ForesterConstants;
  96 import org.forester.util.ForesterUtil;
  97
  98 public class surfacing {
  99
 100     private static final int                                  MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING                                  = 1000;
 101     public final static String                                DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS                           = "graph_analysis_out";
 102     public final static String                                DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS                       = "_dc.dot";
 103     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS        = "_fitch_present_dc.dot";
 104     public final static String                                DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX                                    = ".dcc";
 105     // gain/loss:
 106     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS                                      = "_dollo_gl_d";
 107     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS                          = "_dollo_gl_dc";
 108     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS                                      = "_fitch_gl_d";
 109     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS                          = "_fitch_gl_dc";
 110     // gain/loss counts:
 111     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS                               = "_dollo_glc_d";
 112     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS                   = "_dollo_glc_dc";
 113     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS                               = "_fitch_glc_d";
 114     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS                   = "_fitch_glc_dc";
 115     // tables:
 116     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_BC                                               = "_fitch_gains_dc";
 117     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC                                          = "_fitch_gains_dc.html";
 118     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_BC                                              = "_fitch_losses_dc";
 119     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC                                         = "_fitch_losses_dc.html";
 120     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC                                             = "_fitch_present_dc";
 121     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC                                        = "_fitch_present_dc.html";
 122     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_D                                                = "_dollo_gains_d";
 123     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D                                           = "_dollo_gains_d.html";
 124     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_D                                               = "_dollo_losses_d";
 125     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D                                          = "_dollo_losses_d.html";
 126     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_D                                              = "_dollo_present_d";
 127     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D                                         = "_dollo_present_d.html";
 128     public final static String                                DOMAINS_PRESENT_NEXUS                                                         = "_dom.nex";
 129     public final static String                                BDC_PRESENT_NEXUS                                                             = "_dc.nex";
 130     // ---
 131     public final static String                                PRG_NAME                                                                      = "surfacing";
 132     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                                    = "_d_dollo"
 133                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 134     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                                    = "_d_fitch"
 135                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 136     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                 = "_dc_dollo"
 137                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 138     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                 = "_dc_fitch"
 139                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 140     public static final String                                NEXUS_EXTERNAL_DOMAINS                                                        = "_dom.nex";
 141     public static final String                                NEXUS_EXTERNAL_DOMAIN_COMBINATIONS                                            = "_dc.nex";
 142     public static final String                                NEXUS_SECONDARY_FEATURES                                                      = "_secondary_features.nex";
 143     public static final String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES                           = "_dollo_gl_secondary_features";
 144     public static final String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES                    = "_dollo_glc_secondary_features";
 145     public static final String                                PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES                               = "_dollo_gains_secondary_features";
 146     public static final String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES                              = "_dollo_losses_secondary_features";
 147     public static final String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES                             = "_dollo_present_secondary_features";
 148     public static final String                                SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                         = "_secondary_features_dollo"
 149                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 150     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES                              = "_dollo_goid_d";
 151     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES                             = "_fitch_goid_dc";
 152     final static private String                               HELP_OPTION_1                                                                 = "help";
 153     final static private String                               HELP_OPTION_2                                                                 = "h";
 154     final static private String                               OUTPUT_DIR_OPTION                                                             = "out_dir";
 155     final static private String                               SCORING_OPTION                                                                = "scoring";
 156     private static final DomainSimilarityScoring              SCORING_DEFAULT                                                               = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 157     final static private String                               SCORING_DOMAIN_COUNT_BASED                                                    = "domains";
 158     final static private String                               SCORING_PROTEIN_COUNT_BASED                                                   = "proteins";
 159     final static private String                               SCORING_COMBINATION_BASED                                                     = "combinations";
 160     final static private String                               DETAILEDNESS_OPTION                                                           = "detail";
 161     private final static Detailedness                         DETAILEDNESS_DEFAULT                                                          = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 162     final static private String                               SPECIES_MATRIX_OPTION                                                         = "smatrix";
 163     final static private String                               DETAILEDNESS_BASIC                                                            = "basic";
 164     final static private String                               DETAILEDNESS_LIST_IDS                                                         = "list_ids";
 165     final static private String                               DETAILEDNESS_PUNCTILIOUS                                                      = "punctilious";
 166     final static private String                               DOMAIN_SIMILARITY_SORT_OPTION                                                 = "sort";
 167     private static final DomainSimilaritySortField            DOMAIN_SORT_FILD_DEFAULT                                                      = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 168     final static private String                               DOMAIN_SIMILARITY_SORT_MIN                                                    = "min";
 169     final static private String                               DOMAIN_SIMILARITY_SORT_MAX                                                    = "max";
 170     final static private String                               DOMAIN_SIMILARITY_SORT_SD                                                     = "sd";
 171     final static private String                               DOMAIN_SIMILARITY_SORT_MEAN                                                   = "mean";
 172     final static private String                               DOMAIN_SIMILARITY_SORT_DIFF                                                   = "diff";
 173     final static private String                               DOMAIN_SIMILARITY_SORT_COUNTS_DIFF                                            = "count_diff";
 174     final static private String                               DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF                                        = "abs_count_diff";
 175     final static private String                               DOMAIN_SIMILARITY_SORT_SPECIES_COUNT                                          = "species";
 176     final static private String                               DOMAIN_SIMILARITY_SORT_ALPHA                                                  = "alpha";
 177     final static private String                               DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION                          = "species_first";
 178     final static private String                               DOMAIN_COUNT_SORT_OPTION                                                      = "dc_sort";
 179     private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT                                                    = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
 180     final static private String                               DOMAIN_COUNT_SORT_ALPHA                                                       = "alpha";
 181     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT                                            = "dom";
 182     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT                                   = "prot";
 183     final static private String                               DOMAIN_COUNT_SORT_COMBINATIONS_COUNT                                          = "comb";
 184     final static private String                               CUTOFF_SCORE_FILE_OPTION                                                      = "cos";
 185     final static private String                               NOT_IGNORE_DUFS_OPTION                                                        = "dufs";
 186     final static private String                               MAX_E_VALUE_OPTION                                                            = "e";
 187     final static private String                               MAX_ALLOWED_OVERLAP_OPTION                                                    = "mo";
 188     final static private String                               NO_ENGULFING_OVERLAP_OPTION                                                   = "no_eo";
 189     final static private String                               IGNORE_COMBINATION_WITH_SAME_OPTION                                           = "ignore_self_comb";
 190     final static private String                               PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION                                       = "dc_regain_stats";
 191     final static private String                               DA_ANALYSIS_OPTION                                                            = "DA_analyis";
 192     final static private String                               USE_LAST_IN_FITCH_OPTION                                                      = "last";
 193     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
 194     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_OPTION                                            = "pwc";
 195     final static private String                               OUTPUT_FILE_OPTION                                                            = "o";
 196     final static private String                               PFAM_TO_GO_FILE_USE_OPTION                                                    = "p2g";
 197     final static private String                               GO_OBO_FILE_USE_OPTION                                                        = "obo";
 198     final static private String                               GO_NAMESPACE_LIMIT_OPTION                                                     = "go_namespace";
 199     final static private String                               GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION                                  = "molecular_function";
 200     final static private String                               GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS                                  = "biological_process";
 201     final static private String                               GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT                                  = "cellular_component";
 202     final static private String                               SECONDARY_FEATURES_PARSIMONY_MAP_FILE                                         = "secondary";
 203     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED                           = "simple_tab";
 204     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML                                    = "simple_html";
 205     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML                                  = "detailed_html";
 206     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION                                                = "ds_output";
 207     private static final PRINT_OPTION                         DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT                                        = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 208     final static private String                               IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION                     = "ignore_singlet_domains";
 209     final static private String                               IGNORE_VIRAL_IDS                                                              = "ignore_viral_ids";
 210     final static private boolean                              IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT                    = false;
 211     final static private String                               IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION                                 = "ignore_species_specific_domains";
 212     final static private boolean                              IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT                         = false;
 213     final static private String                               MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                                = "_mean_score.pwd";
 214     final static private String                               MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                            = "_domains.pwd";
 215     final static private String                               MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                   = "_bin_combinations.pwd";
 216     final static private String                               NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                               = "_mean_score_NJ"
 217                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 218     final static private String                               NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                           = "_domains_NJ"
 219                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 220     final static private String                               NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                  = "_bin_combinations_NJ"
 221                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 222     final static private String                               FILTER_POSITIVE_OPTION                                                        = "pos_filter";
 223     final static private String                               FILTER_NEGATIVE_OPTION                                                        = "neg_filter";
 224     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                                = "neg_dom_filter";
 225     final static private String                               INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
 226     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
 227     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
 228     final static private String                               PRG_VERSION                                                                   = "2.280";
 229     final static private String                               PRG_DATE                                                                      = "130701";
 230     final static private String                               E_MAIL                                                                        = "czmasek@burnham.org";
 231     final static private String                               WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
 232     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;
 233     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
 234     final static private double                               MAX_E_VALUE_DEFAULT                                                           = -1;
 235     final static private int                                  MAX_ALLOWED_OVERLAP_DEFAULT                                                   = -1;
 236     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                        = "random_seed";
 237     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                                      = "consider_bdc_direction";
 238     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                        = "consider_bdc_adj";
 239     private static final String                               SEQ_EXTRACT_SUFFIX                                                            = ".prot";
 240     private static final String                               PLUS_MINUS_ANALYSIS_OPTION                                                    = "plus_minus";
 241     private static final String                               PLUS_MINUS_DOM_SUFFIX                                                         = "_plus_minus_dom.txt";
 242     private static final String                               PLUS_MINUS_DOM_SUFFIX_HTML                                                    = "_plus_minus_dom.html";
 243     private static final String                               PLUS_MINUS_DC_SUFFIX_HTML                                                     = "_plus_minus_dc.html";
 244     private static final int                                  PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                          = 0;
 245     private static final double                               PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                            = 1.0;
 246     private static final String                               PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                              = "_plus_minus_go_ids_all.txt";
 247     private static final String                               PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                          = "_plus_minus_go_ids_passing.txt";
 248     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                           = "all_prot";
 249     final static private String                               OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION                         = "all_prot_e";
 250     private static final boolean                              VERBOSE                                                                       = false;
 251     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX              = "_fitch_dc_gains_counts";
 252     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX                = "_fitch_dc_losses_counts";
 253     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                                = "_domain_lengths_analysis";
 254     private static final boolean                              PERFORM_DOMAIN_LENGTH_ANALYSIS                                                = true;
 255     public static final String                                ALL_PFAMS_ENCOUNTERED_SUFFIX                                                  = "_all_encountered_pfams";
 256     public static final String                                ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX                               = "_all_encountered_pfams_with_go_annotation";
 257     public static final String                                ENCOUNTERED_PFAMS_SUMMARY_SUFFIX                                              = "_encountered_pfams_summary";
 258     public static final String                                ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX                                            = "_all_pfams_gained_as_domains";
 259     public static final String                                ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX                                              = "_all_pfams_lost_as_domains";
 260     public static final String                                ALL_PFAMS_GAINED_AS_DC_SUFFIX                                                 = "_all_pfams_gained_as_dc";
 261     public static final String                                ALL_PFAMS_LOST_AS_DC_SUFFIX                                                   = "_all_pfams_lost_as_dc";
 262     public static final String                                BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES                                = "PER_NODE_EVENTS";
 263     public static final String                                BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES                             = "PER_SUBTREE_EVENTS";
 264     public static final String                                D_PROMISCUITY_FILE_SUFFIX                                                     = "_domain_promiscuities";
 265     private static final String                               LOG_FILE_SUFFIX                                                               = "_log.txt";
 266     private static final String                               DATA_FILE_SUFFIX                                                              = "_domain_combination_data.txt";
 267     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";
 268     private static final String                               WRITE_TO_NEXUS_OPTION                                                         = "nexus";
 269     private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                               = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;                                                                                                                                                      //TODO look at me! change?
 270     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX                          = "_indep_dc_gains_fitch_counts.txt";
 271     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                              = "_indep_dc_gains_fitch_lists.txt";
 272     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX               = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
 273     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
 274     public static final String                                LIMIT_SPEC_FOR_PROT_EX                                                        = null;                                                                                                                                                                                       // e.g. "HUMAN"; set to null for not using this feature (default).
 275     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED          = "_dc_MAPPED_secondary_features_fitch"
 276                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 277     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX                   = "_indep_dc_gains_fitch_counts_MAPPED.txt";
 278     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists_MAPPED.txt";
 279     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
 280     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
 281
 282     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
 283                                                                  final String[][] input_file_properties,
 284                                                                  final String automated_pairwise_comparison_suffix,
 285                                                                  final File outdir ) {
 286         for( int i = 0; i < input_file_properties.length; ++i ) {
 287             for( int j = 0; j < i; ++j ) {
 288                 final String species_i = input_file_properties[ i ][ 1 ];
 289                 final String species_j = input_file_properties[ j ][ 1 ];
 290                 String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
 291                         + species_j + automated_pairwise_comparison_suffix;
 292                 switch ( domain_similarity_print_option ) {
 293                     case HTML:
 294                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 295                             pairwise_similarities_output_file_str += ".html";
 296                         }
 297                         break;
 298                 }
 299                 final String error = ForesterUtil
 300                         .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
 301                                 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 302                 if ( !ForesterUtil.isEmpty( error ) ) {
 303                     ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 304                 }
 305             }
 306         }
 307     }
 308
 309     private static StringBuilder createParametersAsString( final boolean ignore_dufs,
 310                                                            final double e_value_max,
 311                                                            final int max_allowed_overlap,
 312                                                            final boolean no_engulfing_overlaps,
 313                                                            final File cutoff_scores_file,
 314                                                            final BinaryDomainCombination.DomainCombinationType dc_type ) {
 315         final StringBuilder parameters_sb = new StringBuilder();
 316         parameters_sb.append( "E-value: " + e_value_max );
 317         if ( cutoff_scores_file != null ) {
 318             parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
 319         }
 320         else {
 321             parameters_sb.append( ", Cutoff-scores-file: not-set" );
 322         }
 323         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
 324             parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
 325         }
 326         else {
 327             parameters_sb.append( ", Max-overlap: not-set" );
 328         }
 329         if ( no_engulfing_overlaps ) {
 330             parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
 331         }
 332         else {
 333             parameters_sb.append( ", Engulfing-overlaps: allowed" );
 334         }
 335         if ( ignore_dufs ) {
 336             parameters_sb.append( ", Ignore-dufs: true" );
 337         }
 338         else {
 339             parameters_sb.append( ", Ignore-dufs: false" );
 340         }
 341         parameters_sb.append( ", DC type (if applicable): " + dc_type );
 342         return parameters_sb;
 343     }
 344
 345     /**
 346      * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
 347      *
 348      *
 349      * @param output_file
 350      * @param all_bin_domain_combinations_changed
 351      * @param sum_of_all_domains_encountered
 352      * @param all_bin_domain_combinations_encountered
 353      * @param is_gains_analysis
 354      * @param protein_length_stats_by_dc
 355      * @throws IOException
 356      */
 357     private static void executeFitchGainsAnalysis( final File output_file,
 358                                                    final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
 359                                                    final int sum_of_all_domains_encountered,
 360                                                    final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
 361                                                    final boolean is_gains_analysis ) throws IOException {
 362         SurfacingUtil.checkForOutputFileWriteability( output_file );
 363         final Writer out = ForesterUtil.createBufferedWriter( output_file );
 364         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
 365                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
 366         final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
 367         final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
 368         int above_one = 0;
 369         int one = 0;
 370         for( final Object bdc_object : bdc_to_counts.keySet() ) {
 371             final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
 372             final int count = bdc_to_counts.get( bdc_object );
 373             if ( count < 1 ) {
 374                 ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
 375             }
 376             out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 377             if ( count > 1 ) {
 378                 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
 379                 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
 380                 above_one++;
 381             }
 382             else if ( count == 1 ) {
 383                 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
 384                 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
 385                 one++;
 386             }
 387         }
 388         final int all = all_bin_domain_combinations_encountered.size();
 389         int never_lost = -1;
 390         if ( !is_gains_analysis ) {
 391             all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
 392             never_lost = all_bin_domain_combinations_encountered.size();
 393             for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
 394                 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
 395             }
 396         }
 397         if ( is_gains_analysis ) {
 398             out.write( "Sum of all distinct domain combinations appearing once               : " + one
 399                     + ForesterUtil.LINE_SEPARATOR );
 400             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
 401                     + ForesterUtil.LINE_SEPARATOR );
 402             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
 403                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 404             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
 405                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 406         }
 407         else {
 408             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
 409                     + ForesterUtil.LINE_SEPARATOR );
 410             out.write( "Sum of all distinct domain combinations lost once                    : " + one
 411                     + ForesterUtil.LINE_SEPARATOR );
 412             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
 413                     + ForesterUtil.LINE_SEPARATOR );
 414             out.write( "Sum of all distinct domains in combinations lost only once           : "
 415                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 416             out.write( "Sum of all distinct domains in combinations lost more than once: "
 417                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 418         }
 419         out.write( "All binary combinations                                              : " + all
 420                 + ForesterUtil.LINE_SEPARATOR );
 421         out.write( "All domains                                                          : "
 422                 + sum_of_all_domains_encountered );
 423         out.close();
 424         ForesterUtil.programMessage( surfacing.PRG_NAME,
 425                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
 426                                              + "\"" );
 427     }
 428
 429     private static void executePlusMinusAnalysis( final File output_file,
 430                                                   final List<String> plus_minus_analysis_high_copy_base,
 431                                                   final List<String> plus_minus_analysis_high_copy_target,
 432                                                   final List<String> plus_minus_analysis_low_copy,
 433                                                   final List<GenomeWideCombinableDomains> gwcd_list,
 434                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species,
 435                                                   final Map<String, List<GoId>> domain_id_to_go_ids_map,
 436                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 437                                                   final List<Object> plus_minus_analysis_numbers ) {
 438         final Set<String> all_spec = new HashSet<String>();
 439         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 440             all_spec.add( gwcd.getSpecies().getSpeciesId() );
 441         }
 442         final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
 443         final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
 444         final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
 445         final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
 446         final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
 447         final File proteins_file_base = new File( output_file + "" );
 448         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
 449         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
 450         try {
 451             DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
 452                                                                        protein_lists_per_species,
 453                                                                        plus_minus_analysis_high_copy_base,
 454                                                                        plus_minus_analysis_high_copy_target,
 455                                                                        plus_minus_analysis_low_copy,
 456                                                                        min_diff,
 457                                                                        factor,
 458                                                                        plain_out_dom,
 459                                                                        html_out_dom,
 460                                                                        html_out_dc,
 461                                                                        domain_id_to_go_ids_map,
 462                                                                        go_id_to_term_map,
 463                                                                        all_domains_go_ids_out_dom,
 464                                                                        passing_domains_go_ids_out_dom,
 465                                                                        proteins_file_base );
 466         }
 467         catch ( final IOException e ) {
 468             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 469         }
 470         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 471                 + html_out_dom + "\"" );
 472         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 473                 + plain_out_dom + "\"" );
 474         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
 475                 + "\"" );
 476         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
 477                 + passing_domains_go_ids_out_dom + "\"" );
 478         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
 479                 + all_domains_go_ids_out_dom + "\"" );
 480     }
 481
 482     private static Phylogeny[] getIntrees( final File[] intree_files,
 483                                            final int number_of_genomes,
 484                                            final String[][] input_file_properties ) {
 485         final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
 486         int i = 0;
 487         for( final File intree_file : intree_files ) {
 488             Phylogeny intree = null;
 489             final String error = ForesterUtil.isReadableFile( intree_file );
 490             if ( !ForesterUtil.isEmpty( error ) ) {
 491                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
 492                         + error );
 493             }
 494             try {
 495                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
 496                         .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
 497                 if ( p_array.length < 1 ) {
 498                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 499                             + "] does not contain any phylogeny in phyloXML format" );
 500                 }
 501                 else if ( p_array.length > 1 ) {
 502                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 503                             + "] contains more than one phylogeny in phyloXML format" );
 504                 }
 505                 intree = p_array[ 0 ];
 506             }
 507             catch ( final Exception e ) {
 508                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
 509                         + "]: " + error );
 510             }
 511             if ( ( intree == null ) || intree.isEmpty() ) {
 512                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
 513             }
 514             if ( !intree.isRooted() ) {
 515                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
 516             }
 517             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
 518                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 519                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
 520                                                  + "] of input tree [" + intree_file
 521                                                  + "] is smaller than the number of genomes the be analyzed ["
 522                                                  + number_of_genomes + "]" );
 523             }
 524             final StringBuilder parent_names = new StringBuilder();
 525             final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
 526             if ( nodes_lacking_name > 0 ) {
 527                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
 528                         + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
 529             }
 530             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
 531             if ( !intree.isCompletelyBinary() ) {
 532                 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
 533                         + "] is not completely binary" );
 534             }
 535             intrees[ i++ ] = intree;
 536         }
 537         return intrees;
 538     }
 539
 540     private static void log( final String msg, final Writer w ) {
 541         try {
 542             w.write( msg );
 543             w.write( ForesterUtil.LINE_SEPARATOR );
 544         }
 545         catch ( final IOException e ) {
 546             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 547         }
 548     }
 549
 550     public static void main( final String args[] ) {
 551         final long start_time = new Date().getTime();
 552         // final StringBuffer log = new StringBuffer();
 553         final StringBuilder html_desc = new StringBuilder();
 554         ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
 555                                               surfacing.PRG_VERSION,
 556                                               surfacing.PRG_DATE,
 557                                               surfacing.E_MAIL,
 558                                               surfacing.WWW );
 559         final String nl = ForesterUtil.LINE_SEPARATOR;
 560         html_desc.append( "<table>" + nl );
 561         html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
 562         html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
 563         html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
 564         html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
 565         html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
 566         CommandLineArguments cla = null;
 567         try {
 568             cla = new CommandLineArguments( args );
 569         }
 570         catch ( final Exception e ) {
 571             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 572         }
 573         if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
 574             surfacing.printHelp();
 575             System.exit( 0 );
 576         }
 577         if ( ( args.length < 1 ) ) {
 578             surfacing.printHelp();
 579             System.exit( -1 );
 580         }
 581         final List<String> allowed_options = new ArrayList<String>();
 582         allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
 583         allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
 584         allowed_options.add( surfacing.DETAILEDNESS_OPTION );
 585         allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
 586         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
 587         allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
 588         allowed_options.add( surfacing.SCORING_OPTION );
 589         allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 590         allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
 591         allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
 592         allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
 593         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
 594         allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
 595         allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
 596         allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
 597         allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
 598         allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
 599         allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
 600         allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 601         allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
 602         allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
 603         //allowed_options.add( JACKNIFE_OPTION );
 604         // allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
 605         // allowed_options.add( JACKNIFE_RATIO_OPTION );
 606         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
 607         allowed_options.add( FILTER_POSITIVE_OPTION );
 608         allowed_options.add( FILTER_NEGATIVE_OPTION );
 609         allowed_options.add( INPUT_GENOMES_FILE_OPTION );
 610         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 611         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
 612         allowed_options.add( IGNORE_VIRAL_IDS );
 613         allowed_options.add( SEQ_EXTRACT_OPTION );
 614         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 615         allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
 616         allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
 617         allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
 618         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
 619         allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
 620         allowed_options.add( WRITE_TO_NEXUS_OPTION );
 621         allowed_options.add( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION );
 622         allowed_options.add( DA_ANALYSIS_OPTION );
 623         allowed_options.add( USE_LAST_IN_FITCH_OPTION );
 624         boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
 625         boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
 626         double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
 627         int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
 628         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 629         if ( dissallowed_options.length() > 0 ) {
 630             ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
 631         }
 632         boolean use_last_in_fitch_parsimony = false;
 633         if ( cla.isOptionSet( USE_LAST_IN_FITCH_OPTION ) ) {
 634             use_last_in_fitch_parsimony = true;
 635         }
 636         boolean write_to_nexus = false;
 637         if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) {
 638             write_to_nexus = true;
 639         }
 640         boolean perform_dc_regain_proteins_stats = false;
 641         if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) {
 642             perform_dc_regain_proteins_stats = true;
 643         }
 644         boolean da_analysis = false;
 645         if ( cla.isOptionSet( DA_ANALYSIS_OPTION ) ) {
 646             da_analysis = true;
 647         }
 648         boolean output_binary_domain_combinationsfor_graph_analysis = false;
 649         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
 650             output_binary_domain_combinationsfor_graph_analysis = true;
 651         }
 652         if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
 653             try {
 654                 e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
 655             }
 656             catch ( final Exception e ) {
 657                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
 658             }
 659         }
 660         if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
 661             try {
 662                 max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 663             }
 664             catch ( final Exception e ) {
 665                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
 666             }
 667         }
 668         boolean no_engulfing_overlaps = false;
 669         if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
 670             no_engulfing_overlaps = true;
 671         }
 672         boolean ignore_virus_like_ids = false;
 673         if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
 674             ignore_virus_like_ids = true;
 675         }
 676         if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
 677             ignore_dufs = false;
 678         }
 679         if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
 680             ignore_combination_with_same = true;
 681         }
 682         boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
 683         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
 684             ignore_domains_without_combs_in_all_spec = true;
 685         }
 686         boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
 687         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
 688             ignore_species_specific_domains = true;
 689         }
 690         File output_file = null;
 691         if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 692             if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 693                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 694                                          "no value for domain combinations similarities output file: -"
 695                                                  + surfacing.OUTPUT_FILE_OPTION + "=<file>" );
 696             }
 697             output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
 698             SurfacingUtil.checkForOutputFileWriteability( output_file );
 699         }
 700         File cutoff_scores_file = null;
 701         Map<String, Double> individual_score_cutoffs = null;
 702         if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 703             if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 704                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
 705                         + surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
 706             }
 707             cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
 708             final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
 709             if ( !ForesterUtil.isEmpty( error ) ) {
 710                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
 711                         + error );
 712             }
 713             try {
 714                 final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, ' ' );
 715                 individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
 716             }
 717             catch ( final IOException e ) {
 718                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
 719             }
 720         }
 721         BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
 722         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
 723             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
 724         }
 725         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
 726             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
 727         }
 728         File out_dir = null;
 729         if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 730             if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 731                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
 732                         + surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
 733             }
 734             out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
 735             if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
 736                 ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
 737             }
 738             if ( !out_dir.exists() ) {
 739                 final boolean success = out_dir.mkdir();
 740                 if ( !success || !out_dir.exists() ) {
 741                     ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
 742                 }
 743             }
 744             if ( !out_dir.canWrite() ) {
 745                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
 746             }
 747         }
 748         File positive_filter_file = null;
 749         File negative_filter_file = null;
 750         File negative_domains_filter_file = null;
 751         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 752             ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
 753         }
 754         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
 755                 && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
 756                         .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
 757             ForesterUtil
 758                     .fatalError( surfacing.PRG_NAME,
 759                                  "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
 760         }
 761         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 762             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 763                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
 764                         + surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
 765             }
 766             negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
 767             final String msg = ForesterUtil.isReadableFile( negative_filter_file );
 768             if ( !ForesterUtil.isEmpty( msg ) ) {
 769                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
 770                         + msg );
 771             }
 772         }
 773         else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 774             if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 775                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
 776                         + surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
 777             }
 778             positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
 779             final String msg = ForesterUtil.isReadableFile( positive_filter_file );
 780             if ( !ForesterUtil.isEmpty( msg ) ) {
 781                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
 782                         + msg );
 783             }
 784         }
 785         else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 786             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 787                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
 788                         + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
 789             }
 790             negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
 791             final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
 792             if ( !ForesterUtil.isEmpty( msg ) ) {
 793                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
 794                         + "\": " + msg );
 795             }
 796         }
 797         final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
 798         final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
 799         final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
 800         final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
 801         processPlusMinusAnalysisOption( cla,
 802                                         plus_minus_analysis_high_copy_base_species,
 803                                         plus_minus_analysis_high_copy_target_species,
 804                                         plus_minus_analysis_high_low_copy_species,
 805                                         plus_minus_analysis_numbers );
 806         File input_genomes_file = null;
 807         if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
 808             if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
 809                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -"
 810                         + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
 811             }
 812             input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) );
 813             final String msg = ForesterUtil.isReadableFile( input_genomes_file );
 814             if ( !ForesterUtil.isEmpty( msg ) ) {
 815                 ForesterUtil
 816                         .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg );
 817             }
 818         }
 819         else {
 820             ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
 821                     + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
 822         }
 823         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
 824         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
 825             if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
 826                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 827                                          "no value for scoring method for domain combinations similarity calculation: -"
 828                                                  + surfacing.SCORING_OPTION + "=<"
 829                                                  + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 830                                                  + surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
 831                                                  + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 832             }
 833             final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
 834             if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
 835                 scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
 836             }
 837             else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
 838                 scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 839             }
 840             else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
 841                 scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
 842             }
 843             else {
 844                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
 845                         + "\" for scoring method for domain combinations similarity calculation: \"-"
 846                         + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 847                         + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 848             }
 849         }
 850         boolean sort_by_species_count_first = false;
 851         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
 852             sort_by_species_count_first = true;
 853         }
 854         boolean species_matrix = false;
 855         if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
 856             species_matrix = true;
 857         }
 858         boolean output_protein_lists_for_all_domains = false;
 859         double output_list_of_all_proteins_per_domain_e_value_max = -1;
 860         if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
 861             output_protein_lists_for_all_domains = true;
 862             if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
 863                 try {
 864                     output_list_of_all_proteins_per_domain_e_value_max = cla
 865                             .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 866                 }
 867                 catch ( final Exception e ) {
 868                     ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
 869                 }
 870             }
 871         }
 872         Detailedness detailedness = DETAILEDNESS_DEFAULT;
 873         if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
 874             if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
 875                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
 876                         + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
 877                         + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 878             }
 879             final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
 880             if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
 881                 detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
 882             }
 883             else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
 884                 detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
 885             }
 886             else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
 887                 detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 888             }
 889             else {
 890                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
 891                         + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
 892                         + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 893             }
 894         }
 895         String automated_pairwise_comparison_suffix = null;
 896         boolean perform_pwc = false;
 897         boolean write_pwc_files = false;
 898         if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 899             perform_pwc = true;
 900             if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 901                 write_pwc_files = false;
 902             }
 903             else {
 904                 write_pwc_files = true;
 905                 automated_pairwise_comparison_suffix = "_"
 906                         + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 907             }
 908         }
 909         String query_domain_ids = null;
 910         if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 911             if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 912                 ForesterUtil
 913                         .fatalError( surfacing.PRG_NAME,
 914                                      "no domain ids given for sequences with given domains to be extracted : -"
 915                                              + surfacing.SEQ_EXTRACT_OPTION
 916                                              + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
 917             }
 918             query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
 919         }
 920         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
 921         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
 922         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 923             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 924                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
 925                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 926                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 927                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 928                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 929                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
 930                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 931                         + ">\"" );
 932             }
 933             final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
 934             if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
 935                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 936                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 937             }
 938             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
 939                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
 940                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 941             }
 942             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
 943                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
 944                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 945             }
 946             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
 947                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
 948                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
 949             }
 950             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
 951                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
 952                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 953             }
 954             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
 955                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
 956                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 957             }
 958             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
 959                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 960                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 961             }
 962             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
 963                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 964                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 965             }
 966             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
 967                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 968                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 969             }
 970             else {
 971                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
 972                         + "\" for domain combinations similarities sorting: \"-"
 973                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 974                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 975                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 976                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 977                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
 978                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 979                         + ">\"" );
 980             }
 981         }
 982         PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
 983         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 984             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 985                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
 986                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 987                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 988                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 989             }
 990             final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
 991             if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
 992                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 993             }
 994             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
 995                 ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
 996             }
 997             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
 998                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
 999             }
1000             else {
1001                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
1002                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
1003                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
1004                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
1005             }
1006         }
1007         GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
1008         if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1009             if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1010                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
1011                         + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
1012                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1013                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1014                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1015             }
1016             final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
1017             if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
1018                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
1019             }
1020             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
1021                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
1022             }
1023             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
1024                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
1025             }
1026             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
1027                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
1028             }
1029             else {
1030                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
1031                         + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
1032                         + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1033                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1034                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1035             }
1036         }
1037         final String[][] input_file_properties = processInputGenomesFile( input_genomes_file );
1038         final int number_of_genomes = input_file_properties.length;
1039         if ( number_of_genomes < 2 ) {
1040             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
1041         }
1042         if ( ( number_of_genomes < 3 ) && perform_pwc ) {
1043             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
1044                     + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1045                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
1046         }
1047         checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
1048                                                  input_file_properties,
1049                                                  automated_pairwise_comparison_suffix,
1050                                                  out_dir );
1051         for( int i = 0; i < number_of_genomes; i++ ) {
1052             File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
1053                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1054             if ( out_dir != null ) {
1055                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
1056             }
1057             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
1058         }
1059         File pfam_to_go_file = null;
1060         Map<String, List<GoId>> domain_id_to_go_ids_map = null;
1061         int domain_id_to_go_ids_count = 0;
1062         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1063             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1064                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
1065                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
1066             }
1067             pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
1068             final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
1069             if ( !ForesterUtil.isEmpty( error ) ) {
1070                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
1071             }
1072             try {
1073                 final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
1074                 final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
1075                 domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
1076                 if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
1077                     ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
1078                                                        "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
1079                 }
1080                 domain_id_to_go_ids_count = parser.getMappingCount();
1081             }
1082             catch ( final IOException e ) {
1083                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
1084             }
1085         }
1086         File go_obo_file = null;
1087         List<GoTerm> go_terms = null;
1088         if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1089             if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1090                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
1091                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
1092             }
1093             if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
1094                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
1095                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
1096                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1097             }
1098             go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
1099             final String error = ForesterUtil.isReadableFile( go_obo_file );
1100             if ( !ForesterUtil.isEmpty( error ) ) {
1101                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
1102             }
1103             try {
1104                 final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
1105                 go_terms = parser.parse();
1106                 if ( parser.getGoTermCount() != go_terms.size() ) {
1107                     ForesterUtil
1108                             .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
1109                 }
1110             }
1111             catch ( final IOException e ) {
1112                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
1113             }
1114         }
1115         Map<GoId, GoTerm> go_id_to_term_map = null;
1116         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
1117                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
1118             go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
1119         }
1120         GoNameSpace go_namespace_limit = null;
1121         if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1122             if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1123                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
1124                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
1125                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
1126                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1127             }
1128             if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1129                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
1130                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1131                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1132                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1133                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1134             }
1135             final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
1136                     .toLowerCase();
1137             if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
1138                 go_namespace_limit = GoNameSpace.createMolecularFunction();
1139             }
1140             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
1141                 go_namespace_limit = GoNameSpace.createBiologicalProcess();
1142             }
1143             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
1144                 go_namespace_limit = GoNameSpace.createCellularComponent();
1145             }
1146             else {
1147                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
1148                         + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1149                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1150                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1151                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1152             }
1153         }
1154         if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
1155                 && ( number_of_genomes > 2 ) ) {
1156             domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
1157         }
1158         File[] intree_files = null;
1159         Phylogeny[] intrees = null;
1160         if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1161             if ( number_of_genomes < 3 ) {
1162                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
1163                         + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
1164                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1165                         + "=<suffix for pairwise comparison output files>)" );
1166             }
1167             if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1168                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
1169                         + surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
1170             }
1171             final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
1172             if ( intrees_str.indexOf( "#" ) > 0 ) {
1173                 final String[] intrees_strs = intrees_str.split( "#" );
1174                 intree_files = new File[ intrees_strs.length ];
1175                 int i = 0;
1176                 for( final String s : intrees_strs ) {
1177                     intree_files[ i++ ] = new File( s.trim() );
1178                 }
1179             }
1180             else {
1181                 intree_files = new File[ 1 ];
1182                 intree_files[ 0 ] = new File( intrees_str );
1183             }
1184             intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
1185         }
1186         long random_number_seed_for_fitch_parsimony = 0l;
1187         boolean radomize_fitch_parsimony = false;
1188         if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1189             if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1190                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
1191                         + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
1192             }
1193             try {
1194                 random_number_seed_for_fitch_parsimony = cla
1195                         .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
1196             }
1197             catch ( final IOException e ) {
1198                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1199             }
1200             radomize_fitch_parsimony = true;
1201         }
1202         SortedSet<String> filter = null;
1203         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1204                 || ( negative_domains_filter_file != null ) ) {
1205             filter = new TreeSet<String>();
1206             if ( positive_filter_file != null ) {
1207                 processFilter( positive_filter_file, filter );
1208             }
1209             else if ( negative_filter_file != null ) {
1210                 processFilter( negative_filter_file, filter );
1211             }
1212             else if ( negative_domains_filter_file != null ) {
1213                 processFilter( negative_domains_filter_file, filter );
1214             }
1215         }
1216         Map<String, Set<String>>[] domain_id_to_secondary_features_maps = null;
1217         File[] secondary_features_map_files = null;
1218         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1219                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
1220         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1221             SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
1222         }
1223         if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1224             if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1225                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
1226                         + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
1227             }
1228             final String[] secondary_features_map_files_strs = cla
1229                     .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
1230             secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
1231             domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
1232             int i = 0;
1233             for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
1234                 secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
1235                 final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
1236                 if ( !ForesterUtil.isEmpty( error ) ) {
1237                     ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
1238                 }
1239                 try {
1240                     domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
1241                             .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
1242                 }
1243                 catch ( final IOException e ) {
1244                     ForesterUtil.fatalError( surfacing.PRG_NAME,
1245                                              "cannot read secondary features map file: " + e.getMessage() );
1246                 }
1247                 catch ( final Exception e ) {
1248                     ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
1249                             + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
1250                 }
1251                 i++;
1252             }
1253         }
1254         if ( out_dir == null ) {
1255             ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
1256                     + surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
1257         }
1258         if ( output_file == null ) {
1259             ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
1260                     + surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
1261         }
1262         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
1263             ForesterUtil.fatalError( surfacing.PRG_NAME,
1264                                      "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
1265                                              + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1266         }
1267         if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1268             ForesterUtil.fatalError( surfacing.PRG_NAME,
1269                                      "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
1270                                              + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1271         }
1272         System.out.println( "Output directory            : " + out_dir );
1273         System.out.println( "Input genomes from          : " + input_genomes_file );
1274         html_desc.append( "<tr><td>Input genomes from:</td><td>" + input_genomes_file + "</td></tr>" + nl );
1275         if ( positive_filter_file != null ) {
1276             final int filter_size = filter.size();
1277             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
1278                     + " domain ids]" );
1279             html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
1280                     + " domain ids]</td></tr>" + nl );
1281         }
1282         if ( negative_filter_file != null ) {
1283             final int filter_size = filter.size();
1284             System.out.println( "Negative protein filter     : " + negative_filter_file + " [" + filter_size
1285                     + " domain ids]" );
1286             html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
1287                     + " domain ids]</td></tr>" + nl );
1288         }
1289         if ( negative_domains_filter_file != null ) {
1290             final int filter_size = filter.size();
1291             System.out.println( "Negative domain filter      : " + negative_domains_filter_file + " [" + filter_size
1292                     + " domain ids]" );
1293             html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
1294                     + filter_size + " domain ids]</td></tr>" + nl );
1295         }
1296         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1297             String plus0 = "";
1298             for( final String s : plus_minus_analysis_high_copy_base_species ) {
1299                 plus0 += "+" + s + " ";
1300             }
1301             String plus1 = "";
1302             for( final String s : plus_minus_analysis_high_copy_target_species ) {
1303                 plus1 += "*" + s + " ";
1304             }
1305             String minus = "";
1306             for( final String s : plus_minus_analysis_high_low_copy_species ) {
1307                 minus += "-" + s + " ";
1308             }
1309             System.out.println( "Plus-minus analysis         : " + plus1 + "&& " + plus0 + "&& " + minus );
1310             html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
1311                     + "</td></tr>" + nl );
1312         }
1313         if ( cutoff_scores_file != null ) {
1314             System.out.println( "Cutoff scores file          : " + cutoff_scores_file );
1315             html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
1316         }
1317         if ( e_value_max >= 0.0 ) {
1318             System.out.println( "E-value maximum (inclusive) : " + e_value_max );
1319             html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
1320         }
1321         if ( output_protein_lists_for_all_domains ) {
1322             System.out.println( "Domain E-value max          : " + output_list_of_all_proteins_per_domain_e_value_max );
1323             html_desc.append( "<tr><td>Protein lists: E-value maximum per domain (inclusive):</td><td>"
1324                     + output_list_of_all_proteins_per_domain_e_value_max + "</td></tr>" + nl );
1325         }
1326         System.out.println( "Ignore DUFs                 : " + ignore_dufs );
1327         if ( ignore_virus_like_ids ) {
1328             System.out.println( "Ignore virus like ids       : " + ignore_virus_like_ids );
1329             html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
1330                     + ignore_virus_like_ids + "</td></tr>" + nl );
1331         }
1332         html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
1333         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1334             System.out.println( "Max allowed domain overlap  : " + max_allowed_overlap );
1335             html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
1336         }
1337         if ( no_engulfing_overlaps ) {
1338             System.out.println( "Ignore engulfed domains     : " + no_engulfing_overlaps );
1339             html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
1340                     + "</td></tr>" + nl );
1341         }
1342         System.out.println( "Ignore singlet domains      : " + ignore_domains_without_combs_in_all_spec );
1343         html_desc
1344                 .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1345                         + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
1346         System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
1347         html_desc
1348                 .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1349                         + ignore_species_specific_domains + "</td></tr>" + nl );
1350         System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
1351         html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
1352                 + ignore_combination_with_same + "</td></tr>" + nl );
1353         System.out.println( "Consider directedness       : "
1354                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
1355         html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
1356                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
1357         if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
1358             System.out.println( "Consider adjacency          : "
1359                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
1360             html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
1361                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
1362                     + nl );
1363         }
1364         System.out.println( "Use last in Fitch parimony  : " + use_last_in_fitch_parsimony );
1365         html_desc.append( "<tr><td>Use last in Fitch parimon:</td><td>" + use_last_in_fitch_parsimony + "</td></tr>"
1366                 + nl );
1367         System.out.println( "Write to Nexus files        : " + write_to_nexus );
1368         html_desc.append( "<tr><td>Write to Nexus files:</td><td>" + write_to_nexus + "</td></tr>" + nl );
1369         System.out.println( "DC regain prot stats        : " + perform_dc_regain_proteins_stats );
1370         html_desc.append( "<tr><td>DC regain prot stats:</td><td>" + perform_dc_regain_proteins_stats + "</td></tr>"
1371                 + nl );
1372         System.out.println( "DA analysis                 : " + da_analysis );
1373         html_desc.append( "<tr><td>DA analysis :</td><td>" + da_analysis + "</td></tr>" + nl );
1374         System.out.print( "Domain counts sort order    : " );
1375         html_desc.append( "<tr><td>Domain counts sort order:</td><td>" );
1376         switch ( dc_sort_order ) {
1377             case ALPHABETICAL_KEY_ID:
1378                 System.out.println( "alphabetical" );
1379                 html_desc.append( "alphabetical" + "</td></tr>" + nl );
1380                 break;
1381             case KEY_DOMAIN_COUNT:
1382                 System.out.println( "domain count" );
1383                 html_desc.append( "domain count" + "</td></tr>" + nl );
1384                 break;
1385             case KEY_DOMAIN_PROTEINS_COUNT:
1386                 System.out.println( "domain proteins count" );
1387                 html_desc.append( "domain proteins count" + "</td></tr>" + nl );
1388                 break;
1389             case COMBINATIONS_COUNT:
1390                 System.out.println( "domain combinations count" );
1391                 html_desc.append( "domain combinations count" + "</td></tr>" + nl );
1392                 break;
1393             default:
1394                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
1395         }
1396         if ( domain_id_to_go_ids_map != null ) {
1397             System.out.println( "Pfam to GO mappings from    : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
1398                     + " mappings]" );
1399             html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
1400                     + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
1401         }
1402         if ( go_terms != null ) {
1403             System.out.println( "GO terms from               : " + go_obo_file + " [" + go_terms.size() + " terms]" );
1404             html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
1405                     + "</td></tr>" + nl );
1406         }
1407         if ( go_namespace_limit != null ) {
1408             System.out.println( "Limit GO terms to           : " + go_namespace_limit.toString() );
1409             html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
1410         }
1411         if ( perform_pwc ) {
1412             System.out.println( "Suffix for PWC files        : " + automated_pairwise_comparison_suffix );
1413             html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
1414                     + "</td></tr>" + nl );
1415         }
1416         if ( out_dir != null ) {
1417             System.out.println( "Output directory            : " + out_dir );
1418         }
1419         if ( query_domain_ids != null ) {
1420             System.out.println( "Query domains (ordered)     : " + query_domain_ids );
1421             html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
1422         }
1423         System.out.println( "Write similarities to       : " + output_file );
1424         System.out.print( "  Scoring method            : " );
1425         html_desc.append( "<tr><td>Scoring method:</td><td>" );
1426         switch ( scoring ) {
1427             case COMBINATIONS:
1428                 System.out.println( "domain combinations based" );
1429                 html_desc.append( "domain combinations based" + "</td></tr>" + nl );
1430                 break;
1431             case DOMAINS:
1432                 System.out.println( "domain counts based" );
1433                 html_desc.append( "domain counts based" + "</td></tr>" + nl );
1434                 break;
1435             case PROTEINS:
1436                 System.out.println( "domain proteins counts based" );
1437                 html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
1438                 break;
1439             default:
1440                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
1441         }
1442         System.out.print( "  Sort by                   : " );
1443         html_desc.append( "<tr><td>Sort by:</td><td>" );
1444         switch ( domain_similarity_sort_field ) {
1445             case MIN:
1446                 System.out.print( "score minimum" );
1447                 html_desc.append( "score minimum" );
1448                 break;
1449             case MAX:
1450                 System.out.print( "score maximum" );
1451                 html_desc.append( "score maximum" );
1452                 break;
1453             case MEAN:
1454                 System.out.print( "score mean" );
1455                 html_desc.append( "score mean" );
1456                 break;
1457             case SD:
1458                 System.out.print( "score standard deviation" );
1459                 html_desc.append( "score standard deviation" );
1460                 break;
1461             case SPECIES_COUNT:
1462                 System.out.print( "species number" );
1463                 html_desc.append( "species number" );
1464                 break;
1465             case DOMAIN_ID:
1466                 System.out.print( "alphabetical domain identifier" );
1467                 html_desc.append( "alphabetical domain identifier" );
1468                 break;
1469             case MAX_DIFFERENCE:
1470                 System.out.print( "(maximal) difference" );
1471                 html_desc.append( "(maximal) difference" );
1472                 break;
1473             case ABS_MAX_COUNTS_DIFFERENCE:
1474                 System.out.print( "absolute (maximal) counts difference" );
1475                 html_desc.append( "absolute (maximal) counts difference" );
1476                 break;
1477             case MAX_COUNTS_DIFFERENCE:
1478                 System.out.print( "(maximal) counts difference" );
1479                 html_desc.append( "(maximal) counts  difference" );
1480                 break;
1481             default:
1482                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1483         }
1484         if ( sort_by_species_count_first ) {
1485             System.out.println( " (sort by species count first)" );
1486             html_desc.append( " (sort by species count first)" );
1487         }
1488         else {
1489             System.out.println();
1490         }
1491         html_desc.append( "</td></tr>" + nl );
1492         System.out.print( "  Detailedness              : " );
1493         switch ( detailedness ) {
1494             case BASIC:
1495                 System.out.println( "basic" );
1496                 break;
1497             case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
1498                 System.out.println( "list combining domains for each species" );
1499                 break;
1500             case PUNCTILIOUS:
1501                 System.out.println( "punctilious" );
1502                 break;
1503             default:
1504                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" );
1505         }
1506         System.out.print( "  Print option              : " );
1507         switch ( domain_similarity_print_option ) {
1508             case HTML:
1509                 System.out.println( "HTML" );
1510                 break;
1511             case SIMPLE_TAB_DELIMITED:
1512                 System.out.println( "simple tab delimited" );
1513                 break;
1514             default:
1515                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
1516         }
1517         System.out.print( "  Species matrix            : " + species_matrix );
1518         System.out.println();
1519         final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
1520         System.out.println( "Domain comb data output     : " + dc_data_file );
1521         html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
1522         System.out.println();
1523         if ( perform_pwc ) {
1524             System.out.println( "Pairwise comparisons: " );
1525             html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
1526             System.out.print( "  Sort by                   : " );
1527             html_desc.append( "<tr><td>Sort by:</td><td>" );
1528             switch ( domain_similarity_sort_field_for_automated_pwc ) {
1529                 case MEAN:
1530                     System.out.print( "score mean" );
1531                     html_desc.append( "score mean" );
1532                     break;
1533                 case DOMAIN_ID:
1534                     System.out.print( "alphabetical domain identifier" );
1535                     html_desc.append( "alphabetical domain identifier" );
1536                     break;
1537                 case MAX_DIFFERENCE:
1538                     System.out.print( "difference" );
1539                     html_desc.append( "difference" );
1540                     break;
1541                 case ABS_MAX_COUNTS_DIFFERENCE:
1542                     System.out.print( "absolute counts difference" );
1543                     html_desc.append( "absolute counts difference" );
1544                     break;
1545                 case MAX_COUNTS_DIFFERENCE:
1546                     System.out.print( "counts difference" );
1547                     html_desc.append( "counts difference" );
1548                     break;
1549                 default:
1550                     ForesterUtil
1551                             .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1552             }
1553             System.out.println();
1554             html_desc.append( "</td></tr>" + nl );
1555             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
1556                 for( final File intree_file : intree_files ) {
1557                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
1558                             + "</td></tr>" + nl );
1559                     System.out.println( "  Intree for gain/loss pars.: " + intree_file );
1560                 }
1561             }
1562             if ( radomize_fitch_parsimony ) {
1563                 html_desc.append( "<tr><td>    Random number seed for Fitch parsimony analysis:</td><td>"
1564                         + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
1565                 System.out.println( "    Random number seed      : " + random_number_seed_for_fitch_parsimony );
1566             }
1567             if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1568                 for( int i = 0; i < secondary_features_map_files.length; i++ ) {
1569                     html_desc.append( "<tr><td>Secondary features map file:</td><td>"
1570                             + secondary_features_map_files[ i ] + "</td></tr>" + nl );
1571                     System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
1572                             + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
1573                     if ( VERBOSE ) {
1574                         System.out.println();
1575                         System.out.println( "Domain ids to secondary features map:" );
1576                         for( final String domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
1577                             System.out.print( domain_id );
1578                             System.out.print( " => " );
1579                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
1580                                 System.out.print( sec );
1581                                 System.out.print( " " );
1582                             }
1583                             System.out.println();
1584                         }
1585                     }
1586                 }
1587             }
1588         } // if ( perform_pwc ) {
1589         System.out.println();
1590         html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
1591         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
1592         BufferedWriter[] query_domains_writer_ary = null;
1593         List<String>[] query_domain_ids_array = null;
1594         if ( query_domain_ids != null ) {
1595             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
1596             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
1597             query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
1598             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
1599                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
1600                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
1601                 final List<String> query = new ArrayList<String>();
1602                 for( final String element : query_domain_ids_str_ary ) {
1603                     query.add( element );
1604                 }
1605                 query_domain_ids_array[ i ] = query;
1606                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
1607                 String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX;
1608                 if ( out_dir != null ) {
1609                     protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
1610                 }
1611                 try {
1612                     query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
1613                 }
1614                 catch ( final IOException e ) {
1615                     ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
1616                             + e.getLocalizedMessage() );
1617                 }
1618             }
1619         }
1620         SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
1621         boolean need_protein_lists_per_species = false;
1622         if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
1623             need_protein_lists_per_species = true;
1624         }
1625         if ( need_protein_lists_per_species ) {
1626             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
1627         }
1628         List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
1629         final SortedSet<String> all_domains_encountered = new TreeSet<String>();
1630         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
1631         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
1632         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
1633         if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
1634             all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
1635             all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
1636         }
1637         final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
1638         final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
1639                 + output_file + D_PROMISCUITY_FILE_SUFFIX );
1640         BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
1641         try {
1642             per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
1643             per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
1644             per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
1645             per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
1646             per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
1647             per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
1648             per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
1649             per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
1650             per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
1651                     + ForesterUtil.LINE_SEPARATOR );
1652         }
1653         catch ( final IOException e2 ) {
1654             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1655         }
1656         final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
1657         BufferedWriter log_writer = null;
1658         try {
1659             log_writer = new BufferedWriter( new FileWriter( log_file ) );
1660         }
1661         catch ( final IOException e2 ) {
1662             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1663         }
1664         BufferedWriter dc_data_writer = null;
1665         try {
1666             dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
1667             dc_data_writer.write( DATA_FILE_DESC );
1668             dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
1669         }
1670         catch ( final IOException e2 ) {
1671             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1672         }
1673         final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics();
1674         final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics();
1675         final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
1676         final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
1677         final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
1678         final SortedSet<String> domains_which_never_single = new TreeSet<String>();
1679         BufferedWriter domains_per_potein_stats_writer = null;
1680         try {
1681             domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
1682                     + output_file + "_domains_per_potein_stats.txt" ) );
1683             domains_per_potein_stats_writer.write( "Genome" );
1684             domains_per_potein_stats_writer.write( "\t" );
1685             domains_per_potein_stats_writer.write( "Mean" );
1686             domains_per_potein_stats_writer.write( "\t" );
1687             domains_per_potein_stats_writer.write( "SD" );
1688             domains_per_potein_stats_writer.write( "\t" );
1689             domains_per_potein_stats_writer.write( "Median" );
1690             domains_per_potein_stats_writer.write( "\t" );
1691             domains_per_potein_stats_writer.write( "N" );
1692             domains_per_potein_stats_writer.write( "\t" );
1693             domains_per_potein_stats_writer.write( "Min" );
1694             domains_per_potein_stats_writer.write( "\t" );
1695             domains_per_potein_stats_writer.write( "Max" );
1696             domains_per_potein_stats_writer.write( "\n" );
1697         }
1698         catch ( final IOException e3 ) {
1699             e3.printStackTrace();
1700         }
1701         Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
1702         Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
1703         final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
1704         if ( perform_dc_regain_proteins_stats ) {
1705             protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1706             domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1707         }
1708         // Main loop:
1709         final SortedMap<String, Set<String>> distinct_domain_architecutures_per_genome = new TreeMap<String, Set<String>>();
1710         final SortedMap<String, Integer> distinct_domain_architecuture_counts = new TreeMap<String, Integer>();
1711         for( int i = 0; i < number_of_genomes; ++i ) {
1712             System.out.println();
1713             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
1714             log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
1715             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 1 ]
1716                     + " [" + input_file_properties[ i ][ 0 ] + "]" );
1717             log( "Genome                                         : " + input_file_properties[ i ][ 1 ] + " ["
1718                     + input_file_properties[ i ][ 0 ] + "]", log_writer );
1719             HmmscanPerDomainTableParser parser = null;
1720             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
1721             if ( individual_score_cutoffs != null ) {
1722                 ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
1723             }
1724             if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1725                     || ( negative_domains_filter_file != null ) ) {
1726                 HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
1727                 if ( positive_filter_file != null ) {
1728                     filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
1729                 }
1730                 else if ( negative_filter_file != null ) {
1731                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
1732                 }
1733                 else if ( negative_domains_filter_file != null ) {
1734                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
1735                 }
1736                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1737                                                           input_file_properties[ i ][ 1 ],
1738                                                           filter,
1739                                                           filter_type,
1740                                                           ind_score_cutoff,
1741                                                           true );
1742             }
1743             else {
1744                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1745                                                           input_file_properties[ i ][ 1 ],
1746                                                           ind_score_cutoff,
1747                                                           true );
1748             }
1749             if ( e_value_max >= 0.0 ) {
1750                 parser.setEValueMaximum( e_value_max );
1751             }
1752             parser.setIgnoreDufs( ignore_dufs );
1753             parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
1754             parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
1755             if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1756                 parser.setMaxAllowedOverlap( max_allowed_overlap );
1757             }
1758             parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
1759             if ( individual_score_cutoffs != null ) {
1760                 parser.setIndividualScoreCutoffs( individual_score_cutoffs );
1761             }
1762             List<Protein> protein_list = null;
1763             try {
1764                 protein_list = parser.parse();
1765             }
1766             catch ( final IOException e ) {
1767                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1768             }
1769             catch ( final Exception e ) {
1770                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
1771             }
1772             if ( VERBOSE ) {
1773                 System.out.println( "Domains ignored due to negative domain filter: " );
1774                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
1775                 System.out.println( "Domains ignored due to virus like id: " );
1776                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
1777             }
1778             final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
1779             protein_coverage_stats.addValue( coverage );
1780             int distinct_das = -1;
1781             if ( da_analysis ) {
1782                 final String genome = input_file_properties[ i ][ 0 ];
1783                 distinct_das = SurfacingUtil.storeDomainArchitectures( genome,
1784                                                                        distinct_domain_architecutures_per_genome,
1785                                                                        protein_list,
1786                                                                        distinct_domain_architecuture_counts );
1787             }
1788             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
1789             log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(), log_writer );
1790             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
1791             log( "Number of proteins stored                      : " + protein_list.size(), log_writer );
1792             System.out.println( "Coverage                                       : "
1793                     + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
1794             log( "Coverage                                       : " + ForesterUtil.roundToInt( 100.0 * coverage )
1795                     + "%", log_writer );
1796             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
1797             log( "Domains encountered                            : " + parser.getDomainsEncountered(), log_writer );
1798             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
1799             log( "Domains stored                                 : " + parser.getDomainsStored(), log_writer );
1800             System.out.println( "Distinct domains stored                        : "
1801                     + parser.getDomainsStoredSet().size() );
1802             log( "Distinct domains stored                        : " + parser.getDomainsStoredSet().size(), log_writer );
1803             System.out.println( "Domains ignored due to individual score cutoffs: "
1804                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
1805             log( "Domains ignored due to individual score cutoffs: "
1806                          + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
1807                  log_writer );
1808             System.out.println( "Domains ignored due to E-value                 : "
1809                     + parser.getDomainsIgnoredDueToEval() );
1810             log( "Domains ignored due to E-value                 : " + parser.getDomainsIgnoredDueToEval(), log_writer );
1811             System.out.println( "Domains ignored due to DUF designation         : "
1812                     + parser.getDomainsIgnoredDueToDuf() );
1813             log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
1814             if ( ignore_virus_like_ids ) {
1815                 System.out.println( "Domains ignored due virus like ids             : "
1816                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
1817                 log( "Domains ignored due virus like ids             : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
1818                      log_writer );
1819             }
1820             System.out.println( "Domains ignored due negative domain filter     : "
1821                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
1822             log( "Domains ignored due negative domain filter     : "
1823                          + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
1824                  log_writer );
1825             System.out.println( "Domains ignored due to overlap                 : "
1826                     + parser.getDomainsIgnoredDueToOverlap() );
1827             log( "Domains ignored due to overlap                 : " + parser.getDomainsIgnoredDueToOverlap(),
1828                  log_writer );
1829             if ( negative_filter_file != null ) {
1830                 System.out.println( "Proteins ignored due to negative filter        : "
1831                         + parser.getProteinsIgnoredDueToFilter() );
1832                 log( "Proteins ignored due to negative filter        : " + parser.getProteinsIgnoredDueToFilter(),
1833                      log_writer );
1834             }
1835             if ( positive_filter_file != null ) {
1836                 System.out.println( "Proteins ignored due to positive filter        : "
1837                         + parser.getProteinsIgnoredDueToFilter() );
1838                 log( "Proteins ignored due to positive filter        : " + parser.getProteinsIgnoredDueToFilter(),
1839                      log_writer );
1840             }
1841             if ( da_analysis ) {
1842                 System.out.println( "Distinct domain architectures stored           : " + distinct_das );
1843                 log( "Distinct domain architectures stored           : " + distinct_das, log_writer );
1844             }
1845             System.out.println( "Time for processing                            : " + parser.getTime() + "ms" );
1846             log( "", log_writer );
1847             html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + ":</td><td>doms analyzed: "
1848                     + parser.getDomainsStored() + "; doms ignored: [ind score cutoffs: "
1849                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
1850                     + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
1851                     + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds() + "] [negative dom filter: "
1852                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() + "] [overlap: "
1853                     + parser.getDomainsIgnoredDueToOverlap() + "]" );
1854             if ( negative_filter_file != null ) {
1855                 html_desc.append( "; proteins ignored due to negative filter: "
1856                         + parser.getProteinsIgnoredDueToFilter() );
1857             }
1858             if ( positive_filter_file != null ) {
1859                 html_desc.append( "; proteins ignored due to positive filter: "
1860                         + parser.getProteinsIgnoredDueToFilter() );
1861             }
1862             html_desc.append( "</td></tr>" + nl );
1863             try {
1864                 int count = 0;
1865                 for( final Protein protein : protein_list ) {
1866                     dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
1867                             .toString() );
1868                     ++count;
1869                     for( final Domain d : protein.getProteinDomains() ) {
1870                         final String d_str = d.getDomainId().toString();
1871                         if ( !domain_length_stats_by_domain.containsKey( d_str ) ) {
1872                             domain_length_stats_by_domain.put( d_str, new BasicDescriptiveStatistics() );
1873                         }
1874                         domain_length_stats_by_domain.get( d_str ).addValue( d.getLength() );
1875                     }
1876                 }
1877             }
1878             catch ( final IOException e ) {
1879                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
1880             }
1881             SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ],
1882                                                         protein_list,
1883                                                         all_genomes_domains_per_potein_stats,
1884                                                         all_genomes_domains_per_potein_histo,
1885                                                         domains_which_are_always_single,
1886                                                         domains_which_are_sometimes_single_sometimes_not,
1887                                                         domains_which_never_single,
1888                                                         domains_per_potein_stats_writer );
1889             domain_lengths_table.addLengths( protein_list );
1890             if ( !da_analysis ) {
1891                 gwcd_list.add( BasicGenomeWideCombinableDomains
1892                         .createInstance( protein_list,
1893                                          ignore_combination_with_same,
1894                                          new BasicSpecies( input_file_properties[ i ][ 1 ] ),
1895                                          domain_id_to_go_ids_map,
1896                                          dc_type,
1897                                          protein_length_stats_by_dc,
1898                                          domain_number_stats_by_dc ) );
1899                 if ( gwcd_list.get( i ).getSize() > 0 ) {
1900                     SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
1901                                                                      out_dir,
1902                                                                      per_genome_domain_promiscuity_statistics_writer,
1903                                                                      gwcd_list.get( i ),
1904                                                                      i,
1905                                                                      dc_sort_order );
1906                     if ( output_binary_domain_combinationsfor_graph_analysis ) {
1907                         SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
1908                                                                                          out_dir,
1909                                                                                          gwcd_list.get( i ),
1910                                                                                          i,
1911                                                                                          dc_sort_order );
1912                     }
1913                     SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
1914                     SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
1915                                                                       all_bin_domain_combinations_encountered );
1916                 }
1917             }
1918             if ( query_domains_writer_ary != null ) {
1919                 for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1920                     try {
1921                         SurfacingUtil.extractProteinNames( protein_list,
1922                                                            query_domain_ids_array[ j ],
1923                                                            query_domains_writer_ary[ j ],
1924                                                            "\t",
1925                                                            LIMIT_SPEC_FOR_PROT_EX );
1926                         query_domains_writer_ary[ j ].flush();
1927                     }
1928                     catch ( final IOException e ) {
1929                         e.printStackTrace();
1930                     }
1931                 }
1932             }
1933             if ( need_protein_lists_per_species ) {
1934                 protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
1935             }
1936             try {
1937                 log_writer.flush();
1938             }
1939             catch ( final IOException e2 ) {
1940                 ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1941             }
1942             System.gc();
1943         } // for( int i = 0; i < number_of_genomes; ++i ) {
1944         ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
1945                 + per_genome_domain_promiscuity_statistics_file );
1946         //
1947         if ( da_analysis ) {
1948             SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
1949                                                              distinct_domain_architecuture_counts,
1950                                                              10,
1951                                                              new File( out_dir.toString() + "/" + output_file
1952                                                                      + "_DA_counts.txt" ),
1953                                                              new File( out_dir.toString() + "/" + output_file
1954                                                                      + "_unique_DAs.txt" ) );
1955             distinct_domain_architecutures_per_genome.clear();
1956             distinct_domain_architecuture_counts.clear();
1957             System.gc();
1958         }
1959         try {
1960             domains_per_potein_stats_writer.write( "ALL" );
1961             domains_per_potein_stats_writer.write( "\t" );
1962             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" );
1963             domains_per_potein_stats_writer.write( "\t" );
1964             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" );
1965             domains_per_potein_stats_writer.write( "\t" );
1966             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" );
1967             domains_per_potein_stats_writer.write( "\t" );
1968             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" );
1969             domains_per_potein_stats_writer.write( "\t" );
1970             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" );
1971             domains_per_potein_stats_writer.write( "\t" );
1972             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
1973             domains_per_potein_stats_writer.write( "\n" );
1974             domains_per_potein_stats_writer.close();
1975             printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
1976             ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1977                     + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
1978             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1979                     + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
1980             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1981                     + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
1982             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1983                     + "_domains_always_combined.txt" ), domains_which_never_single, "\n" );
1984             ForesterUtil.programMessage( PRG_NAME,
1985                                          "Average of proteins with a least one domain assigned: "
1986                                                  + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
1987                                                  + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" );
1988             ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: "
1989                     + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() )
1990                     + "%" );
1991             log( "Average of prot with a least one dom assigned  : " + ( 100 * protein_coverage_stats.arithmeticMean() )
1992                     + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
1993             log( "Range of prot with a least one dom assigned    : " + ( 100 * protein_coverage_stats.getMin() ) + "%-"
1994                     + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer );
1995         }
1996         catch ( final IOException e2 ) {
1997             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1998         }
1999         if ( query_domains_writer_ary != null ) {
2000             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
2001                 try {
2002                     query_domains_writer_ary[ j ].close();
2003                 }
2004                 catch ( final IOException e ) {
2005                     ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
2006                 }
2007             }
2008         }
2009         try {
2010             per_genome_domain_promiscuity_statistics_writer.close();
2011             dc_data_writer.close();
2012             log_writer.close();
2013         }
2014         catch ( final IOException e2 ) {
2015             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2016         }
2017         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
2018             try {
2019                 SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
2020                                                            number_of_genomes,
2021                                                            domain_lengths_table,
2022                                                            domain_lengths_analysis_outfile );
2023             }
2024             catch ( final IOException e1 ) {
2025                 ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
2026             }
2027             System.out.println();
2028             ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
2029             System.out.println();
2030         }
2031         final long analysis_start_time = new Date().getTime();
2032         PairwiseDomainSimilarityCalculator pw_calc = null;
2033         // double[] values_for_all_scores_histogram = null;
2034         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
2035                                                                                      sort_by_species_count_first,
2036                                                                                      number_of_genomes == 2 );
2037         switch ( scoring ) {
2038             case COMBINATIONS:
2039                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
2040                 break;
2041             case DOMAINS:
2042                 pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
2043                 break;
2044             case PROTEINS:
2045                 pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
2046                 break;
2047             default:
2048                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
2049         }
2050         DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
2051         if ( domain_id_to_go_ids_map != null ) {
2052             go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
2053         }
2054         final SortedSet<DomainSimilarity> similarities = calc
2055                 .calculateSimilarities( pw_calc,
2056                                         gwcd_list,
2057                                         ignore_domains_without_combs_in_all_spec,
2058                                         ignore_species_specific_domains );
2059         SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
2060         final Map<String, Integer> tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] );
2061         try {
2062             String my_outfile = output_file.toString();
2063             Map<Character, Writer> split_writers = null;
2064             Writer writer = null;
2065             if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
2066                 if ( my_outfile.endsWith( ".html" ) ) {
2067                     my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
2068                 }
2069                 split_writers = new HashMap<Character, Writer>();
2070                 createSplitWriters( out_dir, my_outfile, split_writers );
2071             }
2072             else if ( !my_outfile.endsWith( ".html" ) ) {
2073                 my_outfile += ".html";
2074                 writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
2075             }
2076             List<Species> species_order = null;
2077             if ( species_matrix ) {
2078                 species_order = new ArrayList<Species>();
2079                 for( int i = 0; i < number_of_genomes; i++ ) {
2080                     species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
2081                 }
2082             }
2083             html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
2084                     + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
2085             html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
2086                     + "</td></tr>" + nl );
2087             html_desc.append( "<tr><td>Analysis date/time:</td><td>"
2088                     + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
2089                     + "</td></tr>" + nl );
2090             html_desc.append( "</table>" + nl );
2091             final DescriptiveStatistics pw_stats = SurfacingUtil
2092                     .writeDomainSimilaritiesToFile( html_desc,
2093                                                     new StringBuilder( number_of_genomes + " genomes" ),
2094                                                     writer,
2095                                                     split_writers,
2096                                                     similarities,
2097                                                     number_of_genomes == 2,
2098                                                     species_order,
2099                                                     domain_similarity_print_option,
2100                                                     domain_similarity_sort_field,
2101                                                     scoring,
2102                                                     true,
2103                                                     tax_code_to_id_map );
2104             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
2105                     + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
2106         }
2107         catch ( final IOException e ) {
2108             ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
2109                     + e.getMessage() + "]" );
2110         }
2111         System.out.println();
2112         final Species[] species = new Species[ number_of_genomes ];
2113         for( int i = 0; i < number_of_genomes; ++i ) {
2114             species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
2115         }
2116         List<Phylogeny> inferred_trees = null;
2117         if ( ( number_of_genomes > 2 ) && perform_pwc ) {
2118             final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
2119             pwgc.performPairwiseComparisons( html_desc,
2120                                              sort_by_species_count_first,
2121                                              detailedness,
2122                                              ignore_domains_without_combs_in_all_spec,
2123                                              ignore_species_specific_domains,
2124                                              domain_similarity_sort_field_for_automated_pwc,
2125                                              domain_similarity_print_option,
2126                                              scoring,
2127                                              domain_id_to_go_ids_map,
2128                                              go_id_to_term_map,
2129                                              go_namespace_limit,
2130                                              species,
2131                                              number_of_genomes,
2132                                              gwcd_list,
2133                                              pw_calc,
2134                                              automated_pairwise_comparison_suffix,
2135                                              true,
2136                                              surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
2137                                              surfacing.PRG_NAME,
2138                                              out_dir,
2139                                              write_pwc_files,
2140                                              tax_code_to_id_map );
2141             String matrix_output_file = new String( output_file.toString() );
2142             if ( matrix_output_file.indexOf( '.' ) > 1 ) {
2143                 matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
2144             }
2145             if ( out_dir != null ) {
2146                 matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
2147                 output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2148             }
2149             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2150                     + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
2151             SurfacingUtil
2152                     .writeMatrixToFile( new File( matrix_output_file
2153                                                 + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2154                                         pwgc.getSharedBinaryCombinationsBasedDistances() );
2155             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2156                                                      + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2157                                              pwgc.getSharedDomainsBasedDistances() );
2158             final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2159                     + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
2160                     .get( 0 ) );
2161             final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2162                     + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2163                     .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
2164             final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2165                     + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2166                     .getSharedDomainsBasedDistances().get( 0 ) );
2167             inferred_trees = new ArrayList<Phylogeny>();
2168             inferred_trees.add( nj_gd );
2169             inferred_trees.add( nj_bc );
2170             inferred_trees.add( nj_d );
2171         } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
2172         if ( ( out_dir != null ) && ( !perform_pwc ) ) {
2173             output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2174         }
2175         if ( write_to_nexus ) {
2176             writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
2177         }
2178         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
2179             final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2180                                                                           e_value_max,
2181                                                                           max_allowed_overlap,
2182                                                                           no_engulfing_overlaps,
2183                                                                           cutoff_scores_file,
2184                                                                           dc_type );
2185             String s = "_";
2186             if ( radomize_fitch_parsimony ) {
2187                 s += random_number_seed_for_fitch_parsimony + "_";
2188             }
2189             int i = 0;
2190             for( final Phylogeny intree : intrees ) {
2191                 final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
2192                         + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
2193                 final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
2194                                                                                                              gwcd_list );
2195                 SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2196                                                         radomize_fitch_parsimony,
2197                                                         outfile_name,
2198                                                         domain_parsimony,
2199                                                         intree,
2200                                                         domain_id_to_go_ids_map,
2201                                                         go_id_to_term_map,
2202                                                         go_namespace_limit,
2203                                                         parameters_sb.toString(),
2204                                                         domain_id_to_secondary_features_maps,
2205                                                         positive_filter_file == null ? null : filter,
2206                                                         output_binary_domain_combinationsfor_graph_analysis,
2207                                                         all_bin_domain_combinations_gained_fitch,
2208                                                         all_bin_domain_combinations_lost_fitch,
2209                                                         dc_type,
2210                                                         protein_length_stats_by_dc,
2211                                                         domain_number_stats_by_dc,
2212                                                         domain_length_stats_by_domain,
2213                                                         tax_code_to_id_map,
2214                                                         write_to_nexus,
2215                                                         use_last_in_fitch_parsimony );
2216                 // Listing of all domain combinations gained is only done if only one input tree is used.
2217                 if ( ( domain_id_to_secondary_features_maps != null )
2218                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
2219                     int j = 0;
2220                     for( final Map<String, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
2221                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
2222                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
2223                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
2224                         SurfacingUtil
2225                                 .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
2226                                                                                        + "_"
2227                                                                                        + secondary_features_map_files[ j++ ],
2228                                                                                secondary_features_parsimony,
2229                                                                                intree,
2230                                                                                parameters_sb.toString(),
2231                                                                                mapping_results_map,
2232                                                                                use_last_in_fitch_parsimony );
2233                         if ( i == 0 ) {
2234                             System.out.println();
2235                             System.out.println( "Mapping to secondary features:" );
2236                             for( final Species spec : mapping_results_map.keySet() ) {
2237                                 final MappingResults mapping_results = mapping_results_map.get( spec );
2238                                 final int total_domains = mapping_results.getSumOfFailures()
2239                                         + mapping_results.getSumOfSuccesses();
2240                                 System.out.print( spec + ":" );
2241                                 System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
2242                                 System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
2243                                 if ( total_domains > 0 ) {
2244                                     System.out.println( ", mapped ratio = "
2245                                             + ( ( 100 * mapping_results.getSumOfSuccesses() ) / total_domains ) + "%" );
2246                                 }
2247                                 else {
2248                                     System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
2249                                 }
2250                             }
2251                         }
2252                     }
2253                 }
2254                 i++;
2255             } // for( final Phylogeny intree : intrees ) {
2256         }
2257         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
2258             executePlusMinusAnalysis( output_file,
2259                                       plus_minus_analysis_high_copy_base_species,
2260                                       plus_minus_analysis_high_copy_target_species,
2261                                       plus_minus_analysis_high_low_copy_species,
2262                                       gwcd_list,
2263                                       protein_lists_per_species,
2264                                       domain_id_to_go_ids_map,
2265                                       go_id_to_term_map,
2266                                       plus_minus_analysis_numbers );
2267         }
2268         if ( output_protein_lists_for_all_domains ) {
2269             writeProteinListsForAllSpecies( out_dir,
2270                                             protein_lists_per_species,
2271                                             gwcd_list,
2272                                             output_list_of_all_proteins_per_domain_e_value_max );
2273         }
2274         gwcd_list = null;
2275         if ( all_bin_domain_combinations_gained_fitch != null ) {
2276             try {
2277                 executeFitchGainsAnalysis( new File( output_file
2278                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2279                                            all_bin_domain_combinations_gained_fitch,
2280                                            all_domains_encountered.size(),
2281                                            all_bin_domain_combinations_encountered,
2282                                            true );
2283             }
2284             catch ( final IOException e ) {
2285                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2286             }
2287         }
2288         if ( all_bin_domain_combinations_lost_fitch != null ) {
2289             try {
2290                 executeFitchGainsAnalysis( new File( output_file
2291                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2292                                            all_bin_domain_combinations_lost_fitch,
2293                                            all_domains_encountered.size(),
2294                                            all_bin_domain_combinations_encountered,
2295                                            false );
2296             }
2297             catch ( final IOException e ) {
2298                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2299             }
2300         }
2301         final Runtime rt = java.lang.Runtime.getRuntime();
2302         final long free_memory = rt.freeMemory() / 1000000;
2303         final long total_memory = rt.totalMemory() / 1000000;
2304         ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time )
2305                 + "ms" );
2306         ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
2307         ForesterUtil.programMessage( PRG_NAME, "Free memory       : " + free_memory + "MB, total memory: "
2308                 + total_memory + "MB" );
2309         ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" );
2310         ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
2311         ForesterUtil.programMessage( PRG_NAME, "OK" );
2312         System.out.println();
2313     }
2314
2315     private static void createSplitWriters( final File out_dir,
2316                                             final String my_outfile,
2317                                             final Map<Character, Writer> split_writers ) throws IOException {
2318         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2319                 + "_domains_A.html" ) ) );
2320         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2321                 + "_domains_B.html" ) ) );
2322         split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2323                 + "_domains_C.html" ) ) );
2324         split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2325                 + "_domains_D.html" ) ) );
2326         split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2327                 + "_domains_E.html" ) ) );
2328         split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2329                 + "_domains_F.html" ) ) );
2330         split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2331                 + "_domains_G.html" ) ) );
2332         split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2333                 + "_domains_H.html" ) ) );
2334         split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2335                 + "_domains_I.html" ) ) );
2336         split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2337                 + "_domains_J.html" ) ) );
2338         split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2339                 + "_domains_K.html" ) ) );
2340         split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2341                 + "_domains_L.html" ) ) );
2342         split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2343                 + "_domains_M.html" ) ) );
2344         split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2345                 + "_domains_N.html" ) ) );
2346         split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2347                 + "_domains_O.html" ) ) );
2348         split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2349                 + "_domains_P.html" ) ) );
2350         split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2351                 + "_domains_Q.html" ) ) );
2352         split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2353                 + "_domains_R.html" ) ) );
2354         split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2355                 + "_domains_S.html" ) ) );
2356         split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2357                 + "_domains_T.html" ) ) );
2358         split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2359                 + "_domains_U.html" ) ) );
2360         split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2361                 + "_domains_V.html" ) ) );
2362         split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2363                 + "_domains_W.html" ) ) );
2364         split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2365                 + "_domains_X.html" ) ) );
2366         split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2367                 + "_domains_Y.html" ) ) );
2368         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2369                 + "_domains_Z.html" ) ) );
2370         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2371                 + "_domains_0.html" ) ) );
2372     }
2373
2374     private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2375                                                                  final Writer log_writer ) {
2376         int sum = 0;
2377         for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
2378             sum += entry.getValue();
2379         }
2380         final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
2381         ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
2382         log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
2383     }
2384
2385     private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
2386                                                               final String[][] input_file_properties ) {
2387         final String[] genomes = new String[ input_file_properties.length ];
2388         for( int i = 0; i < input_file_properties.length; ++i ) {
2389             if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
2390                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2391                         + "] is not unique in input tree " + intree.getName() );
2392             }
2393             genomes[ i ] = input_file_properties[ i ][ 1 ];
2394         }
2395         //
2396         final PhylogenyNodeIterator it = intree.iteratorPostorder();
2397         while ( it.hasNext() ) {
2398             final PhylogenyNode n = it.next();
2399             if ( ForesterUtil.isEmpty( n.getName() ) ) {
2400                 if ( n.getNodeData().isHasTaxonomy()
2401                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
2402                     n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
2403                 }
2404                 else if ( n.getNodeData().isHasTaxonomy()
2405                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
2406                     n.setName( n.getNodeData().getTaxonomy().getScientificName() );
2407                 }
2408                 else if ( n.getNodeData().isHasTaxonomy()
2409                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
2410                     n.setName( n.getNodeData().getTaxonomy().getCommonName() );
2411                 }
2412                 else {
2413                     ForesterUtil
2414                             .fatalError( surfacing.PRG_NAME,
2415                                          "node with no name, scientific name, common name, or taxonomy code present" );
2416                 }
2417             }
2418         }
2419         //
2420         final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
2421         if ( igns.size() > 0 ) {
2422             System.out.println( "Not using the following " + igns.size() + " nodes:" );
2423             for( int i = 0; i < igns.size(); ++i ) {
2424                 System.out.println( " " + i + ": " + igns.get( i ) );
2425             }
2426             System.out.println( "--" );
2427         }
2428         for( final String[] input_file_propertie : input_file_properties ) {
2429             try {
2430                 intree.getNode( input_file_propertie[ 1 ] );
2431             }
2432             catch ( final IllegalArgumentException e ) {
2433                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
2434                         + "] not present/not unique in input tree" );
2435             }
2436         }
2437     }
2438
2439     private static void printHelp() {
2440         System.out.println();
2441         System.out.println( "Usage:" );
2442         System.out.println();
2443         System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME
2444                 + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
2445         System.out.println();
2446         System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
2447         System.out
2448                 .println( "       hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
2449         System.out.println();
2450         System.out.println( " Options: " );
2451         System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
2452                 + DETAILEDNESS_DEFAULT + ")" );
2453         System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
2454                 + ": to ignore combinations with self (default: not to ignore)" );
2455         System.out
2456                 .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
2457                         + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2458         System.out
2459                 .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
2460                         + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2461         System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
2462                 + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
2463         System.out
2464                 .println( surfacing.IGNORE_VIRAL_IDS
2465                         + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
2466         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
2467                 + DOMAIN_SORT_FILD_DEFAULT + ")" );
2468         System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
2469         System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
2470         System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
2471         System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
2472         System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
2473         System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
2474         System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
2475                 + DOMAINS_SORT_ORDER_DEFAULT + ")" );
2476         System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
2477                 + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
2478         System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
2479         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
2480                 + ": sort by species count first" );
2481         System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
2482         System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
2483         System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
2484         System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
2485         System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
2486                 + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
2487         System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
2488                 + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
2489         System.out
2490                 .println( surfacing.INPUT_SPECIES_TREE_OPTION
2491                         + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
2492         System.out.println( surfacing.FILTER_POSITIVE_OPTION
2493                 + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
2494         System.out.println( surfacing.FILTER_NEGATIVE_OPTION
2495                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
2496         System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
2497                 + "=<file>: to filter out (ignore) domains listed in <file>" );
2498         System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>: to read input files from <file>" );
2499         System.out
2500                 .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
2501                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
2502         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
2503                 + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
2504         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
2505                 + ": to consider directedness and adjacency in binary combinations" );
2506         System.out
2507                 .println( surfacing.SEQ_EXTRACT_OPTION
2508                         + "=<domain ids (Pfam names)>: 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')" );
2509         System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
2510                 + "=<file>: to perfom parsimony analysis on secondary features" );
2511         System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
2512         System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
2513                 + ": to output binary domain combinations for (downstream) graph analysis" );
2514         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
2515         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
2516                 + ": e value max per domain for output of all proteins per domain" );
2517         System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" );
2518         System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" );
2519         System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" );
2520         System.out.println( DA_ANALYSIS_OPTION + ": to do DA analysis" );
2521         System.out.println();
2522         System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2523                 + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
2524                 + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o "
2525                 + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
2526         System.out.println();
2527         System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2528                 + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
2529                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
2530                 + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
2531                 + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
2532         System.out.println();
2533     }
2534
2535     private static void processFilter( final File filter_file, final SortedSet<String> filter ) {
2536         SortedSet<String> filter_str = null;
2537         try {
2538             filter_str = ForesterUtil.file2set( filter_file );
2539         }
2540         catch ( final IOException e ) {
2541             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2542         }
2543         if ( filter_str != null ) {
2544             for( final String string : filter_str ) {
2545                 filter.add( string );
2546             }
2547         }
2548         if ( VERBOSE ) {
2549             System.out.println( "Filter:" );
2550             for( final String domainId : filter ) {
2551                 System.out.println( domainId );
2552             }
2553         }
2554     }
2555
2556     private static String[][] processInputGenomesFile( final File input_genomes ) {
2557         String[][] input_file_properties = null;
2558         try {
2559             input_file_properties = ForesterUtil.file22dArray( input_genomes );
2560         }
2561         catch ( final IOException e ) {
2562             ForesterUtil.fatalError( surfacing.PRG_NAME,
2563                                      "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
2564                                              + e.getLocalizedMessage() );
2565         }
2566         final Set<String> specs = new HashSet<String>();
2567         final Set<String> paths = new HashSet<String>();
2568         for( int i = 0; i < input_file_properties.length; ++i ) {
2569             if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
2570                 ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
2571                         + input_file_properties[ i ][ 1 ] );
2572             }
2573             if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
2574                 ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
2575                         + " is not unique" );
2576             }
2577             specs.add( input_file_properties[ i ][ 1 ] );
2578             if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
2579                 ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
2580                         + " is not unique" );
2581             }
2582             paths.add( input_file_properties[ i ][ 0 ] );
2583             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
2584             if ( !ForesterUtil.isEmpty( error ) ) {
2585                 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
2586             }
2587         }
2588         return input_file_properties;
2589     }
2590
2591     private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
2592                                                         final List<String> high_copy_base,
2593                                                         final List<String> high_copy_target,
2594                                                         final List<String> low_copy,
2595                                                         final List<Object> numbers ) {
2596         if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2597             if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2598                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
2599                         + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
2600             }
2601             final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
2602             final String msg = ForesterUtil.isReadableFile( plus_minus_file );
2603             if ( !ForesterUtil.isEmpty( msg ) ) {
2604                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
2605             }
2606             processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
2607         }
2608     }
2609
2610     // First numbers is minimal difference, second is factor.
2611     private static void processPlusMinusFile( final File plus_minus_file,
2612                                               final List<String> high_copy_base,
2613                                               final List<String> high_copy_target,
2614                                               final List<String> low_copy,
2615                                               final List<Object> numbers ) {
2616         Set<String> species_set = null;
2617         int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
2618         double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
2619         try {
2620             species_set = ForesterUtil.file2set( plus_minus_file );
2621         }
2622         catch ( final IOException e ) {
2623             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2624         }
2625         if ( species_set != null ) {
2626             for( final String species : species_set ) {
2627                 final String species_trimmed = species.substring( 1 );
2628                 if ( species.startsWith( "+" ) ) {
2629                     if ( low_copy.contains( species_trimmed ) ) {
2630                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2631                                                  "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
2632                                                          + species_trimmed + "\"" );
2633                     }
2634                     high_copy_base.add( species_trimmed );
2635                 }
2636                 else if ( species.startsWith( "*" ) ) {
2637                     if ( low_copy.contains( species_trimmed ) ) {
2638                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2639                                                  "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
2640                                                          + species_trimmed + "\"" );
2641                     }
2642                     high_copy_target.add( species_trimmed );
2643                 }
2644                 else if ( species.startsWith( "-" ) ) {
2645                     if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
2646                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2647                                                  "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
2648                                                          + species_trimmed + "\"" );
2649                     }
2650                     low_copy.add( species_trimmed );
2651                 }
2652                 else if ( species.startsWith( "$D" ) ) {
2653                     try {
2654                         min_diff = Integer.parseInt( species.substring( 3 ) );
2655                     }
2656                     catch ( final NumberFormatException e ) {
2657                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2658                                                  "could not parse integer value for minimal difference from: \""
2659                                                          + species.substring( 3 ) + "\"" );
2660                     }
2661                 }
2662                 else if ( species.startsWith( "$F" ) ) {
2663                     try {
2664                         factor = Double.parseDouble( species.substring( 3 ) );
2665                     }
2666                     catch ( final NumberFormatException e ) {
2667                         ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
2668                                 + species.substring( 3 ) + "\"" );
2669                     }
2670                 }
2671                 else if ( species.startsWith( "#" ) ) {
2672                     // Comment, ignore.
2673                 }
2674                 else {
2675                     ForesterUtil
2676                             .fatalError( surfacing.PRG_NAME,
2677                                          "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
2678                                                  + species + "\"" );
2679                 }
2680                 numbers.add( new Integer( min_diff + "" ) );
2681                 numbers.add( new Double( factor + "" ) );
2682             }
2683         }
2684         else {
2685             ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
2686         }
2687     }
2688
2689     private static void writePresentToNexus( final File output_file,
2690                                              final File positive_filter_file,
2691                                              final SortedSet<String> filter,
2692                                              final List<GenomeWideCombinableDomains> gwcd_list ) {
2693         try {
2694             SurfacingUtil
2695                     .writeMatrixToFile( DomainParsimonyCalculator
2696                             .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
2697                                     : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
2698             SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
2699                     .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
2700                     + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
2701         }
2702         catch ( final Exception e ) {
2703             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2704         }
2705     }
2706
2707     private static void writeProteinListsForAllSpecies( final File output_dir,
2708                                                         final SortedMap<Species, List<Protein>> protein_lists_per_species,
2709                                                         final List<GenomeWideCombinableDomains> gwcd_list,
2710                                                         final double domain_e_cutoff ) {
2711         final SortedSet<String> all_domains = new TreeSet<String>();
2712         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2713             all_domains.addAll( gwcd.getAllDomainIds() );
2714         }
2715         for( final String domain : all_domains ) {
2716             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
2717             SurfacingUtil.checkForOutputFileWriteability( out );
2718             try {
2719                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2720                 SurfacingUtil.extractProteinNames( protein_lists_per_species,
2721                                                    domain,
2722                                                    proteins_file_writer,
2723                                                    "\t",
2724                                                    LIMIT_SPEC_FOR_PROT_EX,
2725                                                    domain_e_cutoff );
2726                 proteins_file_writer.close();
2727             }
2728             catch ( final IOException e ) {
2729                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2730             }
2731             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2732         }
2733     }
2734 }