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.List;
  38 import java.util.Map;
  39 import java.util.Set;
  40 import java.util.SortedMap;
  41 import java.util.SortedSet;
  42 import java.util.TreeMap;
  43 import java.util.TreeSet;
  44
  45 import org.forester.go.GoId;
  46 import org.forester.go.GoNameSpace;
  47 import org.forester.go.GoTerm;
  48 import org.forester.go.GoUtils;
  49 import org.forester.go.OBOparser;
  50 import org.forester.go.PfamToGoMapping;
  51 import org.forester.go.PfamToGoParser;
  52 import org.forester.io.parsers.HmmscanPerDomainTableParser;
  53 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
  54 import org.forester.phylogeny.Phylogeny;
  55 import org.forester.protein.BinaryDomainCombination;
  56 import org.forester.protein.Domain;
  57 import org.forester.protein.Protein;
  58 import org.forester.species.BasicSpecies;
  59 import org.forester.species.Species;
  60 import org.forester.surfacing.BasicDomainSimilarityCalculator;
  61 import org.forester.surfacing.BasicGenomeWideCombinableDomains;
  62 import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
  63 import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
  64 import org.forester.surfacing.DomainLengthsTable;
  65 import org.forester.surfacing.DomainParsimonyCalculator;
  66 import org.forester.surfacing.DomainSimilarity;
  67 import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
  68 import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
  69 import org.forester.surfacing.DomainSimilarityCalculator;
  70 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  71 import org.forester.surfacing.GenomeWideCombinableDomains;
  72 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  73 import org.forester.surfacing.MappingResults;
  74 import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
  75 import org.forester.surfacing.PairwiseGenomeComparator;
  76 import org.forester.surfacing.PrintableDomainSimilarity;
  77 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  78 import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
  79 import org.forester.surfacing.SurfacingUtil;
  80 import org.forester.util.BasicDescriptiveStatistics;
  81 import org.forester.util.BasicTable;
  82 import org.forester.util.BasicTableParser;
  83 import org.forester.util.CommandLineArguments;
  84 import org.forester.util.DescriptiveStatistics;
  85 import org.forester.util.ForesterConstants;
  86 import org.forester.util.ForesterUtil;
  87
  88 public class surfacing {
  89
  90     private static final int                                  MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING                                  = 1000;
  91     public final static String                                DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS                           = "graph_analysis_out";
  92     public final static String                                DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS                       = "_dc.dot";
  93     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS        = "_fitch_present_dc.dot";
  94     public final static String                                DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX                                    = ".dcc";
  95     // gain/loss:
  96     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS                                      = "_dollo_gl_d";
  97     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS                          = "_dollo_gl_dc";
  98     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS                                      = "_fitch_gl_d";
  99     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS                          = "_fitch_gl_dc";
 100     // gain/loss counts:
 101     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS                               = "_dollo_glc_d";
 102     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS                   = "_dollo_glc_dc";
 103     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS                               = "_fitch_glc_d";
 104     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS                   = "_fitch_glc_dc";
 105     // tables:
 106     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_BC                                               = "_fitch_gains_dc";
 107     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC                                          = "_fitch_gains_dc.html";
 108     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_BC                                              = "_fitch_losses_dc";
 109     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC                                         = "_fitch_losses_dc.html";
 110     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC                                             = "_fitch_present_dc";
 111     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC                                        = "_fitch_present_dc.html";
 112     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_D                                                = "_dollo_gains_d";
 113     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D                                           = "_dollo_gains_d.html";
 114     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_D                                               = "_dollo_losses_d";
 115     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D                                          = "_dollo_losses_d.html";
 116     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_D                                              = "_dollo_present_d";
 117     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D                                         = "_dollo_present_d.html";
 118     public final static String                                DOMAINS_PRESENT_NEXUS                                                         = "_dom.nex";
 119     public final static String                                BDC_PRESENT_NEXUS                                                             = "_dc.nex";
 120     // ---
 121     public final static String                                PRG_NAME                                                                      = "surfacing";
 122     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                                    = "_d_dollo"
 123                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 124     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                                    = "_d_fitch"
 125                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 126     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                 = "_dc_dollo"
 127                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 128     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                 = "_dc_fitch"
 129                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 130     public static final String                                NEXUS_EXTERNAL_DOMAINS                                                        = "_dom.nex";
 131     public static final String                                NEXUS_EXTERNAL_DOMAIN_COMBINATIONS                                            = "_dc.nex";
 132     public static final String                                NEXUS_SECONDARY_FEATURES                                                      = "_secondary_features.nex";
 133     public static final String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES                           = "_dollo_gl_secondary_features";
 134     public static final String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES                    = "_dollo_glc_secondary_features";
 135     public static final String                                PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES                               = "_dollo_gains_secondary_features";
 136     public static final String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES                              = "_dollo_losses_secondary_features";
 137     public static final String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES                             = "_dollo_present_secondary_features";
 138     public static final String                                SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                         = "_secondary_features_dollo"
 139                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 140     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES                              = "_dollo_goid_d";
 141     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES                             = "_fitch_goid_dc";
 142     final static private String                               HELP_OPTION_1                                                                 = "help";
 143     final static private String                               HELP_OPTION_2                                                                 = "h";
 144     final static private String                               OUTPUT_DIR_OPTION                                                             = "out_dir";
 145     final static private String                               SCORING_OPTION                                                                = "scoring";
 146     private static final DomainSimilarityScoring              SCORING_DEFAULT                                                               = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 147     final static private String                               SCORING_DOMAIN_COUNT_BASED                                                    = "domains";
 148     final static private String                               SCORING_PROTEIN_COUNT_BASED                                                   = "proteins";
 149     final static private String                               SCORING_COMBINATION_BASED                                                     = "combinations";
 150     final static private String                               DETAILEDNESS_OPTION                                                           = "detail";
 151     private final static Detailedness                         DETAILEDNESS_DEFAULT                                                          = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 152     final static private String                               SPECIES_MATRIX_OPTION                                                         = "smatrix";
 153     final static private String                               DETAILEDNESS_BASIC                                                            = "basic";
 154     final static private String                               DETAILEDNESS_LIST_IDS                                                         = "list_ids";
 155     final static private String                               DETAILEDNESS_PUNCTILIOUS                                                      = "punctilious";
 156     final static private String                               DOMAIN_SIMILARITY_SORT_OPTION                                                 = "sort";
 157     private static final DomainSimilaritySortField            DOMAIN_SORT_FILD_DEFAULT                                                      = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 158     final static private String                               DOMAIN_SIMILARITY_SORT_MIN                                                    = "min";
 159     final static private String                               DOMAIN_SIMILARITY_SORT_MAX                                                    = "max";
 160     final static private String                               DOMAIN_SIMILARITY_SORT_SD                                                     = "sd";
 161     final static private String                               DOMAIN_SIMILARITY_SORT_MEAN                                                   = "mean";
 162     final static private String                               DOMAIN_SIMILARITY_SORT_DIFF                                                   = "diff";
 163     final static private String                               DOMAIN_SIMILARITY_SORT_COUNTS_DIFF                                            = "count_diff";
 164     final static private String                               DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF                                        = "abs_count_diff";
 165     final static private String                               DOMAIN_SIMILARITY_SORT_SPECIES_COUNT                                          = "species";
 166     final static private String                               DOMAIN_SIMILARITY_SORT_ALPHA                                                  = "alpha";
 167     final static private String                               DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION                          = "species_first";
 168     final static private String                               DOMAIN_COUNT_SORT_OPTION                                                      = "dc_sort";
 169     private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT                                                    = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
 170     final static private String                               DOMAIN_COUNT_SORT_ALPHA                                                       = "alpha";
 171     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT                                            = "dom";
 172     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT                                   = "prot";
 173     final static private String                               DOMAIN_COUNT_SORT_COMBINATIONS_COUNT                                          = "comb";
 174     final static private String                               CUTOFF_SCORE_FILE_OPTION                                                      = "cos";
 175     final static private String                               NOT_IGNORE_DUFS_OPTION                                                        = "dufs";
 176     final static private String                               MAX_E_VALUE_OPTION                                                            = "e";
 177     final static private String                               MAX_ALLOWED_OVERLAP_OPTION                                                    = "mo";
 178     final static private String                               NO_ENGULFING_OVERLAP_OPTION                                                   = "no_eo";
 179     final static private String                               IGNORE_COMBINATION_WITH_SAME_OPTION                                           = "ignore_self_comb";
 180     final static private String                               PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION                                       = "dc_regain_stats";
 181     final static private String                               DA_ANALYSIS_OPTION                                                            = "DA_analyis";
 182     final static private String                               USE_LAST_IN_FITCH_OPTION                                                      = "last";
 183     public final static String                                PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
 184     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_OPTION                                            = "pwc";
 185     final static private String                               OUTPUT_FILE_OPTION                                                            = "o";
 186     final static private String                               PFAM_TO_GO_FILE_USE_OPTION                                                    = "p2g";
 187     final static private String                               GO_OBO_FILE_USE_OPTION                                                        = "obo";
 188     final static private String                               GO_NAMESPACE_LIMIT_OPTION                                                     = "go_namespace";
 189     final static private String                               GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION                                  = "molecular_function";
 190     final static private String                               GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS                                  = "biological_process";
 191     final static private String                               GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT                                  = "cellular_component";
 192     final static private String                               SECONDARY_FEATURES_PARSIMONY_MAP_FILE                                         = "secondary";
 193     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED                           = "simple_tab";
 194     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML                                    = "simple_html";
 195     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML                                  = "detailed_html";
 196     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION                                                = "ds_output";
 197     private static final PRINT_OPTION                         DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT                                        = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 198     final static private String                               IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION                     = "ignore_singlet_domains";
 199     final static private String                               IGNORE_VIRAL_IDS                                                              = "ignore_viral_ids";
 200     final static private boolean                              IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT                    = false;
 201     final static private String                               IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION                                 = "ignore_species_specific_domains";
 202     final static private boolean                              IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT                         = false;
 203     final static private String                               MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                                = "_mean_score.pwd";
 204     final static private String                               MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                            = "_domains.pwd";
 205     final static private String                               MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                   = "_bin_combinations.pwd";
 206     final static private String                               NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                               = "_mean_score_NJ"
 207                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 208     final static private String                               NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                           = "_domains_NJ"
 209                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 210     final static private String                               NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                  = "_bin_combinations_NJ"
 211                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 212     final static private String                               FILTER_POSITIVE_OPTION                                                        = "pos_filter";
 213     final static private String                               FILTER_NEGATIVE_OPTION                                                        = "neg_filter";
 214     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                                = "neg_dom_filter";
 215     final static private String                               INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
 216     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
 217     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
 218     final static private String                               PRG_VERSION                                                                   = "2.304";
 219     final static private String                               PRG_DATE                                                                      = "131024";
 220     final static private String                               E_MAIL                                                                        = "czmasek@burnham.org";
 221     final static private String                               WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
 222     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;
 223     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
 224     final static private double                               MAX_E_VALUE_DEFAULT                                                           = -1;
 225     public final static int                                   MAX_ALLOWED_OVERLAP_DEFAULT                                                   = -1;
 226     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                        = "random_seed";
 227     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                                      = "consider_bdc_direction";
 228     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                        = "consider_bdc_adj";
 229     public static final String                                SEQ_EXTRACT_SUFFIX                                                            = ".prot";
 230     public static final String                                PLUS_MINUS_ANALYSIS_OPTION                                                    = "plus_minus";
 231     public static final String                                PLUS_MINUS_DOM_SUFFIX                                                         = "_plus_minus_dom.txt";
 232     public static final String                                PLUS_MINUS_DOM_SUFFIX_HTML                                                    = "_plus_minus_dom.html";
 233     public static final String                                PLUS_MINUS_DC_SUFFIX_HTML                                                     = "_plus_minus_dc.html";
 234     public static final int                                   PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                          = 0;
 235     public static final double                                PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                            = 1.0;
 236     public static final String                                PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                              = "_plus_minus_go_ids_all.txt";
 237     public static final String                                PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                          = "_plus_minus_go_ids_passing.txt";
 238     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                           = "all_prot";
 239     final static private String                               OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION                         = "all_prot_e";
 240     public static final boolean                               VERBOSE                                                                       = false;
 241     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX              = "_fitch_dc_gains_counts";
 242     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX                = "_fitch_dc_losses_counts";
 243     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                                = "_domain_lengths_analysis";
 244     private static final boolean                              PERFORM_DOMAIN_LENGTH_ANALYSIS                                                = true;
 245     public static final String                                ALL_PFAMS_ENCOUNTERED_SUFFIX                                                  = "_all_encountered_pfams";
 246     public static final String                                ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX                               = "_all_encountered_pfams_with_go_annotation";
 247     public static final String                                ENCOUNTERED_PFAMS_SUMMARY_SUFFIX                                              = "_encountered_pfams_summary";
 248     public static final String                                ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX                                            = "_all_pfams_gained_as_domains";
 249     public static final String                                ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX                                              = "_all_pfams_lost_as_domains";
 250     public static final String                                ALL_PFAMS_GAINED_AS_DC_SUFFIX                                                 = "_all_pfams_gained_as_dc";
 251     public static final String                                ALL_PFAMS_LOST_AS_DC_SUFFIX                                                   = "_all_pfams_lost_as_dc";
 252     public static final String                                BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES                                = "PER_NODE_EVENTS";
 253     public static final String                                BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES                             = "PER_SUBTREE_EVENTS";
 254     public static final String                                D_PROMISCUITY_FILE_SUFFIX                                                     = "_domain_promiscuities";
 255     private static final String                               LOG_FILE_SUFFIX                                                               = "_log.txt";
 256     private static final String                               DATA_FILE_SUFFIX                                                              = "_domain_combination_data.txt";
 257     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";
 258     private static final String                               WRITE_TO_NEXUS_OPTION                                                         = "nexus";
 259     private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                               = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;                                                                                                                                                      //TODO look at me! change?
 260     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX                          = "_indep_dc_gains_fitch_counts.txt";
 261     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                              = "_indep_dc_gains_fitch_lists.txt";
 262     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX               = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
 263     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";
 264     public static final String                                LIMIT_SPEC_FOR_PROT_EX                                                        = null;                                                                                                                                                                                       // e.g. "HUMAN"; set to null for not using this feature (default).
 265     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED          = "_dc_MAPPED_secondary_features_fitch"
 266                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 267     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX                   = "_indep_dc_gains_fitch_counts_MAPPED.txt";
 268     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists_MAPPED.txt";
 269     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";
 270     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";
 271     private static final boolean                              CALC_SIMILARITY_SCORES                                                        = false;
 272
 273     public static void main( final String args[] ) {
 274         final long start_time = new Date().getTime();
 275         // final StringBuffer log = new StringBuffer();
 276         final StringBuilder html_desc = new StringBuilder();
 277         ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
 278                                               surfacing.PRG_VERSION,
 279                                               surfacing.PRG_DATE,
 280                                               surfacing.E_MAIL,
 281                                               surfacing.WWW );
 282         final String nl = ForesterUtil.LINE_SEPARATOR;
 283         html_desc.append( "<table>" + nl );
 284         html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
 285         html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
 286         html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
 287         html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
 288         html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
 289         CommandLineArguments cla = null;
 290         try {
 291             cla = new CommandLineArguments( args );
 292         }
 293         catch ( final Exception e ) {
 294             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 295         }
 296         if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
 297             surfacing.printHelp();
 298             System.exit( 0 );
 299         }
 300         if ( ( args.length < 1 ) ) {
 301             surfacing.printHelp();
 302             System.exit( -1 );
 303         }
 304         final List<String> allowed_options = new ArrayList<String>();
 305         allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
 306         allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
 307         allowed_options.add( surfacing.DETAILEDNESS_OPTION );
 308         allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
 309         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
 310         allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
 311         allowed_options.add( surfacing.SCORING_OPTION );
 312         allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 313         allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
 314         allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
 315         allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
 316         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
 317         allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
 318         allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
 319         allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
 320         allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
 321         allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
 322         allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
 323         allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 324         allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
 325         allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
 326         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
 327         allowed_options.add( FILTER_POSITIVE_OPTION );
 328         allowed_options.add( FILTER_NEGATIVE_OPTION );
 329         allowed_options.add( INPUT_GENOMES_FILE_OPTION );
 330         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 331         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
 332         allowed_options.add( IGNORE_VIRAL_IDS );
 333         allowed_options.add( SEQ_EXTRACT_OPTION );
 334         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 335         allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
 336         allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
 337         allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
 338         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
 339         allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
 340         allowed_options.add( WRITE_TO_NEXUS_OPTION );
 341         allowed_options.add( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION );
 342         allowed_options.add( DA_ANALYSIS_OPTION );
 343         allowed_options.add( USE_LAST_IN_FITCH_OPTION );
 344         boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
 345         boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
 346         double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
 347         int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
 348         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 349         if ( dissallowed_options.length() > 0 ) {
 350             ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
 351         }
 352         boolean use_last_in_fitch_parsimony = false;
 353         if ( cla.isOptionSet( USE_LAST_IN_FITCH_OPTION ) ) {
 354             use_last_in_fitch_parsimony = true;
 355         }
 356         boolean write_to_nexus = false;
 357         if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) {
 358             write_to_nexus = true;
 359         }
 360         boolean perform_dc_regain_proteins_stats = false;
 361         if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) {
 362             perform_dc_regain_proteins_stats = true;
 363         }
 364         boolean da_analysis = false;
 365         if ( cla.isOptionSet( DA_ANALYSIS_OPTION ) ) {
 366             da_analysis = true;
 367         }
 368         boolean output_binary_domain_combinationsfor_graph_analysis = false;
 369         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
 370             output_binary_domain_combinationsfor_graph_analysis = true;
 371         }
 372         if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
 373             try {
 374                 e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
 375             }
 376             catch ( final Exception e ) {
 377                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
 378             }
 379         }
 380         if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
 381             try {
 382                 max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 383             }
 384             catch ( final Exception e ) {
 385                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
 386             }
 387         }
 388         boolean no_engulfing_overlaps = false;
 389         if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
 390             no_engulfing_overlaps = true;
 391         }
 392         boolean ignore_virus_like_ids = false;
 393         if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
 394             ignore_virus_like_ids = true;
 395         }
 396         if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
 397             ignore_dufs = false;
 398         }
 399         if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
 400             ignore_combination_with_same = true;
 401         }
 402         boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
 403         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
 404             ignore_domains_without_combs_in_all_spec = true;
 405         }
 406         boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
 407         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
 408             ignore_species_specific_domains = true;
 409         }
 410         if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
 411             ForesterUtil.fatalError( surfacing.PRG_NAME, "no input species tree file given: "
 412                     + surfacing.INPUT_SPECIES_TREE_OPTION + "=<file>" );
 413         }
 414         File output_file = null;
 415         if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 416             if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 417                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 418                                          "no value for domain combinations similarities output file: -"
 419                                                  + surfacing.OUTPUT_FILE_OPTION + "=<file>" );
 420             }
 421             output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
 422             SurfacingUtil.checkForOutputFileWriteability( output_file );
 423         }
 424         File cutoff_scores_file = null;
 425         Map<String, Double> individual_score_cutoffs = null;
 426         if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 427             if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 428                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
 429                         + surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
 430             }
 431             cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
 432             final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
 433             if ( !ForesterUtil.isEmpty( error ) ) {
 434                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
 435                         + error );
 436             }
 437             try {
 438                 final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, ' ' );
 439                 individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
 440             }
 441             catch ( final IOException e ) {
 442                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
 443             }
 444         }
 445         BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
 446         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
 447             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
 448         }
 449         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
 450             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
 451         }
 452         File out_dir = null;
 453         if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 454             if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 455                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
 456                         + surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
 457             }
 458             out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
 459             if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
 460                 ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
 461             }
 462             if ( !out_dir.exists() ) {
 463                 final boolean success = out_dir.mkdir();
 464                 if ( !success || !out_dir.exists() ) {
 465                     ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
 466                 }
 467             }
 468             if ( !out_dir.canWrite() ) {
 469                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
 470             }
 471         }
 472         File positive_filter_file = null;
 473         File negative_filter_file = null;
 474         File negative_domains_filter_file = null;
 475         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 476             ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
 477         }
 478         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
 479                 && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
 480                         .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
 481             ForesterUtil
 482                     .fatalError( surfacing.PRG_NAME,
 483                                  "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
 484         }
 485         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 486             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 487                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
 488                         + surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
 489             }
 490             negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
 491             final String msg = ForesterUtil.isReadableFile( negative_filter_file );
 492             if ( !ForesterUtil.isEmpty( msg ) ) {
 493                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
 494                         + msg );
 495             }
 496         }
 497         else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 498             if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 499                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
 500                         + surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
 501             }
 502             positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
 503             final String msg = ForesterUtil.isReadableFile( positive_filter_file );
 504             if ( !ForesterUtil.isEmpty( msg ) ) {
 505                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
 506                         + msg );
 507             }
 508         }
 509         else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 510             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 511                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
 512                         + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
 513             }
 514             negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
 515             final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
 516             if ( !ForesterUtil.isEmpty( msg ) ) {
 517                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
 518                         + "\": " + msg );
 519             }
 520         }
 521         final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
 522         final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
 523         final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
 524         final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
 525         SurfacingUtil.processPlusMinusAnalysisOption( cla,
 526                                                       plus_minus_analysis_high_copy_base_species,
 527                                                       plus_minus_analysis_high_copy_target_species,
 528                                                       plus_minus_analysis_high_low_copy_species,
 529                                                       plus_minus_analysis_numbers );
 530         File input_genomes_file = null;
 531         if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
 532             if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
 533                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -"
 534                         + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
 535             }
 536             input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) );
 537             final String msg = ForesterUtil.isReadableFile( input_genomes_file );
 538             if ( !ForesterUtil.isEmpty( msg ) ) {
 539                 ForesterUtil
 540                         .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg );
 541             }
 542         }
 543         else {
 544             ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
 545                     + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
 546         }
 547         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
 548         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
 549             if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
 550                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 551                                          "no value for scoring method for domain combinations similarity calculation: -"
 552                                                  + surfacing.SCORING_OPTION + "=<"
 553                                                  + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 554                                                  + surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
 555                                                  + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 556             }
 557             final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
 558             if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
 559                 scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
 560             }
 561             else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
 562                 scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 563             }
 564             else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
 565                 scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
 566             }
 567             else {
 568                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
 569                         + "\" for scoring method for domain combinations similarity calculation: \"-"
 570                         + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 571                         + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 572             }
 573         }
 574         boolean sort_by_species_count_first = false;
 575         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
 576             sort_by_species_count_first = true;
 577         }
 578         boolean species_matrix = false;
 579         if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
 580             species_matrix = true;
 581         }
 582         boolean output_protein_lists_for_all_domains = false;
 583         double output_list_of_all_proteins_per_domain_e_value_max = -1;
 584         if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
 585             output_protein_lists_for_all_domains = true;
 586             if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
 587                 try {
 588                     output_list_of_all_proteins_per_domain_e_value_max = cla
 589                             .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 590                 }
 591                 catch ( final Exception e ) {
 592                     ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
 593                 }
 594             }
 595         }
 596         Detailedness detailedness = DETAILEDNESS_DEFAULT;
 597         if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
 598             if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
 599                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
 600                         + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
 601                         + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 602             }
 603             final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
 604             if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
 605                 detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
 606             }
 607             else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
 608                 detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
 609             }
 610             else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
 611                 detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 612             }
 613             else {
 614                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
 615                         + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
 616                         + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 617             }
 618         }
 619         String automated_pairwise_comparison_suffix = null;
 620         boolean perform_pwc = false;
 621         boolean write_pwc_files = false;
 622         if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 623             perform_pwc = true;
 624             if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 625                 write_pwc_files = false;
 626             }
 627             else {
 628                 write_pwc_files = true;
 629                 automated_pairwise_comparison_suffix = "_"
 630                         + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 631             }
 632         }
 633         String query_domain_ids = null;
 634         if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 635             if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 636                 ForesterUtil
 637                         .fatalError( surfacing.PRG_NAME,
 638                                      "no domain ids given for sequences with given domains to be extracted : -"
 639                                              + surfacing.SEQ_EXTRACT_OPTION
 640                                              + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
 641             }
 642             query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
 643         }
 644         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
 645         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
 646         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 647             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 648                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
 649                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 650                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 651                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 652                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 653                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
 654                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 655                         + ">\"" );
 656             }
 657             final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
 658             if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
 659                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 660                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 661             }
 662             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
 663                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
 664                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 665             }
 666             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
 667                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
 668                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 669             }
 670             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
 671                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
 672                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
 673             }
 674             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
 675                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
 676                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 677             }
 678             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
 679                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
 680                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 681             }
 682             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
 683                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 684                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 685             }
 686             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
 687                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 688                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 689             }
 690             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
 691                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 692                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 693             }
 694             else {
 695                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
 696                         + "\" for domain combinations similarities sorting: \"-"
 697                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 698                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 699                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 700                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 701                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
 702                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 703                         + ">\"" );
 704             }
 705         }
 706         PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
 707         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 708             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 709                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
 710                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 711                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 712                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 713             }
 714             final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
 715             if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
 716                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 717             }
 718             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
 719                 ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
 720             }
 721             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
 722                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
 723             }
 724             else {
 725                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
 726                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 727                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 728                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 729             }
 730         }
 731         GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
 732         if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
 733             if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
 734                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
 735                         + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
 736                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
 737                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
 738                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
 739             }
 740             final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
 741             if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
 742                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
 743             }
 744             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
 745                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
 746             }
 747             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
 748                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
 749             }
 750             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
 751                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
 752             }
 753             else {
 754                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
 755                         + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
 756                         + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
 757                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
 758                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
 759             }
 760         }
 761         final String[][] input_file_properties = SurfacingUtil.processInputGenomesFile( input_genomes_file );
 762         final int number_of_genomes = input_file_properties.length;
 763         if ( number_of_genomes < 2 ) {
 764             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
 765         }
 766         if ( ( number_of_genomes < 3 ) && perform_pwc ) {
 767             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
 768                     + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
 769                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
 770         }
 771         SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
 772                                                                input_file_properties,
 773                                                                automated_pairwise_comparison_suffix,
 774                                                                out_dir );
 775         for( int i = 0; i < number_of_genomes; i++ ) {
 776             File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
 777                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
 778             if ( out_dir != null ) {
 779                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
 780             }
 781             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
 782         }
 783         File pfam_to_go_file = null;
 784         Map<String, List<GoId>> domain_id_to_go_ids_map = null;
 785         int domain_id_to_go_ids_count = 0;
 786         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
 787             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
 788                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
 789                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
 790             }
 791             pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
 792             final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
 793             if ( !ForesterUtil.isEmpty( error ) ) {
 794                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
 795             }
 796             try {
 797                 final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
 798                 final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
 799                 domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
 800                 if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
 801                     ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
 802                                                        "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
 803                 }
 804                 domain_id_to_go_ids_count = parser.getMappingCount();
 805             }
 806             catch ( final IOException e ) {
 807                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
 808             }
 809         }
 810         File go_obo_file = null;
 811         List<GoTerm> go_terms = null;
 812         if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
 813             if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
 814                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
 815                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
 816             }
 817             if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
 818                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
 819                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
 820                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
 821             }
 822             go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
 823             final String error = ForesterUtil.isReadableFile( go_obo_file );
 824             if ( !ForesterUtil.isEmpty( error ) ) {
 825                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
 826             }
 827             try {
 828                 final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
 829                 go_terms = parser.parse();
 830                 if ( parser.getGoTermCount() != go_terms.size() ) {
 831                     ForesterUtil
 832                             .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
 833                 }
 834             }
 835             catch ( final IOException e ) {
 836                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
 837             }
 838         }
 839         Map<GoId, GoTerm> go_id_to_term_map = null;
 840         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
 841                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
 842             go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
 843         }
 844         GoNameSpace go_namespace_limit = null;
 845         if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
 846             if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
 847                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
 848                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
 849                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
 850                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
 851             }
 852             if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
 853                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
 854                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
 855                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
 856                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
 857                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
 858             }
 859             final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
 860                     .toLowerCase();
 861             if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
 862                 go_namespace_limit = GoNameSpace.createMolecularFunction();
 863             }
 864             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
 865                 go_namespace_limit = GoNameSpace.createBiologicalProcess();
 866             }
 867             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
 868                 go_namespace_limit = GoNameSpace.createCellularComponent();
 869             }
 870             else {
 871                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
 872                         + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
 873                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
 874                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
 875                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
 876             }
 877         }
 878         if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
 879                 && ( number_of_genomes > 2 ) ) {
 880             domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 881         }
 882         File[] intree_files = null;
 883         Phylogeny[] intrees = null;
 884         if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
 885             if ( number_of_genomes < 3 ) {
 886                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
 887                         + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
 888                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
 889                         + "=<suffix for pairwise comparison output files>)" );
 890             }
 891             if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
 892                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
 893                         + surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
 894             }
 895             final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
 896             if ( intrees_str.indexOf( "#" ) > 0 ) {
 897                 final String[] intrees_strs = intrees_str.split( "#" );
 898                 intree_files = new File[ intrees_strs.length ];
 899                 int i = 0;
 900                 for( final String s : intrees_strs ) {
 901                     intree_files[ i++ ] = new File( s.trim() );
 902                 }
 903             }
 904             else {
 905                 intree_files = new File[ 1 ];
 906                 intree_files[ 0 ] = new File( intrees_str );
 907             }
 908             intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, number_of_genomes, input_file_properties );
 909         }
 910         final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ] );
 911         long random_number_seed_for_fitch_parsimony = 0l;
 912         boolean radomize_fitch_parsimony = false;
 913         if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
 914             if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
 915                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
 916                         + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
 917             }
 918             try {
 919                 random_number_seed_for_fitch_parsimony = cla
 920                         .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 921             }
 922             catch ( final IOException e ) {
 923                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 924             }
 925             radomize_fitch_parsimony = true;
 926         }
 927         SortedSet<String> filter = null;
 928         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
 929                 || ( negative_domains_filter_file != null ) ) {
 930             filter = new TreeSet<String>();
 931             if ( positive_filter_file != null ) {
 932                 SurfacingUtil.processFilter( positive_filter_file, filter );
 933             }
 934             else if ( negative_filter_file != null ) {
 935                 SurfacingUtil.processFilter( negative_filter_file, filter );
 936             }
 937             else if ( negative_domains_filter_file != null ) {
 938                 SurfacingUtil.processFilter( negative_domains_filter_file, filter );
 939             }
 940         }
 941         Map<String, Set<String>>[] domain_id_to_secondary_features_maps = null;
 942         File[] secondary_features_map_files = null;
 943         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
 944                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
 945         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
 946             SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
 947         }
 948         if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
 949             if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
 950                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
 951                         + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
 952             }
 953             final String[] secondary_features_map_files_strs = cla
 954                     .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
 955             secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
 956             domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
 957             int i = 0;
 958             for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
 959                 secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
 960                 final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
 961                 if ( !ForesterUtil.isEmpty( error ) ) {
 962                     ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
 963                 }
 964                 try {
 965                     domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
 966                             .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
 967                 }
 968                 catch ( final IOException e ) {
 969                     ForesterUtil.fatalError( surfacing.PRG_NAME,
 970                                              "cannot read secondary features map file: " + e.getMessage() );
 971                 }
 972                 catch ( final Exception e ) {
 973                     ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
 974                             + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
 975                 }
 976                 i++;
 977             }
 978         }
 979         if ( out_dir == null ) {
 980             ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
 981                     + surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
 982         }
 983         if ( output_file == null ) {
 984             ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
 985                     + surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
 986         }
 987         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
 988             ForesterUtil.fatalError( surfacing.PRG_NAME,
 989                                      "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
 990                                              + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
 991         }
 992         if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
 993             ForesterUtil.fatalError( surfacing.PRG_NAME,
 994                                      "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
 995                                              + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
 996         }
 997         System.out.println( "Output directory            : " + out_dir );
 998         System.out.println( "Input genomes from          : " + input_genomes_file );
 999         html_desc.append( "<tr><td>Input genomes from:</td><td>" + input_genomes_file + "</td></tr>" + nl );
1000         if ( positive_filter_file != null ) {
1001             final int filter_size = filter.size();
1002             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
1003                     + " domain ids]" );
1004             html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
1005                     + " domain ids]</td></tr>" + nl );
1006         }
1007         if ( negative_filter_file != null ) {
1008             final int filter_size = filter.size();
1009             System.out.println( "Negative protein filter     : " + negative_filter_file + " [" + filter_size
1010                     + " domain ids]" );
1011             html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
1012                     + " domain ids]</td></tr>" + nl );
1013         }
1014         if ( negative_domains_filter_file != null ) {
1015             final int filter_size = filter.size();
1016             System.out.println( "Negative domain filter      : " + negative_domains_filter_file + " [" + filter_size
1017                     + " domain ids]" );
1018             html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
1019                     + filter_size + " domain ids]</td></tr>" + nl );
1020         }
1021         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1022             String plus0 = "";
1023             for( final String s : plus_minus_analysis_high_copy_base_species ) {
1024                 plus0 += "+" + s + " ";
1025             }
1026             String plus1 = "";
1027             for( final String s : plus_minus_analysis_high_copy_target_species ) {
1028                 plus1 += "*" + s + " ";
1029             }
1030             String minus = "";
1031             for( final String s : plus_minus_analysis_high_low_copy_species ) {
1032                 minus += "-" + s + " ";
1033             }
1034             System.out.println( "Plus-minus analysis         : " + plus1 + "&& " + plus0 + "&& " + minus );
1035             html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
1036                     + "</td></tr>" + nl );
1037         }
1038         if ( cutoff_scores_file != null ) {
1039             System.out.println( "Cutoff scores file          : " + cutoff_scores_file );
1040             html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
1041         }
1042         if ( e_value_max >= 0.0 ) {
1043             System.out.println( "E-value maximum (inclusive) : " + e_value_max );
1044             html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
1045         }
1046         if ( output_protein_lists_for_all_domains ) {
1047             System.out.println( "Domain E-value max          : " + output_list_of_all_proteins_per_domain_e_value_max );
1048             html_desc.append( "<tr><td>Protein lists: E-value maximum per domain (inclusive):</td><td>"
1049                     + output_list_of_all_proteins_per_domain_e_value_max + "</td></tr>" + nl );
1050         }
1051         System.out.println( "Ignore DUFs                 : " + ignore_dufs );
1052         if ( ignore_virus_like_ids ) {
1053             System.out.println( "Ignore virus like ids       : " + ignore_virus_like_ids );
1054             html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
1055                     + ignore_virus_like_ids + "</td></tr>" + nl );
1056         }
1057         html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
1058         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1059             System.out.println( "Max allowed domain overlap  : " + max_allowed_overlap );
1060             html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
1061         }
1062         if ( no_engulfing_overlaps ) {
1063             System.out.println( "Ignore engulfed domains     : " + no_engulfing_overlaps );
1064             html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
1065                     + "</td></tr>" + nl );
1066         }
1067         System.out.println( "Ignore singlet domains      : " + ignore_domains_without_combs_in_all_spec );
1068         html_desc
1069                 .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1070                         + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
1071         System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
1072         html_desc
1073                 .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1074                         + ignore_species_specific_domains + "</td></tr>" + nl );
1075         System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
1076         html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
1077                 + ignore_combination_with_same + "</td></tr>" + nl );
1078         System.out.println( "Consider directedness       : "
1079                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
1080         html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
1081                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
1082         if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
1083             System.out.println( "Consider adjacency          : "
1084                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
1085             html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
1086                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
1087                     + nl );
1088         }
1089         System.out.println( "Use last in Fitch parimony  : " + use_last_in_fitch_parsimony );
1090         html_desc.append( "<tr><td>Use last in Fitch parimon:</td><td>" + use_last_in_fitch_parsimony + "</td></tr>"
1091                 + nl );
1092         System.out.println( "Write to Nexus files        : " + write_to_nexus );
1093         html_desc.append( "<tr><td>Write to Nexus files:</td><td>" + write_to_nexus + "</td></tr>" + nl );
1094         System.out.println( "DC regain prot stats        : " + perform_dc_regain_proteins_stats );
1095         html_desc.append( "<tr><td>DC regain prot stats:</td><td>" + perform_dc_regain_proteins_stats + "</td></tr>"
1096                 + nl );
1097         System.out.println( "DA analysis                 : " + da_analysis );
1098         html_desc.append( "<tr><td>DA analysis :</td><td>" + da_analysis + "</td></tr>" + nl );
1099         System.out.print( "Domain counts sort order    : " );
1100         html_desc.append( "<tr><td>Domain counts sort order:</td><td>" );
1101         switch ( dc_sort_order ) {
1102             case ALPHABETICAL_KEY_ID:
1103                 System.out.println( "alphabetical" );
1104                 html_desc.append( "alphabetical" + "</td></tr>" + nl );
1105                 break;
1106             case KEY_DOMAIN_COUNT:
1107                 System.out.println( "domain count" );
1108                 html_desc.append( "domain count" + "</td></tr>" + nl );
1109                 break;
1110             case KEY_DOMAIN_PROTEINS_COUNT:
1111                 System.out.println( "domain proteins count" );
1112                 html_desc.append( "domain proteins count" + "</td></tr>" + nl );
1113                 break;
1114             case COMBINATIONS_COUNT:
1115                 System.out.println( "domain combinations count" );
1116                 html_desc.append( "domain combinations count" + "</td></tr>" + nl );
1117                 break;
1118             default:
1119                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
1120         }
1121         if ( domain_id_to_go_ids_map != null ) {
1122             System.out.println( "Pfam to GO mappings from    : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
1123                     + " mappings]" );
1124             html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
1125                     + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
1126         }
1127         if ( go_terms != null ) {
1128             System.out.println( "GO terms from               : " + go_obo_file + " [" + go_terms.size() + " terms]" );
1129             html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
1130                     + "</td></tr>" + nl );
1131         }
1132         if ( go_namespace_limit != null ) {
1133             System.out.println( "Limit GO terms to           : " + go_namespace_limit.toString() );
1134             html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
1135         }
1136         if ( perform_pwc ) {
1137             System.out.println( "Suffix for PWC files        : " + automated_pairwise_comparison_suffix );
1138             html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
1139                     + "</td></tr>" + nl );
1140         }
1141         if ( out_dir != null ) {
1142             System.out.println( "Output directory            : " + out_dir );
1143         }
1144         if ( query_domain_ids != null ) {
1145             System.out.println( "Query domains (ordered)     : " + query_domain_ids );
1146             html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
1147         }
1148         System.out.println( "Write similarities to       : " + output_file );
1149         System.out.print( "  Scoring method            : " );
1150         html_desc.append( "<tr><td>Scoring method:</td><td>" );
1151         switch ( scoring ) {
1152             case COMBINATIONS:
1153                 System.out.println( "domain combinations based" );
1154                 html_desc.append( "domain combinations based" + "</td></tr>" + nl );
1155                 break;
1156             case DOMAINS:
1157                 System.out.println( "domain counts based" );
1158                 html_desc.append( "domain counts based" + "</td></tr>" + nl );
1159                 break;
1160             case PROTEINS:
1161                 System.out.println( "domain proteins counts based" );
1162                 html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
1163                 break;
1164             default:
1165                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
1166         }
1167         System.out.print( "  Sort by                   : " );
1168         html_desc.append( "<tr><td>Sort by:</td><td>" );
1169         switch ( domain_similarity_sort_field ) {
1170             case MIN:
1171                 System.out.print( "score minimum" );
1172                 html_desc.append( "score minimum" );
1173                 break;
1174             case MAX:
1175                 System.out.print( "score maximum" );
1176                 html_desc.append( "score maximum" );
1177                 break;
1178             case MEAN:
1179                 System.out.print( "score mean" );
1180                 html_desc.append( "score mean" );
1181                 break;
1182             case SD:
1183                 System.out.print( "score standard deviation" );
1184                 html_desc.append( "score standard deviation" );
1185                 break;
1186             case SPECIES_COUNT:
1187                 System.out.print( "species number" );
1188                 html_desc.append( "species number" );
1189                 break;
1190             case DOMAIN_ID:
1191                 System.out.print( "alphabetical domain identifier" );
1192                 html_desc.append( "alphabetical domain identifier" );
1193                 break;
1194             case MAX_DIFFERENCE:
1195                 System.out.print( "(maximal) difference" );
1196                 html_desc.append( "(maximal) difference" );
1197                 break;
1198             case ABS_MAX_COUNTS_DIFFERENCE:
1199                 System.out.print( "absolute (maximal) counts difference" );
1200                 html_desc.append( "absolute (maximal) counts difference" );
1201                 break;
1202             case MAX_COUNTS_DIFFERENCE:
1203                 System.out.print( "(maximal) counts difference" );
1204                 html_desc.append( "(maximal) counts  difference" );
1205                 break;
1206             default:
1207                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1208         }
1209         if ( sort_by_species_count_first ) {
1210             System.out.println( " (sort by species count first)" );
1211             html_desc.append( " (sort by species count first)" );
1212         }
1213         else {
1214             System.out.println();
1215         }
1216         html_desc.append( "</td></tr>" + nl );
1217         System.out.print( "  Detailedness              : " );
1218         switch ( detailedness ) {
1219             case BASIC:
1220                 System.out.println( "basic" );
1221                 break;
1222             case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
1223                 System.out.println( "list combining domains for each species" );
1224                 break;
1225             case PUNCTILIOUS:
1226                 System.out.println( "punctilious" );
1227                 break;
1228             default:
1229                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" );
1230         }
1231         System.out.print( "  Print option              : " );
1232         switch ( domain_similarity_print_option ) {
1233             case HTML:
1234                 System.out.println( "HTML" );
1235                 break;
1236             case SIMPLE_TAB_DELIMITED:
1237                 System.out.println( "simple tab delimited" );
1238                 break;
1239             default:
1240                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
1241         }
1242         System.out.print( "  Species matrix            : " + species_matrix );
1243         System.out.println();
1244         final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
1245         System.out.println( "Domain comb data output     : " + dc_data_file );
1246         html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
1247         System.out.println();
1248         if ( perform_pwc ) {
1249             System.out.println( "Pairwise comparisons: " );
1250             html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
1251             System.out.print( "  Sort by                   : " );
1252             html_desc.append( "<tr><td>Sort by:</td><td>" );
1253             switch ( domain_similarity_sort_field_for_automated_pwc ) {
1254                 case MEAN:
1255                     System.out.print( "score mean" );
1256                     html_desc.append( "score mean" );
1257                     break;
1258                 case DOMAIN_ID:
1259                     System.out.print( "alphabetical domain identifier" );
1260                     html_desc.append( "alphabetical domain identifier" );
1261                     break;
1262                 case MAX_DIFFERENCE:
1263                     System.out.print( "difference" );
1264                     html_desc.append( "difference" );
1265                     break;
1266                 case ABS_MAX_COUNTS_DIFFERENCE:
1267                     System.out.print( "absolute counts difference" );
1268                     html_desc.append( "absolute counts difference" );
1269                     break;
1270                 case MAX_COUNTS_DIFFERENCE:
1271                     System.out.print( "counts difference" );
1272                     html_desc.append( "counts difference" );
1273                     break;
1274                 default:
1275                     ForesterUtil
1276                             .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1277             }
1278             System.out.println();
1279             html_desc.append( "</td></tr>" + nl );
1280             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
1281                 for( final File intree_file : intree_files ) {
1282                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
1283                             + "</td></tr>" + nl );
1284                     System.out.println( "  Intree for gain/loss pars.: " + intree_file );
1285                 }
1286             }
1287             if ( radomize_fitch_parsimony ) {
1288                 html_desc.append( "<tr><td>    Random number seed for Fitch parsimony analysis:</td><td>"
1289                         + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
1290                 System.out.println( "    Random number seed      : " + random_number_seed_for_fitch_parsimony );
1291             }
1292             if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1293                 for( int i = 0; i < secondary_features_map_files.length; i++ ) {
1294                     html_desc.append( "<tr><td>Secondary features map file:</td><td>"
1295                             + secondary_features_map_files[ i ] + "</td></tr>" + nl );
1296                     System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
1297                             + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
1298                     if ( VERBOSE ) {
1299                         System.out.println();
1300                         System.out.println( "Domain ids to secondary features map:" );
1301                         for( final String domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
1302                             System.out.print( domain_id );
1303                             System.out.print( " => " );
1304                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
1305                                 System.out.print( sec );
1306                                 System.out.print( " " );
1307                             }
1308                             System.out.println();
1309                         }
1310                     }
1311                 }
1312             }
1313         } // if ( perform_pwc ) {
1314         System.out.println();
1315         html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
1316         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
1317         BufferedWriter[] query_domains_writer_ary = null;
1318         List<String>[] query_domain_ids_array = null;
1319         if ( query_domain_ids != null ) {
1320             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
1321             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
1322             query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
1323             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
1324                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
1325                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
1326                 final List<String> query = new ArrayList<String>();
1327                 for( final String element : query_domain_ids_str_ary ) {
1328                     query.add( element );
1329                 }
1330                 query_domain_ids_array[ i ] = query;
1331                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
1332                 String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX;
1333                 if ( out_dir != null ) {
1334                     protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
1335                 }
1336                 try {
1337                     query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
1338                 }
1339                 catch ( final IOException e ) {
1340                     ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
1341                             + e.getLocalizedMessage() );
1342                 }
1343             }
1344         }
1345         SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
1346         boolean need_protein_lists_per_species = false;
1347         if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
1348             need_protein_lists_per_species = true;
1349         }
1350         if ( need_protein_lists_per_species ) {
1351             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
1352         }
1353         List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
1354         final SortedSet<String> all_domains_encountered = new TreeSet<String>();
1355         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
1356         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
1357         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
1358         if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
1359             all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
1360             all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
1361         }
1362         DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
1363         final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
1364                 + output_file + D_PROMISCUITY_FILE_SUFFIX );
1365         BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
1366         try {
1367             per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
1368             per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
1369             per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
1370             per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
1371             per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
1372             per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
1373             per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
1374             per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
1375             per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
1376                     + ForesterUtil.LINE_SEPARATOR );
1377         }
1378         catch ( final IOException e2 ) {
1379             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1380         }
1381         final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
1382         BufferedWriter log_writer = null;
1383         try {
1384             log_writer = new BufferedWriter( new FileWriter( log_file ) );
1385         }
1386         catch ( final IOException e2 ) {
1387             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1388         }
1389         BufferedWriter dc_data_writer = null;
1390         try {
1391             dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
1392             dc_data_writer.write( DATA_FILE_DESC );
1393             dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
1394         }
1395         catch ( final IOException e2 ) {
1396             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1397         }
1398         final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics();
1399         final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics();
1400         final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
1401         final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
1402         final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
1403         final SortedSet<String> domains_which_never_single = new TreeSet<String>();
1404         BufferedWriter domains_per_potein_stats_writer = null;
1405         try {
1406             domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
1407                     + output_file + "_domains_per_potein_stats.txt" ) );
1408             domains_per_potein_stats_writer.write( "Genome" );
1409             domains_per_potein_stats_writer.write( "\t" );
1410             domains_per_potein_stats_writer.write( "Mean" );
1411             domains_per_potein_stats_writer.write( "\t" );
1412             domains_per_potein_stats_writer.write( "SD" );
1413             domains_per_potein_stats_writer.write( "\t" );
1414             domains_per_potein_stats_writer.write( "Median" );
1415             domains_per_potein_stats_writer.write( "\t" );
1416             domains_per_potein_stats_writer.write( "N" );
1417             domains_per_potein_stats_writer.write( "\t" );
1418             domains_per_potein_stats_writer.write( "Min" );
1419             domains_per_potein_stats_writer.write( "\t" );
1420             domains_per_potein_stats_writer.write( "Max" );
1421             domains_per_potein_stats_writer.write( "\n" );
1422         }
1423         catch ( final IOException e3 ) {
1424             e3.printStackTrace();
1425         }
1426         Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
1427         Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
1428         final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
1429         if ( perform_dc_regain_proteins_stats ) {
1430             protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1431             domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1432         }
1433         // Main loop:
1434         final SortedMap<String, Set<String>> distinct_domain_architecutures_per_genome = new TreeMap<String, Set<String>>();
1435         final SortedMap<String, Integer> distinct_domain_architecuture_counts = new TreeMap<String, Integer>();
1436         for( int i = 0; i < number_of_genomes; ++i ) {
1437             System.out.println();
1438             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
1439             SurfacingUtil.log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
1440             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 1 ]
1441                     + " [" + input_file_properties[ i ][ 0 ] + "]" );
1442             SurfacingUtil.log( "Genome                                         : " + input_file_properties[ i ][ 1 ]
1443                     + " [" + input_file_properties[ i ][ 0 ] + "]", log_writer );
1444             HmmscanPerDomainTableParser parser = null;
1445             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
1446             if ( individual_score_cutoffs != null ) {
1447                 ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
1448             }
1449             if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1450                     || ( negative_domains_filter_file != null ) ) {
1451                 HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
1452                 if ( positive_filter_file != null ) {
1453                     filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
1454                 }
1455                 else if ( negative_filter_file != null ) {
1456                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
1457                 }
1458                 else if ( negative_domains_filter_file != null ) {
1459                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
1460                 }
1461                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1462                                                           input_file_properties[ i ][ 1 ],
1463                                                           filter,
1464                                                           filter_type,
1465                                                           ind_score_cutoff,
1466                                                           true );
1467             }
1468             else {
1469                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1470                                                           input_file_properties[ i ][ 1 ],
1471                                                           ind_score_cutoff,
1472                                                           true );
1473             }
1474             if ( e_value_max >= 0.0 ) {
1475                 parser.setEValueMaximum( e_value_max );
1476             }
1477             parser.setIgnoreDufs( ignore_dufs );
1478             parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
1479             parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
1480             if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1481                 parser.setMaxAllowedOverlap( max_allowed_overlap );
1482             }
1483             parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
1484             if ( individual_score_cutoffs != null ) {
1485                 parser.setIndividualScoreCutoffs( individual_score_cutoffs );
1486             }
1487             List<Protein> protein_list = null;
1488             try {
1489                 protein_list = parser.parse();
1490             }
1491             catch ( final IOException e ) {
1492                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1493             }
1494             catch ( final Exception e ) {
1495                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
1496             }
1497             if ( VERBOSE ) {
1498                 System.out.println( "Domains ignored due to negative domain filter: " );
1499                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
1500                 System.out.println( "Domains ignored due to virus like id: " );
1501                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
1502             }
1503             final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
1504             protein_coverage_stats.addValue( coverage );
1505             int distinct_das = -1;
1506             if ( da_analysis ) {
1507                 final String genome = input_file_properties[ i ][ 0 ];
1508                 distinct_das = SurfacingUtil.storeDomainArchitectures( genome,
1509                                                                        distinct_domain_architecutures_per_genome,
1510                                                                        protein_list,
1511                                                                        distinct_domain_architecuture_counts );
1512             }
1513             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
1514             SurfacingUtil.log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(),
1515                                log_writer );
1516             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
1517             SurfacingUtil.log( "Number of proteins stored                      : " + protein_list.size(), log_writer );
1518             System.out.println( "Coverage                                       : "
1519                     + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
1520             SurfacingUtil.log( "Coverage                                       : "
1521                                        + ForesterUtil.roundToInt( 100.0 * coverage ) + "%",
1522                                log_writer );
1523             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
1524             SurfacingUtil.log( "Domains encountered                            : " + parser.getDomainsEncountered(),
1525                                log_writer );
1526             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
1527             SurfacingUtil.log( "Domains stored                                 : " + parser.getDomainsStored(),
1528                                log_writer );
1529             System.out.println( "Distinct domains stored                        : "
1530                     + parser.getDomainsStoredSet().size() );
1531             SurfacingUtil.log( "Distinct domains stored                        : "
1532                     + parser.getDomainsStoredSet().size(), log_writer );
1533             System.out.println( "Domains ignored due to individual score cutoffs: "
1534                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
1535             SurfacingUtil.log( "Domains ignored due to individual score cutoffs: "
1536                                        + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
1537                                log_writer );
1538             System.out.println( "Domains ignored due to E-value                 : "
1539                     + parser.getDomainsIgnoredDueToEval() );
1540             SurfacingUtil.log( "Domains ignored due to E-value                 : "
1541                                        + parser.getDomainsIgnoredDueToEval(),
1542                                log_writer );
1543             System.out.println( "Domains ignored due to DUF designation         : "
1544                     + parser.getDomainsIgnoredDueToDuf() );
1545             SurfacingUtil
1546                     .log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(),
1547                           log_writer );
1548             if ( ignore_virus_like_ids ) {
1549                 System.out.println( "Domains ignored due virus like ids             : "
1550                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
1551                 SurfacingUtil.log( "Domains ignored due virus like ids             : "
1552                                            + parser.getDomainsIgnoredDueToVirusLikeIds(),
1553                                    log_writer );
1554             }
1555             System.out.println( "Domains ignored due negative domain filter     : "
1556                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
1557             SurfacingUtil.log( "Domains ignored due negative domain filter     : "
1558                                        + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
1559                                log_writer );
1560             System.out.println( "Domains ignored due to overlap                 : "
1561                     + parser.getDomainsIgnoredDueToOverlap() );
1562             SurfacingUtil.log( "Domains ignored due to overlap                 : "
1563                                        + parser.getDomainsIgnoredDueToOverlap(),
1564                                log_writer );
1565             if ( negative_filter_file != null ) {
1566                 System.out.println( "Proteins ignored due to negative filter        : "
1567                         + parser.getProteinsIgnoredDueToFilter() );
1568                 SurfacingUtil.log( "Proteins ignored due to negative filter        : "
1569                                            + parser.getProteinsIgnoredDueToFilter(),
1570                                    log_writer );
1571             }
1572             if ( positive_filter_file != null ) {
1573                 System.out.println( "Proteins ignored due to positive filter        : "
1574                         + parser.getProteinsIgnoredDueToFilter() );
1575                 SurfacingUtil.log( "Proteins ignored due to positive filter        : "
1576                                            + parser.getProteinsIgnoredDueToFilter(),
1577                                    log_writer );
1578             }
1579             if ( da_analysis ) {
1580                 System.out.println( "Distinct domain architectures stored           : " + distinct_das );
1581                 SurfacingUtil.log( "Distinct domain architectures stored           : " + distinct_das, log_writer );
1582             }
1583             System.out.println( "Time for processing                            : " + parser.getTime() + "ms" );
1584             SurfacingUtil.log( "", log_writer );
1585             try {
1586                 int count = 0;
1587                 for( final Protein protein : protein_list ) {
1588                     dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
1589                             .toString() );
1590                     ++count;
1591                     for( final Domain d : protein.getProteinDomains() ) {
1592                         final String d_str = d.getDomainId().toString();
1593                         if ( !domain_length_stats_by_domain.containsKey( d_str ) ) {
1594                             domain_length_stats_by_domain.put( d_str, new BasicDescriptiveStatistics() );
1595                         }
1596                         domain_length_stats_by_domain.get( d_str ).addValue( d.getLength() );
1597                     }
1598                 }
1599             }
1600             catch ( final IOException e ) {
1601                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
1602             }
1603             SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ],
1604                                                         protein_list,
1605                                                         all_genomes_domains_per_potein_stats,
1606                                                         all_genomes_domains_per_potein_histo,
1607                                                         domains_which_are_always_single,
1608                                                         domains_which_are_sometimes_single_sometimes_not,
1609                                                         domains_which_never_single,
1610                                                         domains_per_potein_stats_writer );
1611             domain_lengths_table.addLengths( protein_list );
1612             if ( !da_analysis ) {
1613                 gwcd_list.add( BasicGenomeWideCombinableDomains
1614                         .createInstance( protein_list,
1615                                          ignore_combination_with_same,
1616                                          new BasicSpecies( input_file_properties[ i ][ 1 ] ),
1617                                          domain_id_to_go_ids_map,
1618                                          dc_type,
1619                                          protein_length_stats_by_dc,
1620                                          domain_number_stats_by_dc ) );
1621                 if ( gwcd_list.get( i ).getSize() > 0 ) {
1622                     SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
1623                                                                      out_dir,
1624                                                                      per_genome_domain_promiscuity_statistics_writer,
1625                                                                      gwcd_list.get( i ),
1626                                                                      i,
1627                                                                      dc_sort_order );
1628                     if ( output_binary_domain_combinationsfor_graph_analysis ) {
1629                         SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
1630                                                                                          out_dir,
1631                                                                                          gwcd_list.get( i ),
1632                                                                                          i,
1633                                                                                          dc_sort_order );
1634                     }
1635                     SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
1636                     SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
1637                                                                       all_bin_domain_combinations_encountered );
1638                 }
1639             }
1640             if ( query_domains_writer_ary != null ) {
1641                 for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1642                     try {
1643                         SurfacingUtil.extractProteinNames( protein_list,
1644                                                            query_domain_ids_array[ j ],
1645                                                            query_domains_writer_ary[ j ],
1646                                                            "\t",
1647                                                            LIMIT_SPEC_FOR_PROT_EX );
1648                         query_domains_writer_ary[ j ].flush();
1649                     }
1650                     catch ( final IOException e ) {
1651                         e.printStackTrace();
1652                     }
1653                 }
1654             }
1655             if ( need_protein_lists_per_species ) {
1656                 protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
1657             }
1658             try {
1659                 log_writer.flush();
1660             }
1661             catch ( final IOException e2 ) {
1662                 ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1663             }
1664             System.gc();
1665         } // for( int i = 0; i < number_of_genomes; ++i ) {
1666         ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
1667                 + per_genome_domain_promiscuity_statistics_file );
1668         //
1669         if ( da_analysis ) {
1670             SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
1671                                                              distinct_domain_architecuture_counts,
1672                                                              10,
1673                                                              new File( out_dir.toString() + "/" + output_file
1674                                                                      + "_DA_counts.txt" ),
1675                                                              new File( out_dir.toString() + "/" + output_file
1676                                                                      + "_unique_DAs.txt" ) );
1677             distinct_domain_architecutures_per_genome.clear();
1678             distinct_domain_architecuture_counts.clear();
1679             System.gc();
1680         }
1681         try {
1682             domains_per_potein_stats_writer.write( "ALL" );
1683             domains_per_potein_stats_writer.write( "\t" );
1684             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" );
1685             domains_per_potein_stats_writer.write( "\t" );
1686             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" );
1687             domains_per_potein_stats_writer.write( "\t" );
1688             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" );
1689             domains_per_potein_stats_writer.write( "\t" );
1690             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" );
1691             domains_per_potein_stats_writer.write( "\t" );
1692             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" );
1693             domains_per_potein_stats_writer.write( "\t" );
1694             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
1695             domains_per_potein_stats_writer.write( "\n" );
1696             domains_per_potein_stats_writer.close();
1697             SurfacingUtil.printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
1698             ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1699                     + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
1700             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1701                     + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
1702             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1703                     + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
1704             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1705                     + "_domains_always_combined.txt" ), domains_which_never_single, "\n" );
1706             ForesterUtil.programMessage( PRG_NAME,
1707                                          "Average of proteins with a least one domain assigned: "
1708                                                  + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
1709                                                  + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" );
1710             ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: "
1711                     + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() )
1712                     + "%" );
1713             SurfacingUtil.log( "Average of prot with a least one dom assigned  : "
1714                                        + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
1715                                        + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)",
1716                                log_writer );
1717             SurfacingUtil.log( "Range of prot with a least one dom assigned    : "
1718                                        + ( 100 * protein_coverage_stats.getMin() ) + "%-"
1719                                        + ( 100 * protein_coverage_stats.getMax() ) + "%",
1720                                log_writer );
1721         }
1722         catch ( final IOException e2 ) {
1723             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1724         }
1725         if ( query_domains_writer_ary != null ) {
1726             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1727                 try {
1728                     query_domains_writer_ary[ j ].close();
1729                 }
1730                 catch ( final IOException e ) {
1731                     ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
1732                 }
1733             }
1734         }
1735         try {
1736             per_genome_domain_promiscuity_statistics_writer.close();
1737             dc_data_writer.close();
1738             log_writer.close();
1739         }
1740         catch ( final IOException e2 ) {
1741             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1742         }
1743         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1744             try {
1745                 SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
1746                                                            number_of_genomes,
1747                                                            domain_lengths_table,
1748                                                            domain_lengths_analysis_outfile );
1749             }
1750             catch ( final IOException e1 ) {
1751                 ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
1752             }
1753             System.out.println();
1754             ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
1755             System.out.println();
1756         }
1757         domain_lengths_table = null;
1758         final long analysis_start_time = new Date().getTime();
1759         PairwiseDomainSimilarityCalculator pw_calc = null;
1760         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
1761                                                                                      sort_by_species_count_first,
1762                                                                                      number_of_genomes == 2,
1763                                                                                      CALC_SIMILARITY_SCORES );
1764         switch ( scoring ) {
1765             case COMBINATIONS:
1766                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
1767                 break;
1768             case DOMAINS:
1769                 pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
1770                 break;
1771             case PROTEINS:
1772                 pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
1773                 break;
1774             default:
1775                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
1776         }
1777         DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
1778         if ( domain_id_to_go_ids_map != null ) {
1779             go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
1780         }
1781         final SortedSet<DomainSimilarity> similarities = calc
1782                 .calculateSimilarities( pw_calc,
1783                                         gwcd_list,
1784                                         ignore_domains_without_combs_in_all_spec,
1785                                         ignore_species_specific_domains );
1786         SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
1787         final Map<String, Integer> tax_code_to_id_map = SurfacingUtil.createTaxCodeToIdMap( intrees[ 0 ] );
1788         try {
1789             String my_outfile = output_file.toString();
1790             Map<Character, Writer> split_writers = null;
1791             Writer writer = null;
1792             if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
1793                 if ( my_outfile.endsWith( ".html" ) ) {
1794                     my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
1795                 }
1796                 split_writers = new HashMap<Character, Writer>();
1797                 SurfacingUtil.createSplitWriters( out_dir, my_outfile, split_writers );
1798             }
1799             else if ( !my_outfile.endsWith( ".html" ) ) {
1800                 my_outfile += ".html";
1801                 writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
1802             }
1803             List<Species> species_order = null;
1804             if ( species_matrix ) {
1805                 species_order = new ArrayList<Species>();
1806                 for( int i = 0; i < number_of_genomes; i++ ) {
1807                     species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
1808                 }
1809             }
1810             html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
1811                     + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
1812             html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
1813                     + "</td></tr>" + nl );
1814             html_desc.append( "<tr><td>Analysis date/time:</td><td>"
1815                     + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
1816                     + "</td></tr>" + nl );
1817             html_desc.append( "</table>" + nl );
1818             final Writer simple_tab_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
1819                     + my_outfile + ".tsv" ) );
1820             SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
1821                                                          new StringBuilder( number_of_genomes + " genomes" ),
1822                                                          simple_tab_writer,
1823                                                          writer,
1824                                                          split_writers,
1825                                                          similarities,
1826                                                          number_of_genomes == 2,
1827                                                          species_order,
1828                                                          domain_similarity_print_option,
1829                                                          scoring,
1830                                                          true,
1831                                                          tax_code_to_id_map,
1832                                                          intree_0_orig );
1833             simple_tab_writer.close();
1834             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
1835                     + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
1836         }
1837         catch ( final IOException e ) {
1838             ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
1839                     + e.getMessage() + "]" );
1840         }
1841         System.out.println();
1842         final Species[] species = new Species[ number_of_genomes ];
1843         for( int i = 0; i < number_of_genomes; ++i ) {
1844             species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
1845         }
1846         List<Phylogeny> inferred_trees = null;
1847         if ( ( number_of_genomes > 2 ) && perform_pwc ) {
1848             final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
1849             pwgc.performPairwiseComparisons( html_desc,
1850                                              sort_by_species_count_first,
1851                                              detailedness,
1852                                              ignore_domains_without_combs_in_all_spec,
1853                                              ignore_species_specific_domains,
1854                                              domain_similarity_sort_field_for_automated_pwc,
1855                                              domain_similarity_print_option,
1856                                              scoring,
1857                                              domain_id_to_go_ids_map,
1858                                              go_id_to_term_map,
1859                                              go_namespace_limit,
1860                                              species,
1861                                              number_of_genomes,
1862                                              gwcd_list,
1863                                              pw_calc,
1864                                              automated_pairwise_comparison_suffix,
1865                                              true,
1866                                              surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
1867                                              surfacing.PRG_NAME,
1868                                              out_dir,
1869                                              write_pwc_files,
1870                                              tax_code_to_id_map,
1871                                              CALC_SIMILARITY_SCORES,
1872                                              intree_0_orig );
1873             String matrix_output_file = new String( output_file.toString() );
1874             if ( matrix_output_file.indexOf( '.' ) > 1 ) {
1875                 matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
1876             }
1877             if ( out_dir != null ) {
1878                 matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
1879                 output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
1880             }
1881             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
1882                     + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
1883             SurfacingUtil
1884                     .writeMatrixToFile( new File( matrix_output_file
1885                                                 + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
1886                                         pwgc.getSharedBinaryCombinationsBasedDistances() );
1887             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
1888                                                      + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
1889                                              pwgc.getSharedDomainsBasedDistances() );
1890             final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
1891                     + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
1892                     .get( 0 ) );
1893             final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
1894                     + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
1895                     .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
1896             final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
1897                     + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
1898                     .getSharedDomainsBasedDistances().get( 0 ) );
1899             inferred_trees = new ArrayList<Phylogeny>();
1900             inferred_trees.add( nj_gd );
1901             inferred_trees.add( nj_bc );
1902             inferred_trees.add( nj_d );
1903         } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
1904         if ( ( out_dir != null ) && ( !perform_pwc ) ) {
1905             output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
1906         }
1907         if ( write_to_nexus ) {
1908             SurfacingUtil.writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
1909         }
1910         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
1911             final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs,
1912                                                                                         e_value_max,
1913                                                                                         max_allowed_overlap,
1914                                                                                         no_engulfing_overlaps,
1915                                                                                         cutoff_scores_file,
1916                                                                                         dc_type );
1917             String s = "_";
1918             if ( radomize_fitch_parsimony ) {
1919                 s += random_number_seed_for_fitch_parsimony + "_";
1920             }
1921             int i = 0;
1922             for( final Phylogeny intree : intrees ) {
1923                 final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
1924                         + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
1925                 final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
1926                                                                                                              gwcd_list );
1927                 SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
1928                                                         radomize_fitch_parsimony,
1929                                                         outfile_name,
1930                                                         domain_parsimony,
1931                                                         intree,
1932                                                         domain_id_to_go_ids_map,
1933                                                         go_id_to_term_map,
1934                                                         go_namespace_limit,
1935                                                         parameters_sb.toString(),
1936                                                         domain_id_to_secondary_features_maps,
1937                                                         positive_filter_file == null ? null : filter,
1938                                                         output_binary_domain_combinationsfor_graph_analysis,
1939                                                         all_bin_domain_combinations_gained_fitch,
1940                                                         all_bin_domain_combinations_lost_fitch,
1941                                                         dc_type,
1942                                                         protein_length_stats_by_dc,
1943                                                         domain_number_stats_by_dc,
1944                                                         domain_length_stats_by_domain,
1945                                                         tax_code_to_id_map,
1946                                                         write_to_nexus,
1947                                                         use_last_in_fitch_parsimony );
1948                 // Listing of all domain combinations gained is only done if only one input tree is used.
1949                 if ( ( domain_id_to_secondary_features_maps != null )
1950                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1951                     int j = 0;
1952                     for( final Map<String, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
1953                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
1954                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
1955                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
1956                         SurfacingUtil
1957                                 .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
1958                                                                                        + "_"
1959                                                                                        + secondary_features_map_files[ j++ ],
1960                                                                                secondary_features_parsimony,
1961                                                                                intree,
1962                                                                                parameters_sb.toString(),
1963                                                                                mapping_results_map,
1964                                                                                use_last_in_fitch_parsimony );
1965                         if ( i == 0 ) {
1966                             System.out.println();
1967                             System.out.println( "Mapping to secondary features:" );
1968                             for( final Species spec : mapping_results_map.keySet() ) {
1969                                 final MappingResults mapping_results = mapping_results_map.get( spec );
1970                                 final int total_domains = mapping_results.getSumOfFailures()
1971                                         + mapping_results.getSumOfSuccesses();
1972                                 System.out.print( spec + ":" );
1973                                 System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
1974                                 System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
1975                                 if ( total_domains > 0 ) {
1976                                     System.out.println( ", mapped ratio = "
1977                                             + ( ( 100 * mapping_results.getSumOfSuccesses() ) / total_domains ) + "%" );
1978                                 }
1979                                 else {
1980                                     System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
1981                                 }
1982                             }
1983                         }
1984                     }
1985                 }
1986                 i++;
1987             } // for( final Phylogeny intree : intrees ) {
1988         }
1989         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1990             SurfacingUtil.executePlusMinusAnalysis( output_file,
1991                                                     plus_minus_analysis_high_copy_base_species,
1992                                                     plus_minus_analysis_high_copy_target_species,
1993                                                     plus_minus_analysis_high_low_copy_species,
1994                                                     gwcd_list,
1995                                                     protein_lists_per_species,
1996                                                     domain_id_to_go_ids_map,
1997                                                     go_id_to_term_map,
1998                                                     plus_minus_analysis_numbers );
1999         }
2000         if ( output_protein_lists_for_all_domains ) {
2001             SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
2002                                                           protein_lists_per_species,
2003                                                           gwcd_list,
2004                                                           output_list_of_all_proteins_per_domain_e_value_max );
2005         }
2006         gwcd_list = null;
2007         if ( all_bin_domain_combinations_gained_fitch != null ) {
2008             try {
2009                 SurfacingUtil
2010                         .executeFitchGainsAnalysis( new File( output_file
2011                                                             + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2012                                                     all_bin_domain_combinations_gained_fitch,
2013                                                     all_domains_encountered.size(),
2014                                                     all_bin_domain_combinations_encountered,
2015                                                     true );
2016             }
2017             catch ( final IOException e ) {
2018                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2019             }
2020         }
2021         if ( all_bin_domain_combinations_lost_fitch != null ) {
2022             try {
2023                 SurfacingUtil
2024                         .executeFitchGainsAnalysis( new File( output_file
2025                                                             + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2026                                                     all_bin_domain_combinations_lost_fitch,
2027                                                     all_domains_encountered.size(),
2028                                                     all_bin_domain_combinations_encountered,
2029                                                     false );
2030             }
2031             catch ( final IOException e ) {
2032                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2033             }
2034         }
2035         final Runtime rt = java.lang.Runtime.getRuntime();
2036         final long free_memory = rt.freeMemory() / 1000000;
2037         final long total_memory = rt.totalMemory() / 1000000;
2038         ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time )
2039                 + "ms" );
2040         ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
2041         ForesterUtil.programMessage( PRG_NAME, "Free memory       : " + free_memory + "MB, total memory: "
2042                 + total_memory + "MB" );
2043         ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" );
2044         ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
2045         ForesterUtil.programMessage( PRG_NAME, "OK" );
2046         System.out.println();
2047     }
2048
2049     private static void printHelp() {
2050         System.out.println();
2051         System.out.println( "Usage:" );
2052         System.out.println();
2053         System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME
2054                 + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
2055         System.out.println();
2056         System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
2057         System.out
2058                 .println( "       hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
2059         System.out.println();
2060         System.out.println( " Options: " );
2061         System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
2062                 + DETAILEDNESS_DEFAULT + ")" );
2063         System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
2064                 + ": to ignore combinations with self (default: not to ignore)" );
2065         System.out
2066                 .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
2067                         + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2068         System.out
2069                 .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
2070                         + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2071         System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
2072                 + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
2073         System.out
2074                 .println( surfacing.IGNORE_VIRAL_IDS
2075                         + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
2076         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
2077                 + DOMAIN_SORT_FILD_DEFAULT + ")" );
2078         System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
2079         System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
2080         System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
2081         System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
2082         System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
2083         System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
2084         System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
2085                 + DOMAINS_SORT_ORDER_DEFAULT + ")" );
2086         System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
2087                 + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
2088         System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
2089         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
2090                 + ": sort by species count first" );
2091         System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
2092         System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
2093         System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
2094         System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
2095         System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
2096                 + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
2097         System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
2098                 + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
2099         System.out
2100                 .println( surfacing.INPUT_SPECIES_TREE_OPTION
2101                         + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
2102         System.out.println( surfacing.FILTER_POSITIVE_OPTION
2103                 + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
2104         System.out.println( surfacing.FILTER_NEGATIVE_OPTION
2105                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
2106         System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
2107                 + "=<file>: to filter out (ignore) domains listed in <file>" );
2108         System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>: to read input files from <file>" );
2109         System.out
2110                 .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
2111                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
2112         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
2113                 + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
2114         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
2115                 + ": to consider directedness and adjacency in binary combinations" );
2116         System.out
2117                 .println( surfacing.SEQ_EXTRACT_OPTION
2118                         + "=<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')" );
2119         System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
2120                 + "=<file>: to perfom parsimony analysis on secondary features" );
2121         System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
2122         System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
2123                 + ": to output binary domain combinations for (downstream) graph analysis" );
2124         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
2125         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
2126                 + ": e value max per domain for output of all proteins per domain" );
2127         System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" );
2128         System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" );
2129         System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" );
2130         System.out.println( DA_ANALYSIS_OPTION + ": to do DA analysis" );
2131         System.out.println();
2132         System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2133                 + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
2134                 + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o "
2135                 + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
2136         System.out.println();
2137         System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2138                 + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
2139                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
2140                 + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
2141                 + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
2142         System.out.println();
2143     }
2144 }