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

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.application;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.util.ArrayList;
  35 import java.util.Date;
  36 import java.util.HashMap;
  37 import java.util.HashSet;
  38 import java.util.Iterator;
  39 import java.util.List;
  40 import java.util.Map;
  41 import java.util.Map.Entry;
  42 import java.util.Set;
  43 import java.util.SortedMap;
  44 import java.util.SortedSet;
  45 import java.util.TreeMap;
  46 import java.util.TreeSet;
  47
  48 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  49 import org.forester.go.GoId;
  50 import org.forester.go.GoNameSpace;
  51 import org.forester.go.GoTerm;
  52 import org.forester.go.GoUtils;
  53 import org.forester.go.OBOparser;
  54 import org.forester.go.PfamToGoMapping;
  55 import org.forester.go.PfamToGoParser;
  56 import org.forester.io.parsers.HmmscanPerDomainTableParser;
  57 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
  58 import org.forester.io.parsers.util.ParserUtils;
  59 import org.forester.phylogeny.Phylogeny;
  60 import org.forester.phylogeny.PhylogenyMethods;
  61 import org.forester.phylogeny.PhylogenyNode;
  62 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  63 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  64 import org.forester.protein.BasicProtein;
  65 import org.forester.protein.BinaryDomainCombination;
  66 import org.forester.protein.Domain;
  67 import org.forester.protein.DomainId;
  68 import org.forester.protein.Protein;
  69 import org.forester.species.BasicSpecies;
  70 import org.forester.species.Species;
  71 import org.forester.surfacing.BasicDomainSimilarityCalculator;
  72 import org.forester.surfacing.BasicGenomeWideCombinableDomains;
  73 import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
  74 import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
  75 import org.forester.surfacing.DomainCountsDifferenceUtil;
  76 import org.forester.surfacing.DomainLengthsTable;
  77 import org.forester.surfacing.DomainParsimonyCalculator;
  78 import org.forester.surfacing.DomainSimilarity;
  79 import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
  80 import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
  81 import org.forester.surfacing.DomainSimilarityCalculator;
  82 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  83 import org.forester.surfacing.GenomeWideCombinableDomains;
  84 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  85 import org.forester.surfacing.MappingResults;
  86 import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
  87 import org.forester.surfacing.PairwiseGenomeComparator;
  88 import org.forester.surfacing.PrintableDomainSimilarity;
  89 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  90 import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
  91 import org.forester.surfacing.SurfacingUtil;
  92 import org.forester.util.BasicDescriptiveStatistics;
  93 import org.forester.util.BasicTable;
  94 import org.forester.util.BasicTableParser;
  95 import org.forester.util.CommandLineArguments;
  96 import org.forester.util.DescriptiveStatistics;
  97 import org.forester.util.ForesterConstants;
  98 import org.forester.util.ForesterUtil;
  99
 100 public class surfacing {
 101
 102     private static final int                                  MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING                                  = 1000;
 103     public final static String                                DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS                           = "graph_analysis_out";
 104     public final static String                                DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS                       = "_dc.dot";
 105     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS        = "_fitch_present_dc.dot";
 106     public final static String                                DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX                                    = ".dcc";
 107     // gain/loss:
 108     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS                                      = "_dollo_gl_d";
 109     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS                          = "_dollo_gl_dc";
 110     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS                                      = "_fitch_gl_d";
 111     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS                          = "_fitch_gl_dc";
 112     // gain/loss counts:
 113     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS                               = "_dollo_glc_d";
 114     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS                   = "_dollo_glc_dc";
 115     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS                               = "_fitch_glc_d";
 116     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS                   = "_fitch_glc_dc";
 117     // tables:
 118     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_BC                                               = "_fitch_gains_dc";
 119     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC                                          = "_fitch_gains_dc.html";
 120     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_BC                                              = "_fitch_losses_dc";
 121     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC                                         = "_fitch_losses_dc.html";
 122     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC                                             = "_fitch_present_dc";
 123     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC                                        = "_fitch_present_dc.html";
 124     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_D                                                = "_dollo_gains_d";
 125     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D                                           = "_dollo_gains_d.html";
 126     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_D                                               = "_dollo_losses_d";
 127     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D                                          = "_dollo_losses_d.html";
 128     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_D                                              = "_dollo_present_d";
 129     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D                                         = "_dollo_present_d.html";
 130     public final static String                                DOMAINS_PRESENT_NEXUS                                                         = "_dom.nex";
 131     public final static String                                BDC_PRESENT_NEXUS                                                             = "_dc.nex";
 132     // ---
 133     public final static String                                PRG_NAME                                                                      = "surfacing";
 134     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                                    = "_d_dollo"
 135                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 136     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                                    = "_d_fitch"
 137                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 138     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                 = "_dc_dollo"
 139                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 140     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                 = "_dc_fitch"
 141                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 142     public static final String                                NEXUS_EXTERNAL_DOMAINS                                                        = "_dom.nex";
 143     public static final String                                NEXUS_EXTERNAL_DOMAIN_COMBINATIONS                                            = "_dc.nex";
 144     public static final String                                NEXUS_SECONDARY_FEATURES                                                      = "_secondary_features.nex";
 145     public static final String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES                           = "_dollo_gl_secondary_features";
 146     public static final String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES                    = "_dollo_glc_secondary_features";
 147     public static final String                                PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES                               = "_dollo_gains_secondary_features";
 148     public static final String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES                              = "_dollo_losses_secondary_features";
 149     public static final String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES                             = "_dollo_present_secondary_features";
 150     public static final String                                SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                         = "_secondary_features_dollo"
 151                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 152     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES                              = "_dollo_goid_d";
 153     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES                             = "_fitch_goid_dc";
 154     final static private String                               HELP_OPTION_1                                                                 = "help";
 155     final static private String                               HELP_OPTION_2                                                                 = "h";
 156     final static private String                               OUTPUT_DIR_OPTION                                                             = "out_dir";
 157     final static private String                               SCORING_OPTION                                                                = "scoring";
 158     private static final DomainSimilarityScoring              SCORING_DEFAULT                                                               = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 159     final static private String                               SCORING_DOMAIN_COUNT_BASED                                                    = "domains";
 160     final static private String                               SCORING_PROTEIN_COUNT_BASED                                                   = "proteins";
 161     final static private String                               SCORING_COMBINATION_BASED                                                     = "combinations";
 162     final static private String                               DETAILEDNESS_OPTION                                                           = "detail";
 163     private final static Detailedness                         DETAILEDNESS_DEFAULT                                                          = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 164     final static private String                               SPECIES_MATRIX_OPTION                                                         = "smatrix";
 165     final static private String                               DETAILEDNESS_BASIC                                                            = "basic";
 166     final static private String                               DETAILEDNESS_LIST_IDS                                                         = "list_ids";
 167     final static private String                               DETAILEDNESS_PUNCTILIOUS                                                      = "punctilious";
 168     final static private String                               DOMAIN_SIMILARITY_SORT_OPTION                                                 = "sort";
 169     private static final DomainSimilaritySortField            DOMAIN_SORT_FILD_DEFAULT                                                      = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 170     final static private String                               DOMAIN_SIMILARITY_SORT_MIN                                                    = "min";
 171     final static private String                               DOMAIN_SIMILARITY_SORT_MAX                                                    = "max";
 172     final static private String                               DOMAIN_SIMILARITY_SORT_SD                                                     = "sd";
 173     final static private String                               DOMAIN_SIMILARITY_SORT_MEAN                                                   = "mean";
 174     final static private String                               DOMAIN_SIMILARITY_SORT_DIFF                                                   = "diff";
 175     final static private String                               DOMAIN_SIMILARITY_SORT_COUNTS_DIFF                                            = "count_diff";
 176     final static private String                               DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF                                        = "abs_count_diff";
 177     final static private String                               DOMAIN_SIMILARITY_SORT_SPECIES_COUNT                                          = "species";
 178     final static private String                               DOMAIN_SIMILARITY_SORT_ALPHA                                                  = "alpha";
 179     final static private String                               DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION                          = "species_first";
 180     final static private String                               DOMAIN_COUNT_SORT_OPTION                                                      = "dc_sort";
 181     private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT                                                    = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
 182     final static private String                               DOMAIN_COUNT_SORT_ALPHA                                                       = "alpha";
 183     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT                                            = "dom";
 184     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT                                   = "prot";
 185     final static private String                               DOMAIN_COUNT_SORT_COMBINATIONS_COUNT                                          = "comb";
 186     final static private String                               CUTOFF_SCORE_FILE_OPTION                                                      = "cos";
 187     final static private String                               NOT_IGNORE_DUFS_OPTION                                                        = "dufs";
 188     final static private String                               MAX_E_VALUE_OPTION                                                            = "e";
 189     final static private String                               MAX_ALLOWED_OVERLAP_OPTION                                                    = "mo";
 190     final static private String                               NO_ENGULFING_OVERLAP_OPTION                                                   = "no_eo";
 191     final static private String                               IGNORE_COMBINATION_WITH_SAME_OPTION                                           = "ignore_self_comb";
 192     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
 193     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_OPTION                                            = "pwc";
 194     final static private String                               OUTPUT_FILE_OPTION                                                            = "o";
 195     final static private String                               PFAM_TO_GO_FILE_USE_OPTION                                                    = "p2g";
 196     final static private String                               GO_OBO_FILE_USE_OPTION                                                        = "obo";
 197     final static private String                               GO_NAMESPACE_LIMIT_OPTION                                                     = "go_namespace";
 198     final static private String                               GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION                                  = "molecular_function";
 199     final static private String                               GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS                                  = "biological_process";
 200     final static private String                               GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT                                  = "cellular_component";
 201     final static private String                               SECONDARY_FEATURES_PARSIMONY_MAP_FILE                                         = "secondary";
 202     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED                           = "simple_tab";
 203     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML                                    = "simple_html";
 204     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML                                  = "detailed_html";
 205     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION                                                = "ds_output";
 206     private static final PRINT_OPTION                         DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT                                        = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 207     final static private String                               IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION                     = "ignore_singlet_domains";
 208     final static private String                               IGNORE_VIRAL_IDS                                                              = "ignore_viral_ids";
 209     final static private boolean                              IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT                    = false;
 210     final static private String                               IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION                                 = "ignore_species_specific_domains";
 211     final static private boolean                              IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT                         = false;
 212     final static private String                               MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                                = "_mean_score.pwd";
 213     final static private String                               MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                            = "_domains.pwd";
 214     final static private String                               MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                   = "_bin_combinations.pwd";
 215     final static private String                               NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                               = "_mean_score_NJ"
 216                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 217     final static private String                               NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                           = "_domains_NJ"
 218                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 219     final static private String                               NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX                  = "_bin_combinations_NJ"
 220                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 221     final static private String                               JACKNIFE_OPTION                                                               = "jack";
 222     final static private String                               JACKNIFE_RANDOM_SEED_OPTION                                                   = "seed";
 223     final static private String                               JACKNIFE_RATIO_OPTION                                                         = "jack_ratio";
 224     private static final int                                  JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT                                        = 100;
 225     final static private long                                 JACKNIFE_RANDOM_SEED_DEFAULT                                                  = 19;
 226     final static private double                               JACKNIFE_RATIO_DEFAULT                                                        = 0.5;
 227     //final static private String  INFER_SPECIES_TREES_OPTION                                             = "species_tree_inference";
 228     final static private String                               FILTER_POSITIVE_OPTION                                                        = "pos_filter";
 229     final static private String                               FILTER_NEGATIVE_OPTION                                                        = "neg_filter";
 230     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                                = "neg_dom_filter";
 231     final static private String                               INPUT_FILES_FROM_FILE_OPTION                                                  = "input";
 232     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
 233     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
 234     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                                    = '#';
 235     final static private String                               PRG_VERSION                                                                   = "2.252";
 236     final static private String                               PRG_DATE                                                                      = "2012.08.01";
 237     final static private String                               E_MAIL                                                                        = "czmasek@burnham.org";
 238     final static private String                               WWW                                                                           = "www.phylosoft.org/forester/applications/surfacing";
 239     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;
 240     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
 241     final static private double                               MAX_E_VALUE_DEFAULT                                                           = -1;
 242     final static private int                                  MAX_ALLOWED_OVERLAP_DEFAULT                                                   = -1;
 243     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                        = "random_seed";
 244     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                                      = "consider_bdc_direction";
 245     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                        = "consider_bdc_adj";
 246     private static final String                               SEQ_EXTRACT_SUFFIX                                                            = ".prot";
 247     private static final String                               PLUS_MINUS_ANALYSIS_OPTION                                                    = "plus_minus";
 248     private static final String                               PLUS_MINUS_DOM_SUFFIX                                                         = "_plus_minus_dom.txt";
 249     private static final String                               PLUS_MINUS_DOM_SUFFIX_HTML                                                    = "_plus_minus_dom.html";
 250     private static final String                               PLUS_MINUS_DC_SUFFIX_HTML                                                     = "_plus_minus_dc.html";
 251     private static final int                                  PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                          = 0;
 252     private static final double                               PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                            = 1.0;
 253     private static final String                               PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                              = "_plus_minus_go_ids_all.txt";
 254     private static final String                               PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                          = "_plus_minus_go_ids_passing.txt";
 255     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                           = "all_prot";
 256     final static private String                               OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION                         = "all_prot_e";
 257     private static final boolean                              VERBOSE                                                                       = false;
 258     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX              = "_fitch_dc_gains_counts";
 259     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX                = "_fitch_dc_losses_counts";
 260     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                                = "_domain_lengths_analysis";
 261     private static final boolean                              PERFORM_DOMAIN_LENGTH_ANALYSIS                                                = true;
 262     public static final String                                ALL_PFAMS_ENCOUNTERED_SUFFIX                                                  = "_all_encountered_pfams";
 263     public static final String                                ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX                               = "_all_encountered_pfams_with_go_annotation";
 264     public static final String                                ENCOUNTERED_PFAMS_SUMMARY_SUFFIX                                              = "_encountered_pfams_summary";
 265     public static final String                                ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX                                            = "_all_pfams_gained_as_domains";
 266     public static final String                                ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX                                              = "_all_pfams_lost_as_domains";
 267     public static final String                                ALL_PFAMS_GAINED_AS_DC_SUFFIX                                                 = "_all_pfams_gained_as_dc";
 268     public static final String                                ALL_PFAMS_LOST_AS_DC_SUFFIX                                                   = "_all_pfams_lost_as_dc";
 269     public static final String                                BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES                                = "PER_NODE_EVENTS";
 270     public static final String                                BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES                             = "PER_SUBTREE_EVENTS";
 271     public static final String                                D_PROMISCUITY_FILE_SUFFIX                                                     = "_domain_promiscuities";
 272     private static final String                               LOG_FILE_SUFFIX                                                               = "_log.txt";
 273     private static final String                               DATA_FILE_SUFFIX                                                              = "_domain_combination_data.txt";
 274     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";
 275     private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                               = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;                                                                                                                                                      //TODO look at me! change?
 276     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX                          = "_indep_dc_gains_fitch_counts.txt";
 277     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                              = "_indep_dc_gains_fitch_lists.txt";
 278     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX               = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
 279     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";
 280     public static final String                                LIMIT_SPEC_FOR_PROT_EX                                                        = null;                                                                                                                                                                                       // e.g. "HUMAN"; set to null for not using this feature (default).
 281     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED          = "_dc_MAPPED_secondary_features_fitch"
 282                                                                                                                                                     + ForesterConstants.PHYLO_XML_SUFFIX;
 283     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX                   = "_indep_dc_gains_fitch_counts_MAPPED.txt";
 284     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists_MAPPED.txt";
 285     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";
 286     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";
 287     private static final boolean                              PERFORM_DC_REGAIN_PROTEINS_STATS                                              = true;
 288     private static final boolean                              DA_ANALYSIS                                                                   = true;
 289
 290     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
 291                                                                  final String[][] input_file_properties,
 292                                                                  final String automated_pairwise_comparison_suffix,
 293                                                                  final File outdir ) {
 294         for( int i = 0; i < input_file_properties.length; ++i ) {
 295             for( int j = 0; j < i; ++j ) {
 296                 final String species_i = input_file_properties[ i ][ 1 ];
 297                 final String species_j = input_file_properties[ j ][ 1 ];
 298                 String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
 299                         + species_j + automated_pairwise_comparison_suffix;
 300                 switch ( domain_similarity_print_option ) {
 301                     case HTML:
 302                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 303                             pairwise_similarities_output_file_str += ".html";
 304                         }
 305                         break;
 306                 }
 307                 final String error = ForesterUtil
 308                         .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
 309                                 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 310                 if ( !ForesterUtil.isEmpty( error ) ) {
 311                     ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 312                 }
 313             }
 314         }
 315     }
 316
 317     private static StringBuilder createParametersAsString( final boolean ignore_dufs,
 318                                                            final double e_value_max,
 319                                                            final int max_allowed_overlap,
 320                                                            final boolean no_engulfing_overlaps,
 321                                                            final File cutoff_scores_file,
 322                                                            final BinaryDomainCombination.DomainCombinationType dc_type ) {
 323         final StringBuilder parameters_sb = new StringBuilder();
 324         parameters_sb.append( "E-value: " + e_value_max );
 325         if ( cutoff_scores_file != null ) {
 326             parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
 327         }
 328         else {
 329             parameters_sb.append( ", Cutoff-scores-file: not-set" );
 330         }
 331         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
 332             parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
 333         }
 334         else {
 335             parameters_sb.append( ", Max-overlap: not-set" );
 336         }
 337         if ( no_engulfing_overlaps ) {
 338             parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
 339         }
 340         else {
 341             parameters_sb.append( ", Engulfing-overlaps: allowed" );
 342         }
 343         if ( ignore_dufs ) {
 344             parameters_sb.append( ", Ignore-dufs: true" );
 345         }
 346         else {
 347             parameters_sb.append( ", Ignore-dufs: false" );
 348         }
 349         parameters_sb.append( ", DC type (if applicable): " + dc_type );
 350         return parameters_sb;
 351     }
 352
 353     /**
 354      * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
 355      *
 356      *
 357      * @param output_file
 358      * @param all_bin_domain_combinations_changed
 359      * @param sum_of_all_domains_encountered
 360      * @param all_bin_domain_combinations_encountered
 361      * @param is_gains_analysis
 362      * @param protein_length_stats_by_dc
 363      * @throws IOException
 364      */
 365     private static void executeFitchGainsAnalysis( final File output_file,
 366                                                    final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
 367                                                    final int sum_of_all_domains_encountered,
 368                                                    final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
 369                                                    final boolean is_gains_analysis ) throws IOException {
 370         SurfacingUtil.checkForOutputFileWriteability( output_file );
 371         final Writer out = ForesterUtil.createBufferedWriter( output_file );
 372         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
 373                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
 374         final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
 375         final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
 376         int above_one = 0;
 377         int one = 0;
 378         for( final Object bdc_object : bdc_to_counts.keySet() ) {
 379             final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
 380             final int count = bdc_to_counts.get( bdc_object );
 381             if ( count < 1 ) {
 382                 ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
 383             }
 384             out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 385             if ( count > 1 ) {
 386                 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
 387                 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
 388                 above_one++;
 389             }
 390             else if ( count == 1 ) {
 391                 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
 392                 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
 393                 one++;
 394             }
 395         }
 396         final int all = all_bin_domain_combinations_encountered.size();
 397         int never_lost = -1;
 398         if ( !is_gains_analysis ) {
 399             all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
 400             never_lost = all_bin_domain_combinations_encountered.size();
 401             for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
 402                 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
 403             }
 404         }
 405         if ( is_gains_analysis ) {
 406             out.write( "Sum of all distinct domain combinations appearing once               : " + one
 407                     + ForesterUtil.LINE_SEPARATOR );
 408             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
 409                     + ForesterUtil.LINE_SEPARATOR );
 410             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
 411                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 412             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
 413                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 414         }
 415         else {
 416             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
 417                     + ForesterUtil.LINE_SEPARATOR );
 418             out.write( "Sum of all distinct domain combinations lost once                    : " + one
 419                     + ForesterUtil.LINE_SEPARATOR );
 420             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
 421                     + ForesterUtil.LINE_SEPARATOR );
 422             out.write( "Sum of all distinct domains in combinations lost only once           : "
 423                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 424             out.write( "Sum of all distinct domains in combinations lost more than once: "
 425                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 426         }
 427         out.write( "All binary combinations                                              : " + all
 428                 + ForesterUtil.LINE_SEPARATOR );
 429         out.write( "All domains                                                          : "
 430                 + sum_of_all_domains_encountered );
 431         out.close();
 432         ForesterUtil.programMessage( surfacing.PRG_NAME,
 433                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
 434                                              + "\"" );
 435     }
 436
 437     private static void executePlusMinusAnalysis( final File output_file,
 438                                                   final List<String> plus_minus_analysis_high_copy_base,
 439                                                   final List<String> plus_minus_analysis_high_copy_target,
 440                                                   final List<String> plus_minus_analysis_low_copy,
 441                                                   final List<GenomeWideCombinableDomains> gwcd_list,
 442                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species,
 443                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 444                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 445                                                   final List<Object> plus_minus_analysis_numbers ) {
 446         final Set<String> all_spec = new HashSet<String>();
 447         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 448             all_spec.add( gwcd.getSpecies().getSpeciesId() );
 449         }
 450         final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
 451         final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
 452         final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
 453         final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
 454         final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
 455         final File proteins_file_base = new File( output_file + "" );
 456         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
 457         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
 458         try {
 459             DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
 460                                                                        protein_lists_per_species,
 461                                                                        plus_minus_analysis_high_copy_base,
 462                                                                        plus_minus_analysis_high_copy_target,
 463                                                                        plus_minus_analysis_low_copy,
 464                                                                        min_diff,
 465                                                                        factor,
 466                                                                        plain_out_dom,
 467                                                                        html_out_dom,
 468                                                                        html_out_dc,
 469                                                                        domain_id_to_go_ids_map,
 470                                                                        go_id_to_term_map,
 471                                                                        all_domains_go_ids_out_dom,
 472                                                                        passing_domains_go_ids_out_dom,
 473                                                                        proteins_file_base );
 474         }
 475         catch ( final IOException e ) {
 476             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 477         }
 478         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 479                 + html_out_dom + "\"" );
 480         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 481                 + plain_out_dom + "\"" );
 482         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
 483                 + "\"" );
 484         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
 485                 + passing_domains_go_ids_out_dom + "\"" );
 486         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
 487                 + all_domains_go_ids_out_dom + "\"" );
 488     }
 489
 490     private static Phylogeny[] getIntrees( final File[] intree_files,
 491                                            final int number_of_genomes,
 492                                            final String[][] input_file_properties ) {
 493         final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
 494         int i = 0;
 495         for( final File intree_file : intree_files ) {
 496             Phylogeny intree = null;
 497             final String error = ForesterUtil.isReadableFile( intree_file );
 498             if ( !ForesterUtil.isEmpty( error ) ) {
 499                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
 500                         + error );
 501             }
 502             try {
 503                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
 504                         .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
 505                 if ( p_array.length < 1 ) {
 506                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 507                             + "] does not contain any phylogeny in phyloXML format" );
 508                 }
 509                 else if ( p_array.length > 1 ) {
 510                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 511                             + "] contains more than one phylogeny in phyloXML format" );
 512                 }
 513                 intree = p_array[ 0 ];
 514             }
 515             catch ( final Exception e ) {
 516                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
 517                         + "]: " + error );
 518             }
 519             if ( ( intree == null ) || intree.isEmpty() ) {
 520                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
 521             }
 522             if ( !intree.isRooted() ) {
 523                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
 524             }
 525             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
 526                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 527                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
 528                                                  + "] of input tree [" + intree_file
 529                                                  + "] is smaller than the number of genomes the be analyzed ["
 530                                                  + number_of_genomes + "]" );
 531             }
 532             final StringBuilder parent_names = new StringBuilder();
 533             final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
 534             if ( nodes_lacking_name > 0 ) {
 535                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
 536                         + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
 537             }
 538             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
 539             if ( !intree.isCompletelyBinary() ) {
 540                 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
 541                         + "] is not completely binary" );
 542             }
 543             intrees[ i++ ] = intree;
 544         }
 545         return intrees;
 546     }
 547
 548     private static void log( final String msg, final Writer w ) {
 549         try {
 550             w.write( msg );
 551             w.write( ForesterUtil.LINE_SEPARATOR );
 552         }
 553         catch ( final IOException e ) {
 554             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 555         }
 556     }
 557
 558     public static void main( final String args[] ) {
 559         final long start_time = new Date().getTime();
 560         // final StringBuffer log = new StringBuffer();
 561         final StringBuilder html_desc = new StringBuilder();
 562         ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
 563                                               surfacing.PRG_VERSION,
 564                                               surfacing.PRG_DATE,
 565                                               surfacing.E_MAIL,
 566                                               surfacing.WWW );
 567         final String nl = ForesterUtil.LINE_SEPARATOR;
 568         html_desc.append( "<table>" + nl );
 569         html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
 570         html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
 571         html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
 572         html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
 573         html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
 574         CommandLineArguments cla = null;
 575         try {
 576             cla = new CommandLineArguments( args );
 577         }
 578         catch ( final Exception e ) {
 579             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 580         }
 581         if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
 582             surfacing.printHelp();
 583             System.exit( 0 );
 584         }
 585         if ( ( args.length < 1 ) ) {
 586             surfacing.printHelp();
 587             System.exit( -1 );
 588         }
 589         final List<String> allowed_options = new ArrayList<String>();
 590         allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
 591         allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
 592         allowed_options.add( surfacing.DETAILEDNESS_OPTION );
 593         allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
 594         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
 595         allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
 596         allowed_options.add( surfacing.SCORING_OPTION );
 597         allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 598         allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
 599         allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
 600         allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
 601         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
 602         allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
 603         allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
 604         allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
 605         allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
 606         allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
 607         allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
 608         allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 609         allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
 610         allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
 611         allowed_options.add( JACKNIFE_OPTION );
 612         allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
 613         allowed_options.add( JACKNIFE_RATIO_OPTION );
 614         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
 615         //allowed_options.add( INFER_SPECIES_TREES_OPTION );
 616         allowed_options.add( FILTER_POSITIVE_OPTION );
 617         allowed_options.add( FILTER_NEGATIVE_OPTION );
 618         allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
 619         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 620         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
 621         allowed_options.add( IGNORE_VIRAL_IDS );
 622         allowed_options.add( SEQ_EXTRACT_OPTION );
 623         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 624         allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
 625         allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
 626         allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
 627         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
 628         allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
 629         boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
 630         boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
 631         double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
 632         int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
 633         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 634         if ( dissallowed_options.length() > 0 ) {
 635             ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
 636         }
 637         boolean output_binary_domain_combinationsfor_graph_analysis = false;
 638         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
 639             output_binary_domain_combinationsfor_graph_analysis = true;
 640         }
 641         if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
 642             try {
 643                 e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
 644             }
 645             catch ( final Exception e ) {
 646                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
 647             }
 648         }
 649         if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
 650             try {
 651                 max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 652             }
 653             catch ( final Exception e ) {
 654                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
 655             }
 656         }
 657         boolean no_engulfing_overlaps = false;
 658         if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
 659             no_engulfing_overlaps = true;
 660         }
 661         boolean ignore_virus_like_ids = false;
 662         if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
 663             ignore_virus_like_ids = true;
 664         }
 665         if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
 666             ignore_dufs = false;
 667         }
 668         if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
 669             ignore_combination_with_same = true;
 670         }
 671         boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
 672         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
 673             ignore_domains_without_combs_in_all_spec = true;
 674         }
 675         boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
 676         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
 677             ignore_species_specific_domains = true;
 678         }
 679         File output_file = null;
 680         if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 681             if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 682                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 683                                          "no value for domain combinations similarities output file: -"
 684                                                  + surfacing.OUTPUT_FILE_OPTION + "=<file>" );
 685             }
 686             output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
 687             SurfacingUtil.checkForOutputFileWriteability( output_file );
 688         }
 689         File cutoff_scores_file = null;
 690         Map<String, Double> individual_score_cutoffs = null;
 691         if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 692             if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 693                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
 694                         + surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
 695             }
 696             cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
 697             final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
 698             if ( !ForesterUtil.isEmpty( error ) ) {
 699                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
 700                         + error );
 701             }
 702             try {
 703                 final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, ' ' );
 704                 individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
 705             }
 706             catch ( final IOException e ) {
 707                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
 708             }
 709         }
 710         BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
 711         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
 712             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
 713         }
 714         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
 715             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
 716         }
 717         File out_dir = null;
 718         if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 719             if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 720                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
 721                         + surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
 722             }
 723             out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
 724             if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
 725                 ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
 726             }
 727             if ( !out_dir.exists() ) {
 728                 final boolean success = out_dir.mkdir();
 729                 if ( !success || !out_dir.exists() ) {
 730                     ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
 731                 }
 732             }
 733             if ( !out_dir.canWrite() ) {
 734                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
 735             }
 736         }
 737         File positive_filter_file = null;
 738         File negative_filter_file = null;
 739         File negative_domains_filter_file = null;
 740         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 741             ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
 742         }
 743         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
 744                 && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
 745                         .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
 746             ForesterUtil
 747                     .fatalError( surfacing.PRG_NAME,
 748                                  "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
 749         }
 750         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 751             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 752                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
 753                         + surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
 754             }
 755             negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
 756             final String msg = ForesterUtil.isReadableFile( negative_filter_file );
 757             if ( !ForesterUtil.isEmpty( msg ) ) {
 758                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
 759                         + msg );
 760             }
 761         }
 762         else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 763             if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 764                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
 765                         + surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
 766             }
 767             positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
 768             final String msg = ForesterUtil.isReadableFile( positive_filter_file );
 769             if ( !ForesterUtil.isEmpty( msg ) ) {
 770                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
 771                         + msg );
 772             }
 773         }
 774         else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 775             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 776                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
 777                         + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
 778             }
 779             negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
 780             final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
 781             if ( !ForesterUtil.isEmpty( msg ) ) {
 782                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
 783                         + "\": " + msg );
 784             }
 785         }
 786         final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
 787         final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
 788         final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
 789         final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
 790         processPlusMinusAnalysisOption( cla,
 791                                         plus_minus_analysis_high_copy_base_species,
 792                                         plus_minus_analysis_high_copy_target_species,
 793                                         plus_minus_analysis_high_low_copy_species,
 794                                         plus_minus_analysis_numbers );
 795         File input_files_file = null;
 796         String[] input_file_names_from_file = null;
 797         if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
 798             if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
 799                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
 800                         + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 801             }
 802             input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
 803             final String msg = ForesterUtil.isReadableFile( input_files_file );
 804             if ( !ForesterUtil.isEmpty( msg ) ) {
 805                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
 806             }
 807             try {
 808                 input_file_names_from_file = ForesterUtil.file2array( input_files_file );
 809             }
 810             catch ( final IOException e ) {
 811                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
 812             }
 813         }
 814         if ( ( cla.getNumberOfNames() < 1 )
 815                 && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
 816             ForesterUtil.fatalError( surfacing.PRG_NAME,
 817                                      "No hmmpfam output file indicated is input: use comand line directly or "
 818                                              + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 819         }
 820         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
 821         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
 822             if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
 823                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 824                                          "no value for scoring method for domain combinations similarity calculation: -"
 825                                                  + surfacing.SCORING_OPTION + "=<"
 826                                                  + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 827                                                  + surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
 828                                                  + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 829             }
 830             final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
 831             if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
 832                 scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
 833             }
 834             else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
 835                 scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 836             }
 837             else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
 838                 scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
 839             }
 840             else {
 841                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
 842                         + "\" for scoring method for domain combinations similarity calculation: \"-"
 843                         + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 844                         + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 845             }
 846         }
 847         boolean sort_by_species_count_first = false;
 848         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
 849             sort_by_species_count_first = true;
 850         }
 851         boolean species_matrix = false;
 852         if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
 853             species_matrix = true;
 854         }
 855         boolean output_protein_lists_for_all_domains = false;
 856         double output_list_of_all_proteins_per_domain_e_value_max = -1;
 857         if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
 858             output_protein_lists_for_all_domains = true;
 859             //
 860             if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
 861                 try {
 862                     output_list_of_all_proteins_per_domain_e_value_max = cla
 863                             .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
 864                 }
 865                 catch ( final Exception e ) {
 866                     ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
 867                 }
 868             }
 869             //
 870         }
 871         Detailedness detailedness = DETAILEDNESS_DEFAULT;
 872         if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
 873             if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
 874                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
 875                         + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
 876                         + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 877             }
 878             final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
 879             if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
 880                 detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
 881             }
 882             else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
 883                 detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
 884             }
 885             else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
 886                 detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 887             }
 888             else {
 889                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
 890                         + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
 891                         + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 892             }
 893         }
 894         String automated_pairwise_comparison_suffix = null;
 895         boolean perform_pwc = false;
 896         boolean write_pwc_files = false;
 897         if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 898             perform_pwc = true;
 899             if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 900                 write_pwc_files = false;
 901             }
 902             else {
 903                 write_pwc_files = true;
 904                 automated_pairwise_comparison_suffix = "_"
 905                         + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 906             }
 907         }
 908         String query_domain_ids = null;
 909         if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 910             if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 911                 ForesterUtil
 912                         .fatalError( surfacing.PRG_NAME,
 913                                      "no domain ids given for sequences with given domains to be extracted : -"
 914                                              + surfacing.SEQ_EXTRACT_OPTION
 915                                              + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
 916             }
 917             query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
 918         }
 919         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
 920         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
 921         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 922             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 923                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
 924                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 925                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 926                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 927                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 928                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
 929                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 930                         + ">\"" );
 931             }
 932             final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
 933             if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
 934                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 935                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 936             }
 937             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
 938                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
 939                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 940             }
 941             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
 942                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
 943                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 944             }
 945             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
 946                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
 947                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
 948             }
 949             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
 950                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
 951                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 952             }
 953             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
 954                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
 955                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 956             }
 957             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
 958                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 959                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 960             }
 961             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
 962                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 963                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 964             }
 965             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
 966                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 967                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 968             }
 969             else {
 970                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
 971                         + "\" for domain combinations similarities sorting: \"-"
 972                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 973                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 974                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 975                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 976                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
 977                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 978                         + ">\"" );
 979             }
 980         }
 981         PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
 982         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 983             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 984                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
 985                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 986                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 987                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 988             }
 989             final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
 990             if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
 991                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 992             }
 993             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
 994                 // domain_similarity_print_option =
 995                 // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
 996                 ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
 997             }
 998             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
 999                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
1000             }
1001             else {
1002                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
1003                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
1004                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
1005                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
1006             }
1007         }
1008         GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
1009         if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1010             if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1011                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
1012                         + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
1013                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1014                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1015                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1016             }
1017             final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
1018             if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
1019                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
1020             }
1021             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
1022                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
1023             }
1024             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
1025                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
1026             }
1027             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
1028                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
1029             }
1030             else {
1031                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
1032                         + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
1033                         + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1034                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1035                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1036             }
1037         }
1038         String[][] input_file_properties = null;
1039         if ( input_file_names_from_file != null ) {
1040             input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
1041         }
1042         else {
1043             input_file_properties = surfacing.processInputFileNames( cla.getNames() );
1044         }
1045         final int number_of_genomes = input_file_properties.length;
1046         if ( number_of_genomes < 2 ) {
1047             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
1048         }
1049         if ( ( number_of_genomes < 3 ) && perform_pwc ) {
1050             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
1051                     + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1052                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
1053         }
1054         checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
1055                                                  input_file_properties,
1056                                                  automated_pairwise_comparison_suffix,
1057                                                  out_dir );
1058         for( int i = 0; i < number_of_genomes; i++ ) {
1059             File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
1060                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1061             if ( out_dir != null ) {
1062                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
1063             }
1064             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
1065         }
1066         File pfam_to_go_file = null;
1067         Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
1068         int domain_id_to_go_ids_count = 0;
1069         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1070             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1071                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
1072                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
1073             }
1074             pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
1075             final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
1076             if ( !ForesterUtil.isEmpty( error ) ) {
1077                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
1078             }
1079             try {
1080                 final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
1081                 final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
1082                 domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
1083                 if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
1084                     ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
1085                                                        "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
1086                 }
1087                 domain_id_to_go_ids_count = parser.getMappingCount();
1088             }
1089             catch ( final IOException e ) {
1090                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
1091             }
1092         }
1093         File go_obo_file = null;
1094         List<GoTerm> go_terms = null;
1095         if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1096             if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1097                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
1098                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
1099             }
1100             if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
1101                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
1102                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
1103                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1104             }
1105             go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
1106             final String error = ForesterUtil.isReadableFile( go_obo_file );
1107             if ( !ForesterUtil.isEmpty( error ) ) {
1108                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
1109             }
1110             try {
1111                 final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
1112                 go_terms = parser.parse();
1113                 if ( parser.getGoTermCount() != go_terms.size() ) {
1114                     ForesterUtil
1115                             .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
1116                 }
1117             }
1118             catch ( final IOException e ) {
1119                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
1120             }
1121         }
1122         Map<GoId, GoTerm> go_id_to_term_map = null;
1123         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
1124                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
1125             go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
1126         }
1127         GoNameSpace go_namespace_limit = null;
1128         if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1129             if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1130                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
1131                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
1132                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
1133                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1134             }
1135             if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1136                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
1137                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1138                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1139                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1140                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1141             }
1142             final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
1143                     .toLowerCase();
1144             if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
1145                 go_namespace_limit = GoNameSpace.createMolecularFunction();
1146             }
1147             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
1148                 go_namespace_limit = GoNameSpace.createBiologicalProcess();
1149             }
1150             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
1151                 go_namespace_limit = GoNameSpace.createCellularComponent();
1152             }
1153             else {
1154                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
1155                         + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1156                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1157                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1158                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1159             }
1160         }
1161         if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
1162                 && ( number_of_genomes > 2 ) ) {
1163             domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
1164         }
1165         boolean jacknifed_distances = false;
1166         int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
1167         double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
1168         long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
1169         if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) {
1170             if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
1171                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-"
1172                         + surfacing.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
1173                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1174                         + "=<suffix for pairwise comparison output files>)" );
1175             }
1176             jacknifed_distances = true;
1177             if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) {
1178                 try {
1179                     jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION );
1180                 }
1181                 catch ( final IOException e ) {
1182                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" );
1183                 }
1184                 if ( jacknife_resamplings < 2 ) {
1185                     ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" );
1186                 }
1187             }
1188             if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION )
1189                     && cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) {
1190                 try {
1191                     jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION );
1192                 }
1193                 catch ( final IOException e ) {
1194                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" );
1195                 }
1196                 if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
1197                     ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: "
1198                             + jacknife_ratio );
1199                 }
1200             }
1201             if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION )
1202                     && cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) {
1203                 try {
1204                     random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION );
1205                 }
1206                 catch ( final IOException e ) {
1207                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" );
1208                 }
1209             }
1210         }
1211         //        boolean infer_species_trees = false;
1212         //        if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
1213         //            if ( ( output_file == null ) || ( number_of_genomes < 3 )
1214         //                    || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
1215         //                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
1216         //                        + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
1217         //                        + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1218         //                        + "=<suffix for pairwise comparison output files>)" );
1219         //            }
1220         //            infer_species_trees = true;
1221         //        }
1222         File[] intree_files = null;
1223         Phylogeny[] intrees = null;
1224         if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1225             // TODO FIXME if jacknife.... maybe not
1226             if ( number_of_genomes < 3 ) {
1227                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
1228                         + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
1229                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1230                         + "=<suffix for pairwise comparison output files>)" );
1231             }
1232             if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1233                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
1234                         + surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
1235             }
1236             final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
1237             if ( intrees_str.indexOf( "#" ) > 0 ) {
1238                 final String[] intrees_strs = intrees_str.split( "#" );
1239                 intree_files = new File[ intrees_strs.length ];
1240                 int i = 0;
1241                 for( final String s : intrees_strs ) {
1242                     intree_files[ i++ ] = new File( s.trim() );
1243                 }
1244             }
1245             else {
1246                 intree_files = new File[ 1 ];
1247                 intree_files[ 0 ] = new File( intrees_str );
1248             }
1249             intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
1250         }
1251         long random_number_seed_for_fitch_parsimony = 0l;
1252         boolean radomize_fitch_parsimony = false;
1253         if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1254             if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1255                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
1256                         + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
1257             }
1258             try {
1259                 random_number_seed_for_fitch_parsimony = cla
1260                         .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
1261             }
1262             catch ( final IOException e ) {
1263                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1264             }
1265             radomize_fitch_parsimony = true;
1266         }
1267         SortedSet<DomainId> filter = null;
1268         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1269                 || ( negative_domains_filter_file != null ) ) {
1270             filter = new TreeSet<DomainId>();
1271             if ( positive_filter_file != null ) {
1272                 processFilter( positive_filter_file, filter );
1273             }
1274             else if ( negative_filter_file != null ) {
1275                 processFilter( negative_filter_file, filter );
1276             }
1277             else if ( negative_domains_filter_file != null ) {
1278                 processFilter( negative_domains_filter_file, filter );
1279             }
1280         }
1281         Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
1282         File[] secondary_features_map_files = null;
1283         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1284                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
1285         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1286             SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
1287         }
1288         if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1289             if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1290                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
1291                         + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
1292             }
1293             final String[] secondary_features_map_files_strs = cla
1294                     .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
1295             secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
1296             domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
1297             int i = 0;
1298             for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
1299                 secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
1300                 final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
1301                 if ( !ForesterUtil.isEmpty( error ) ) {
1302                     ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
1303                 }
1304                 try {
1305                     domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
1306                             .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
1307                 }
1308                 catch ( final IOException e ) {
1309                     ForesterUtil.fatalError( surfacing.PRG_NAME,
1310                                              "cannot read secondary features map file: " + e.getMessage() );
1311                 }
1312                 catch ( final Exception e ) {
1313                     ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
1314                             + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
1315                 }
1316                 i++;
1317             }
1318         }
1319         if ( out_dir == null ) {
1320             ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
1321                     + surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
1322         }
1323         if ( output_file == null ) {
1324             ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
1325                     + surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
1326         }
1327         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
1328             ForesterUtil.fatalError( surfacing.PRG_NAME,
1329                                      "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
1330                                              + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1331         }
1332         if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1333             ForesterUtil.fatalError( surfacing.PRG_NAME,
1334                                      "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
1335                                              + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1336         }
1337         System.out.println( "Output directory            : " + out_dir );
1338         if ( input_file_names_from_file != null ) {
1339             System.out.println( "Input files names from      : " + input_files_file + " ["
1340                     + input_file_names_from_file.length + " input files]" );
1341             html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
1342                     + input_file_names_from_file.length + " input files]</td></tr>" + nl );
1343         }
1344         if ( positive_filter_file != null ) {
1345             final int filter_size = filter.size();
1346             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
1347                     + " domain ids]" );
1348             html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
1349                     + " domain ids]</td></tr>" + nl );
1350         }
1351         if ( negative_filter_file != null ) {
1352             final int filter_size = filter.size();
1353             System.out.println( "Negative protein filter     : " + negative_filter_file + " [" + filter_size
1354                     + " domain ids]" );
1355             html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
1356                     + " domain ids]</td></tr>" + nl );
1357         }
1358         if ( negative_domains_filter_file != null ) {
1359             final int filter_size = filter.size();
1360             System.out.println( "Negative domain filter      : " + negative_domains_filter_file + " [" + filter_size
1361                     + " domain ids]" );
1362             html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
1363                     + filter_size + " domain ids]</td></tr>" + nl );
1364         }
1365         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1366             String plus0 = "";
1367             for( final String s : plus_minus_analysis_high_copy_base_species ) {
1368                 plus0 += "+" + s + " ";
1369             }
1370             String plus1 = "";
1371             for( final String s : plus_minus_analysis_high_copy_target_species ) {
1372                 plus1 += "*" + s + " ";
1373             }
1374             String minus = "";
1375             for( final String s : plus_minus_analysis_high_low_copy_species ) {
1376                 minus += "-" + s + " ";
1377             }
1378             System.out.println( "Plus-minus analysis         : " + plus1 + "&& " + plus0 + "&& " + minus );
1379             html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
1380                     + "</td></tr>" + nl );
1381         }
1382         if ( cutoff_scores_file != null ) {
1383             System.out.println( "Cutoff scores file          : " + cutoff_scores_file );
1384             html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
1385         }
1386         if ( e_value_max >= 0.0 ) {
1387             System.out.println( "E-value maximum (inclusive) : " + e_value_max );
1388             html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
1389         }
1390         if ( output_protein_lists_for_all_domains ) {
1391             System.out.println( "Domain E-value max          : " + output_list_of_all_proteins_per_domain_e_value_max );
1392             html_desc.append( "<tr><td>Protein lists: E-value maximum per domain (inclusive):</td><td>"
1393                     + output_list_of_all_proteins_per_domain_e_value_max + "</td></tr>" + nl );
1394         }
1395         System.out.println( "Ignore DUFs                 : " + ignore_dufs );
1396         if ( ignore_virus_like_ids ) {
1397             System.out.println( "Ignore virus like ids       : " + ignore_virus_like_ids );
1398             html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
1399                     + ignore_virus_like_ids + "</td></tr>" + nl );
1400         }
1401         html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
1402         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1403             System.out.println( "Max allowed domain overlap  : " + max_allowed_overlap );
1404             html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
1405         }
1406         if ( no_engulfing_overlaps ) {
1407             System.out.println( "Ignore engulfed domains     : " + no_engulfing_overlaps );
1408             html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
1409                     + "</td></tr>" + nl );
1410         }
1411         System.out.println( "Ignore singlet domains      : " + ignore_domains_without_combs_in_all_spec );
1412         html_desc
1413                 .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1414                         + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
1415         System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
1416         html_desc
1417                 .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1418                         + ignore_species_specific_domains + "</td></tr>" + nl );
1419         System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
1420         html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
1421                 + ignore_combination_with_same + "</td></tr>" + nl );
1422         System.out.println( "Consider directedness       : "
1423                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
1424         html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
1425                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
1426         if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
1427             System.out.println( "Consider adjacency          : "
1428                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
1429             html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
1430                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
1431                     + nl );
1432         }
1433         System.out.print( "Domain counts sort order    : " );
1434         switch ( dc_sort_order ) {
1435             case ALPHABETICAL_KEY_ID:
1436                 System.out.println( "alphabetical" );
1437                 break;
1438             case KEY_DOMAIN_COUNT:
1439                 System.out.println( "domain count" );
1440                 break;
1441             case KEY_DOMAIN_PROTEINS_COUNT:
1442                 System.out.println( "domain proteins count" );
1443                 break;
1444             case COMBINATIONS_COUNT:
1445                 System.out.println( "domain combinations count" );
1446                 break;
1447             default:
1448                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
1449         }
1450         if ( domain_id_to_go_ids_map != null ) {
1451             System.out.println( "Pfam to GO mappings from    : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
1452                     + " mappings]" );
1453             html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
1454                     + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
1455         }
1456         if ( go_terms != null ) {
1457             System.out.println( "GO terms from               : " + go_obo_file + " [" + go_terms.size() + " terms]" );
1458             html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
1459                     + "</td></tr>" + nl );
1460         }
1461         if ( go_namespace_limit != null ) {
1462             System.out.println( "Limit GO terms to           : " + go_namespace_limit.toString() );
1463             html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
1464         }
1465         if ( perform_pwc ) {
1466             System.out.println( "Suffix for PWC files        : " + automated_pairwise_comparison_suffix );
1467             html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
1468                     + "</td></tr>" + nl );
1469         }
1470         if ( out_dir != null ) {
1471             System.out.println( "Output directory            : " + out_dir );
1472         }
1473         if ( query_domain_ids != null ) {
1474             System.out.println( "Query domains (ordered)     : " + query_domain_ids );
1475             html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
1476         }
1477         System.out.println( "Write similarities to       : " + output_file );
1478         System.out.print( "  Scoring method            : " );
1479         html_desc.append( "<tr><td>Scoring method:</td><td>" );
1480         switch ( scoring ) {
1481             case COMBINATIONS:
1482                 System.out.println( "domain combinations based" );
1483                 html_desc.append( "domain combinations based" + "</td></tr>" + nl );
1484                 break;
1485             case DOMAINS:
1486                 System.out.println( "domain counts based" );
1487                 html_desc.append( "domain counts based" + "</td></tr>" + nl );
1488                 break;
1489             case PROTEINS:
1490                 System.out.println( "domain proteins counts based" );
1491                 html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
1492                 break;
1493             default:
1494                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
1495         }
1496         System.out.print( "  Sort by                   : " );
1497         html_desc.append( "<tr><td>Sort by:</td><td>" );
1498         switch ( domain_similarity_sort_field ) {
1499             case MIN:
1500                 System.out.print( "score minimum" );
1501                 html_desc.append( "score minimum" );
1502                 break;
1503             case MAX:
1504                 System.out.print( "score maximum" );
1505                 html_desc.append( "score maximum" );
1506                 break;
1507             case MEAN:
1508                 System.out.print( "score mean" );
1509                 html_desc.append( "score mean" );
1510                 break;
1511             case SD:
1512                 System.out.print( "score standard deviation" );
1513                 html_desc.append( "score standard deviation" );
1514                 break;
1515             case SPECIES_COUNT:
1516                 System.out.print( "species number" );
1517                 html_desc.append( "species number" );
1518                 break;
1519             case DOMAIN_ID:
1520                 System.out.print( "alphabetical domain identifier" );
1521                 html_desc.append( "alphabetical domain identifier" );
1522                 break;
1523             case MAX_DIFFERENCE:
1524                 System.out.print( "(maximal) difference" );
1525                 html_desc.append( "(maximal) difference" );
1526                 break;
1527             case ABS_MAX_COUNTS_DIFFERENCE:
1528                 System.out.print( "absolute (maximal) counts difference" );
1529                 html_desc.append( "absolute (maximal) counts difference" );
1530                 break;
1531             case MAX_COUNTS_DIFFERENCE:
1532                 System.out.print( "(maximal) counts difference" );
1533                 html_desc.append( "(maximal) counts  difference" );
1534                 break;
1535             default:
1536                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1537         }
1538         if ( sort_by_species_count_first ) {
1539             System.out.println( " (sort by species count first)" );
1540             html_desc.append( " (sort by species count first)" );
1541         }
1542         else {
1543             System.out.println();
1544         }
1545         html_desc.append( "</td></tr>" + nl );
1546         System.out.print( "  Detailedness              : " );
1547         switch ( detailedness ) {
1548             case BASIC:
1549                 System.out.println( "basic" );
1550                 break;
1551             case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
1552                 System.out.println( "list combining domains for each species" );
1553                 break;
1554             case PUNCTILIOUS:
1555                 System.out.println( "punctilious" );
1556                 break;
1557             default:
1558                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" );
1559         }
1560         System.out.print( "  Print option              : " );
1561         switch ( domain_similarity_print_option ) {
1562             case HTML:
1563                 System.out.println( "HTML" );
1564                 break;
1565             case SIMPLE_TAB_DELIMITED:
1566                 System.out.println( "simple tab delimited" );
1567                 break;
1568             default:
1569                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
1570         }
1571         System.out.print( "  Species matrix            : " + species_matrix );
1572         System.out.println();
1573         final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
1574         System.out.println( "Domain comb data output     : " + dc_data_file );
1575         html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
1576         System.out.println();
1577         if ( perform_pwc ) {
1578             System.out.println( "Pairwise comparisons: " );
1579             html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
1580             System.out.print( "  Sort by                   : " );
1581             html_desc.append( "<tr><td>Sort by:</td><td>" );
1582             switch ( domain_similarity_sort_field_for_automated_pwc ) {
1583                 case MEAN:
1584                     System.out.print( "score mean" );
1585                     html_desc.append( "score mean" );
1586                     break;
1587                 case DOMAIN_ID:
1588                     System.out.print( "alphabetical domain identifier" );
1589                     html_desc.append( "alphabetical domain identifier" );
1590                     break;
1591                 case MAX_DIFFERENCE:
1592                     System.out.print( "difference" );
1593                     html_desc.append( "difference" );
1594                     break;
1595                 case ABS_MAX_COUNTS_DIFFERENCE:
1596                     System.out.print( "absolute counts difference" );
1597                     html_desc.append( "absolute counts difference" );
1598                     break;
1599                 case MAX_COUNTS_DIFFERENCE:
1600                     System.out.print( "counts difference" );
1601                     html_desc.append( "counts difference" );
1602                     break;
1603                 default:
1604                     ForesterUtil
1605                             .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1606             }
1607             System.out.println();
1608             html_desc.append( "</td></tr>" + nl );
1609             if ( jacknifed_distances ) {
1610                 html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
1611                 html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
1612                         + "</td></tr>" + nl );
1613                 html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
1614                 System.out.println( "  Jacknife                  : " + jacknife_resamplings + " resamplings" );
1615                 System.out.println( "    Ratio                   : " + ForesterUtil.round( jacknife_ratio, 2 ) );
1616                 System.out.println( "    Random number seed      : " + random_seed );
1617             }
1618             //                if ( infer_species_trees ) {
1619             //                    html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
1620             //                    System.out.println( "  Infer species trees       : true" );
1621             //                }
1622             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
1623                 for( final File intree_file : intree_files ) {
1624                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
1625                             + "</td></tr>" + nl );
1626                     System.out.println( "  Intree for gain/loss pars.: " + intree_file );
1627                 }
1628             }
1629             if ( radomize_fitch_parsimony ) {
1630                 html_desc.append( "<tr><td>    Random number seed for Fitch parsimony analysis:</td><td>"
1631                         + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
1632                 System.out.println( "    Random number seed      : " + random_number_seed_for_fitch_parsimony );
1633             }
1634             if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1635                 for( int i = 0; i < secondary_features_map_files.length; i++ ) {
1636                     html_desc.append( "<tr><td>Secondary features map file:</td><td>"
1637                             + secondary_features_map_files[ i ] + "</td></tr>" + nl );
1638                     System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
1639                             + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
1640                     if ( VERBOSE ) {
1641                         System.out.println();
1642                         System.out.println( "Domain ids to secondary features map:" );
1643                         for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
1644                             System.out.print( domain_id.getId() );
1645                             System.out.print( " => " );
1646                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
1647                                 System.out.print( sec );
1648                                 System.out.print( " " );
1649                             }
1650                             System.out.println();
1651                         }
1652                     }
1653                 }
1654             }
1655         } // if ( perform_pwc ) {
1656         System.out.println();
1657         html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
1658         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
1659         BufferedWriter[] query_domains_writer_ary = null;
1660         List<DomainId>[] query_domain_ids_array = null;
1661         if ( query_domain_ids != null ) {
1662             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
1663             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
1664             query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
1665             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
1666                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
1667                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
1668                 final List<DomainId> query = new ArrayList<DomainId>();
1669                 for( final String element : query_domain_ids_str_ary ) {
1670                     query.add( new DomainId( element ) );
1671                 }
1672                 query_domain_ids_array[ i ] = query;
1673                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
1674                 String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX;
1675                 if ( out_dir != null ) {
1676                     protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
1677                 }
1678                 try {
1679                     query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
1680                 }
1681                 catch ( final IOException e ) {
1682                     ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
1683                             + e.getLocalizedMessage() );
1684                 }
1685             }
1686         }
1687         SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
1688         boolean need_protein_lists_per_species = false;
1689         if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
1690             need_protein_lists_per_species = true;
1691         }
1692         if ( need_protein_lists_per_species ) {
1693             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
1694         }
1695         final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
1696         final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
1697         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
1698         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
1699         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
1700         if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
1701             all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
1702             all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
1703         }
1704         final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
1705         final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
1706                 + output_file + D_PROMISCUITY_FILE_SUFFIX );
1707         BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
1708         try {
1709             per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
1710             per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
1711             per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
1712             per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
1713             per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
1714             per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
1715             per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
1716             per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
1717             per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
1718                     + ForesterUtil.LINE_SEPARATOR );
1719         }
1720         catch ( final IOException e2 ) {
1721             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1722         }
1723         final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
1724         BufferedWriter log_writer = null;
1725         try {
1726             log_writer = new BufferedWriter( new FileWriter( log_file ) );
1727         }
1728         catch ( final IOException e2 ) {
1729             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1730         }
1731         BufferedWriter dc_data_writer = null;
1732         try {
1733             dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
1734             dc_data_writer.write( DATA_FILE_DESC );
1735             dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
1736         }
1737         catch ( final IOException e2 ) {
1738             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1739         }
1740         final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics();
1741         final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics();
1742         final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
1743         final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
1744         final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
1745         final SortedSet<String> domains_which_never_single = new TreeSet<String>();
1746         BufferedWriter domains_per_potein_stats_writer = null;
1747         try {
1748             domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
1749                     + output_file + "__domains_per_potein_stats.txt" ) );
1750             domains_per_potein_stats_writer.write( "Genome" );
1751             domains_per_potein_stats_writer.write( "\t" );
1752             domains_per_potein_stats_writer.write( "Mean" );
1753             domains_per_potein_stats_writer.write( "\t" );
1754             domains_per_potein_stats_writer.write( "SD" );
1755             domains_per_potein_stats_writer.write( "\t" );
1756             domains_per_potein_stats_writer.write( "Median" );
1757             domains_per_potein_stats_writer.write( "\t" );
1758             domains_per_potein_stats_writer.write( "N" );
1759             domains_per_potein_stats_writer.write( "\t" );
1760             domains_per_potein_stats_writer.write( "Min" );
1761             domains_per_potein_stats_writer.write( "\t" );
1762             domains_per_potein_stats_writer.write( "Max" );
1763             domains_per_potein_stats_writer.write( "\n" );
1764         }
1765         catch ( final IOException e3 ) {
1766             e3.printStackTrace();
1767         }
1768         Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
1769         Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
1770         final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
1771         if ( PERFORM_DC_REGAIN_PROTEINS_STATS ) {
1772             protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1773             domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
1774         }
1775         // Main loop:
1776         final SortedMap<String, Set<String>> distinct_domain_architecutures_per_genome = new TreeMap<String, Set<String>>();
1777         final SortedMap<String, Integer> distinct_domain_architecuture_counts = new TreeMap<String, Integer>();
1778         for( int i = 0; i < number_of_genomes; ++i ) {
1779             System.out.println();
1780             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
1781             log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
1782             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 0 ] );
1783             log( "Genome                                         : " + input_file_properties[ i ][ 0 ], log_writer );
1784             HmmscanPerDomainTableParser parser = null;
1785             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
1786             if ( individual_score_cutoffs != null ) {
1787                 ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
1788             }
1789             if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1790                     || ( negative_domains_filter_file != null ) ) {
1791                 HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
1792                 if ( positive_filter_file != null ) {
1793                     filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
1794                 }
1795                 else if ( negative_filter_file != null ) {
1796                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
1797                 }
1798                 else if ( negative_domains_filter_file != null ) {
1799                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
1800                 }
1801                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1802                                                           input_file_properties[ i ][ 1 ],
1803                                                           filter,
1804                                                           filter_type,
1805                                                           ind_score_cutoff,
1806                                                           true );
1807             }
1808             else {
1809                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1810                                                           input_file_properties[ i ][ 1 ],
1811                                                           ind_score_cutoff,
1812                                                           true );
1813             }
1814             if ( e_value_max >= 0.0 ) {
1815                 parser.setEValueMaximum( e_value_max );
1816             }
1817             parser.setIgnoreDufs( ignore_dufs );
1818             parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
1819             parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
1820             if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1821                 parser.setMaxAllowedOverlap( max_allowed_overlap );
1822             }
1823             parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
1824             if ( individual_score_cutoffs != null ) {
1825                 parser.setIndividualScoreCutoffs( individual_score_cutoffs );
1826             }
1827             List<Protein> protein_list = null;
1828             try {
1829                 protein_list = parser.parse();
1830             }
1831             catch ( final IOException e ) {
1832                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1833             }
1834             catch ( final Exception e ) {
1835                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
1836             }
1837             if ( VERBOSE ) {
1838                 System.out.println( "Domains ignored due to negative domain filter: " );
1839                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
1840                 System.out.println( "Domains ignored due to virus like id: " );
1841                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
1842             }
1843             final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
1844             protein_coverage_stats.addValue( coverage );
1845             int distinct_das = -1;
1846             if ( DA_ANALYSIS ) {
1847                 final String genome = input_file_properties[ i ][ 0 ];
1848                 distinct_das = storeDomainArchitectures( genome,
1849                                                          distinct_domain_architecutures_per_genome,
1850                                                          protein_list,
1851                                                          distinct_domain_architecuture_counts );
1852             }
1853             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
1854             log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(), log_writer );
1855             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
1856             log( "Number of proteins stored                      : " + protein_list.size(), log_writer );
1857             System.out.println( "Coverage                                       : "
1858                     + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
1859             log( "Coverage                                       : " + ForesterUtil.roundToInt( 100.0 * coverage )
1860                     + "%", log_writer );
1861             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
1862             log( "Domains encountered                            : " + parser.getDomainsEncountered(), log_writer );
1863             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
1864             log( "Domains stored                                 : " + parser.getDomainsStored(), log_writer );
1865             System.out.println( "Distinct domains stored                        : "
1866                     + parser.getDomainsStoredSet().size() );
1867             log( "Distinct domains stored                        : " + parser.getDomainsStoredSet().size(), log_writer );
1868             System.out.println( "Domains ignored due to individual score cutoffs: "
1869                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
1870             log( "Domains ignored due to individual score cutoffs: "
1871                          + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
1872                  log_writer );
1873             System.out.println( "Domains ignored due to E-value                 : "
1874                     + parser.getDomainsIgnoredDueToEval() );
1875             log( "Domains ignored due to E-value                 : " + parser.getDomainsIgnoredDueToEval(), log_writer );
1876             System.out.println( "Domains ignored due to DUF designation         : "
1877                     + parser.getDomainsIgnoredDueToDuf() );
1878             log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
1879             if ( ignore_virus_like_ids ) {
1880                 System.out.println( "Domains ignored due virus like ids             : "
1881                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
1882                 log( "Domains ignored due virus like ids             : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
1883                      log_writer );
1884             }
1885             System.out.println( "Domains ignored due negative domain filter     : "
1886                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
1887             log( "Domains ignored due negative domain filter     : "
1888                          + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
1889                  log_writer );
1890             System.out.println( "Domains ignored due to overlap                 : "
1891                     + parser.getDomainsIgnoredDueToOverlap() );
1892             log( "Domains ignored due to overlap                 : " + parser.getDomainsIgnoredDueToOverlap(),
1893                  log_writer );
1894             if ( negative_filter_file != null ) {
1895                 System.out.println( "Proteins ignored due to negative filter        : "
1896                         + parser.getProteinsIgnoredDueToFilter() );
1897                 log( "Proteins ignored due to negative filter        : " + parser.getProteinsIgnoredDueToFilter(),
1898                      log_writer );
1899             }
1900             if ( positive_filter_file != null ) {
1901                 System.out.println( "Proteins ignored due to positive filter        : "
1902                         + parser.getProteinsIgnoredDueToFilter() );
1903                 log( "Proteins ignored due to positive filter        : " + parser.getProteinsIgnoredDueToFilter(),
1904                      log_writer );
1905             }
1906             if ( DA_ANALYSIS ) {
1907                 System.out.println( "Distinct domain architectures stored           : " + distinct_das );
1908                 log( "Distinct domain architectures stored           : " + distinct_das, log_writer );
1909             }
1910             System.out.println( "Time for processing                            : " + parser.getTime() + "ms" );
1911             log( "", log_writer );
1912             html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
1913                     + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
1914                     + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
1915                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
1916                     + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
1917                     + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
1918                     + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
1919                     + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
1920             if ( negative_filter_file != null ) {
1921                 html_desc.append( "; proteins ignored due to negative filter: "
1922                         + parser.getProteinsIgnoredDueToFilter() );
1923             }
1924             if ( positive_filter_file != null ) {
1925                 html_desc.append( "; proteins ignored due to positive filter: "
1926                         + parser.getProteinsIgnoredDueToFilter() );
1927             }
1928             html_desc.append( "</td></tr>" + nl );
1929             // domain_partner_counts_array[ i ] =
1930             // Methods.getDomainPartnerCounts( protein_domain_collections_array[
1931             // i ],
1932             // false, input_file_properties[ i ][ 1 ] );
1933             try {
1934                 int count = 0;
1935                 for( final Protein protein : protein_list ) {
1936                     dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
1937                             .toString() );
1938                     ++count;
1939                     for( final Domain d : protein.getProteinDomains() ) {
1940                         final String d_str = d.getDomainId().toString();
1941                         if ( !domain_length_stats_by_domain.containsKey( d_str ) ) {
1942                             domain_length_stats_by_domain.put( d_str, new BasicDescriptiveStatistics() );
1943                         }
1944                         domain_length_stats_by_domain.get( d_str ).addValue( d.getLength() );
1945                     }
1946                 }
1947             }
1948             catch ( final IOException e ) {
1949                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
1950             }
1951             SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ],
1952                                                         protein_list,
1953                                                         all_genomes_domains_per_potein_stats,
1954                                                         all_genomes_domains_per_potein_histo,
1955                                                         domains_which_are_always_single,
1956                                                         domains_which_are_sometimes_single_sometimes_not,
1957                                                         domains_which_never_single,
1958                                                         domains_per_potein_stats_writer );
1959             domain_lengths_table.addLengths( protein_list );
1960             if ( !DA_ANALYSIS ) {
1961                 gwcd_list.add( BasicGenomeWideCombinableDomains
1962                         .createInstance( protein_list,
1963                                          ignore_combination_with_same,
1964                                          new BasicSpecies( input_file_properties[ i ][ 1 ] ),
1965                                          domain_id_to_go_ids_map,
1966                                          dc_type,
1967                                          protein_length_stats_by_dc,
1968                                          domain_number_stats_by_dc ) );
1969                 if ( gwcd_list.get( i ).getSize() > 0 ) {
1970                     SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
1971                                                                      out_dir,
1972                                                                      per_genome_domain_promiscuity_statistics_writer,
1973                                                                      gwcd_list.get( i ),
1974                                                                      i,
1975                                                                      dc_sort_order );
1976                     if ( output_binary_domain_combinationsfor_graph_analysis ) {
1977                         SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
1978                                                                                          out_dir,
1979                                                                                          gwcd_list.get( i ),
1980                                                                                          i,
1981                                                                                          dc_sort_order );
1982                     }
1983                     SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
1984                     SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
1985                                                                       all_bin_domain_combinations_encountered );
1986                 }
1987             }
1988             if ( query_domains_writer_ary != null ) {
1989                 for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1990                     try {
1991                         SurfacingUtil.extractProteinNames( protein_list,
1992                                                            query_domain_ids_array[ j ],
1993                                                            query_domains_writer_ary[ j ],
1994                                                            "\t",
1995                                                            LIMIT_SPEC_FOR_PROT_EX );
1996                         query_domains_writer_ary[ j ].flush();
1997                     }
1998                     catch ( final IOException e ) {
1999                         e.printStackTrace();
2000                     }
2001                 }
2002             }
2003             if ( need_protein_lists_per_species ) {
2004                 protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
2005             }
2006             try {
2007                 log_writer.flush();
2008             }
2009             catch ( final IOException e2 ) {
2010                 ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2011             }
2012             System.gc();
2013         } // for( int i = 0; i < number_of_genomes; ++i ) {
2014         ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
2015                 + per_genome_domain_promiscuity_statistics_file );
2016         //
2017         if ( DA_ANALYSIS ) {
2018             performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
2019                                                distinct_domain_architecuture_counts,
2020                                                10 );
2021             distinct_domain_architecutures_per_genome.clear();
2022             distinct_domain_architecuture_counts.clear();
2023             System.gc();
2024         }
2025         try {
2026             domains_per_potein_stats_writer.write( "ALL" );
2027             domains_per_potein_stats_writer.write( "\t" );
2028             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" );
2029             domains_per_potein_stats_writer.write( "\t" );
2030             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" );
2031             domains_per_potein_stats_writer.write( "\t" );
2032             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" );
2033             domains_per_potein_stats_writer.write( "\t" );
2034             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" );
2035             domains_per_potein_stats_writer.write( "\t" );
2036             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" );
2037             domains_per_potein_stats_writer.write( "\t" );
2038             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
2039             domains_per_potein_stats_writer.write( "\n" );
2040             domains_per_potein_stats_writer.close();
2041             printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
2042             ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
2043                     + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
2044             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
2045                     + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
2046             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
2047                     + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
2048             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
2049                     + "__domains_always_combined.txt" ), domains_which_never_single, "\n" );
2050             ForesterUtil.programMessage( PRG_NAME,
2051                                          "Average of proteins with a least one domain assigned: "
2052                                                  + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
2053                                                  + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" );
2054             ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: "
2055                     + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() )
2056                     + "%" );
2057             log( "Average of prot with a least one dom assigned  : " + ( 100 * protein_coverage_stats.arithmeticMean() )
2058                     + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
2059             log( "Range of prot with a least one dom assigned    : " + ( 100 * protein_coverage_stats.getMin() ) + "%-"
2060                     + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer );
2061         }
2062         catch ( final IOException e2 ) {
2063             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2064         }
2065         if ( query_domains_writer_ary != null ) {
2066             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
2067                 try {
2068                     query_domains_writer_ary[ j ].close();
2069                 }
2070                 catch ( final IOException e ) {
2071                     ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
2072                 }
2073             }
2074         }
2075         try {
2076             per_genome_domain_promiscuity_statistics_writer.close();
2077             dc_data_writer.close();
2078             log_writer.close();
2079         }
2080         catch ( final IOException e2 ) {
2081             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2082         }
2083         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
2084             try {
2085                 SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
2086                                                            number_of_genomes,
2087                                                            domain_lengths_table,
2088                                                            domain_lengths_analysis_outfile );
2089             }
2090             catch ( final IOException e1 ) {
2091                 ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
2092             }
2093             System.out.println();
2094             ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
2095             System.out.println();
2096         }
2097         final long analysis_start_time = new Date().getTime();
2098         PairwiseDomainSimilarityCalculator pw_calc = null;
2099         // double[] values_for_all_scores_histogram = null;
2100         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
2101                                                                                      sort_by_species_count_first,
2102                                                                                      number_of_genomes == 2 );
2103         switch ( scoring ) {
2104             case COMBINATIONS:
2105                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
2106                 break;
2107             case DOMAINS:
2108                 pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
2109                 break;
2110             case PROTEINS:
2111                 pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
2112                 break;
2113             default:
2114                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
2115         }
2116         DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
2117         if ( domain_id_to_go_ids_map != null ) {
2118             go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
2119         }
2120         final SortedSet<DomainSimilarity> similarities = calc
2121                 .calculateSimilarities( pw_calc,
2122                                         gwcd_list,
2123                                         ignore_domains_without_combs_in_all_spec,
2124                                         ignore_species_specific_domains );
2125         SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
2126                                                            detailedness,
2127                                                            go_annotation_output,
2128                                                            go_id_to_term_map,
2129                                                            go_namespace_limit );
2130         DescriptiveStatistics pw_stats = null;
2131         try {
2132             String my_outfile = output_file.toString();
2133             Map<Character, Writer> split_writers = null;
2134             Writer writer = null;
2135             if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
2136                 if ( my_outfile.endsWith( ".html" ) ) {
2137                     my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
2138                 }
2139                 split_writers = new HashMap<Character, Writer>();
2140                 createSplitWriters( out_dir, my_outfile, split_writers );
2141             }
2142             else if ( !my_outfile.endsWith( ".html" ) ) {
2143                 my_outfile += ".html";
2144                 writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
2145             }
2146             List<Species> species_order = null;
2147             if ( species_matrix ) {
2148                 species_order = new ArrayList<Species>();
2149                 for( int i = 0; i < number_of_genomes; i++ ) {
2150                     species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
2151                 }
2152             }
2153             html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
2154                     + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
2155             html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
2156                     + "</td></tr>" + nl );
2157             html_desc.append( "<tr><td>Analysis date/time:</td><td>"
2158                     + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
2159                     + "</td></tr>" + nl );
2160             html_desc.append( "</table>" + nl );
2161             pw_stats = SurfacingUtil
2162                     .writeDomainSimilaritiesToFile( html_desc,
2163                                                     new StringBuilder( number_of_genomes + " genomes" ),
2164                                                     writer,
2165                                                     split_writers,
2166                                                     similarities,
2167                                                     number_of_genomes == 2,
2168                                                     species_order,
2169                                                     domain_similarity_print_option,
2170                                                     domain_similarity_sort_field,
2171                                                     scoring,
2172                                                     true );
2173             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
2174                     + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
2175         }
2176         catch ( final IOException e ) {
2177             ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
2178                     + e.getMessage() + "]" );
2179         }
2180         System.out.println();
2181         // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
2182         final Species[] species = new Species[ number_of_genomes ];
2183         for( int i = 0; i < number_of_genomes; ++i ) {
2184             species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
2185         }
2186         List<Phylogeny> inferred_trees = null;
2187         if ( ( number_of_genomes > 2 ) && perform_pwc ) {
2188             final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
2189             pwgc.performPairwiseComparisons( html_desc,
2190                                              sort_by_species_count_first,
2191                                              detailedness,
2192                                              ignore_domains_without_combs_in_all_spec,
2193                                              ignore_species_specific_domains,
2194                                              domain_similarity_sort_field_for_automated_pwc,
2195                                              domain_similarity_print_option,
2196                                              scoring,
2197                                              domain_id_to_go_ids_map,
2198                                              go_id_to_term_map,
2199                                              go_namespace_limit,
2200                                              species,
2201                                              number_of_genomes,
2202                                              gwcd_list,
2203                                              pw_calc,
2204                                              automated_pairwise_comparison_suffix,
2205                                              true,
2206                                              surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
2207                                              surfacing.PRG_NAME,
2208                                              out_dir,
2209                                              write_pwc_files );
2210             String matrix_output_file = new String( output_file.toString() );
2211             if ( matrix_output_file.indexOf( '.' ) > 1 ) {
2212                 matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
2213             }
2214             if ( out_dir != null ) {
2215                 matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
2216                 output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2217             }
2218             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2219                     + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
2220             SurfacingUtil
2221                     .writeMatrixToFile( new File( matrix_output_file
2222                                                 + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2223                                         pwgc.getSharedBinaryCombinationsBasedDistances() );
2224             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2225                                                      + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2226                                              pwgc.getSharedDomainsBasedDistances() );
2227             final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2228                     + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
2229                     .get( 0 ) );
2230             final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2231                     + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2232                     .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
2233             final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2234                     + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2235                     .getSharedDomainsBasedDistances().get( 0 ) );
2236             inferred_trees = new ArrayList<Phylogeny>();
2237             inferred_trees.add( nj_gd );
2238             inferred_trees.add( nj_bc );
2239             inferred_trees.add( nj_d );
2240             if ( jacknifed_distances ) {
2241                 pwgc.performPairwiseComparisonsJacknifed( species,
2242                                                           number_of_genomes,
2243                                                           gwcd_list,
2244                                                           true,
2245                                                           jacknife_resamplings,
2246                                                           jacknife_ratio,
2247                                                           random_seed );
2248                 SurfacingUtil
2249                         .writeMatrixToFile( new File( matrix_output_file
2250                                                     + "_"
2251                                                     + ForesterUtil.round( jacknife_ratio, 2 )
2252                                                     + "_"
2253                                                     + jacknife_resamplings
2254                                                     + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2255                                             pwgc.getSharedBinaryCombinationsBasedDistances() );
2256                 SurfacingUtil
2257                         .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 )
2258                                                     + "_" + jacknife_resamplings
2259                                                     + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2260                                             pwgc.getSharedDomainsBasedDistances() );
2261                 //                if ( infer_species_trees ) {
2262                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2263                 //                            + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
2264                 //                            .getSharedBinaryCombinationsBasedDistances() );
2265                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2266                 //                            + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
2267                 //                }
2268             }
2269         } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
2270         if ( ( out_dir != null ) && ( !perform_pwc ) ) {
2271             output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2272         }
2273         writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
2274         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
2275             final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2276                                                                           e_value_max,
2277                                                                           max_allowed_overlap,
2278                                                                           no_engulfing_overlaps,
2279                                                                           cutoff_scores_file,
2280                                                                           dc_type );
2281             String s = "_";
2282             if ( radomize_fitch_parsimony ) {
2283                 s += random_number_seed_for_fitch_parsimony + "_";
2284             }
2285             int i = 0;
2286             for( final Phylogeny intree : intrees ) {
2287                 final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
2288                         + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
2289                 final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
2290                                                                                                              gwcd_list );
2291                 SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2292                                                         radomize_fitch_parsimony,
2293                                                         outfile_name,
2294                                                         domain_parsimony,
2295                                                         intree,
2296                                                         domain_id_to_go_ids_map,
2297                                                         go_id_to_term_map,
2298                                                         go_namespace_limit,
2299                                                         parameters_sb.toString(),
2300                                                         domain_id_to_secondary_features_maps,
2301                                                         positive_filter_file == null ? null : filter,
2302                                                         output_binary_domain_combinationsfor_graph_analysis,
2303                                                         all_bin_domain_combinations_gained_fitch,
2304                                                         all_bin_domain_combinations_lost_fitch,
2305                                                         dc_type,
2306                                                         protein_length_stats_by_dc,
2307                                                         domain_number_stats_by_dc,
2308                                                         domain_length_stats_by_domain );
2309                 // Listing of all domain combinations gained is only done if only one input tree is used.
2310                 if ( ( domain_id_to_secondary_features_maps != null )
2311                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
2312                     int j = 0;
2313                     for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
2314                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
2315                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
2316                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
2317                         SurfacingUtil
2318                                 .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
2319                                                                                        + "_"
2320                                                                                        + secondary_features_map_files[ j++ ],
2321                                                                                secondary_features_parsimony,
2322                                                                                intree,
2323                                                                                parameters_sb.toString(),
2324                                                                                mapping_results_map );
2325                         if ( i == 0 ) {
2326                             System.out.println();
2327                             System.out.println( "Mapping to secondary features:" );
2328                             for( final Species spec : mapping_results_map.keySet() ) {
2329                                 final MappingResults mapping_results = mapping_results_map.get( spec );
2330                                 final int total_domains = mapping_results.getSumOfFailures()
2331                                         + mapping_results.getSumOfSuccesses();
2332                                 System.out.print( spec + ":" );
2333                                 System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
2334                                 System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
2335                                 if ( total_domains > 0 ) {
2336                                     System.out.println( ", mapped ratio = "
2337                                             + ( ( 100 * mapping_results.getSumOfSuccesses() ) / total_domains ) + "%" );
2338                                 }
2339                                 else {
2340                                     System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
2341                                 }
2342                             }
2343                         }
2344                     }
2345                 }
2346                 i++;
2347             } // for( final Phylogeny intree : intrees ) {
2348         }
2349         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
2350             executePlusMinusAnalysis( output_file,
2351                                       plus_minus_analysis_high_copy_base_species,
2352                                       plus_minus_analysis_high_copy_target_species,
2353                                       plus_minus_analysis_high_low_copy_species,
2354                                       gwcd_list,
2355                                       protein_lists_per_species,
2356                                       domain_id_to_go_ids_map,
2357                                       go_id_to_term_map,
2358                                       plus_minus_analysis_numbers );
2359         }
2360         if ( output_protein_lists_for_all_domains ) {
2361             writeProteinListsForAllSpecies( out_dir,
2362                                             protein_lists_per_species,
2363                                             gwcd_list,
2364                                             output_list_of_all_proteins_per_domain_e_value_max );
2365         }
2366         if ( all_bin_domain_combinations_gained_fitch != null ) {
2367             try {
2368                 executeFitchGainsAnalysis( new File( output_file
2369                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2370                                            all_bin_domain_combinations_gained_fitch,
2371                                            all_domains_encountered.size(),
2372                                            all_bin_domain_combinations_encountered,
2373                                            true );
2374             }
2375             catch ( final IOException e ) {
2376                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2377             }
2378         }
2379         if ( all_bin_domain_combinations_lost_fitch != null ) {
2380             try {
2381                 executeFitchGainsAnalysis( new File( output_file
2382                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2383                                            all_bin_domain_combinations_lost_fitch,
2384                                            all_domains_encountered.size(),
2385                                            all_bin_domain_combinations_encountered,
2386                                            false );
2387             }
2388             catch ( final IOException e ) {
2389                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2390             }
2391         }
2392         final Runtime rt = java.lang.Runtime.getRuntime();
2393         final long free_memory = rt.freeMemory() / 1000000;
2394         final long total_memory = rt.totalMemory() / 1000000;
2395         ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time )
2396                 + "ms" );
2397         ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
2398         ForesterUtil.programMessage( PRG_NAME, "Free memory       : " + free_memory + "MB, total memory: "
2399                 + total_memory + "MB" );
2400         ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" );
2401         ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
2402         ForesterUtil.programMessage( PRG_NAME, "OK" );
2403         System.out.println();
2404     }
2405
2406     private static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
2407                                                            final SortedMap<String, Integer> domain_architecuture_counts,
2408                                                            final int min_count ) {
2409         final StringBuilder unique_das = new StringBuilder();
2410         final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
2411         System.out.println( "Domain Architecture Counts (min count:  " + min_count + " ):" );
2412         while ( it.hasNext() ) {
2413             final Map.Entry<String, Integer> e = it.next();
2414             final String da = e.getKey();
2415             final int count = e.getValue();
2416             if ( count >= min_count ) {
2417                 System.out.println( da + "\t" + count );
2418             }
2419             if ( count == 1 ) {
2420                 final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
2421                 while ( it2.hasNext() ) {
2422                     final Map.Entry<String, Set<String>> e2 = it2.next();
2423                     final String genome = e2.getKey();
2424                     final Set<String> das = e2.getValue();
2425                     if ( das.contains( da ) ) {
2426                         unique_das.append( genome + "\t" + da + ForesterUtil.LINE_SEPARATOR );
2427                     }
2428                 }
2429             }
2430         }
2431         System.out.println();
2432         System.out.println();
2433         System.out.println( "Unique Domain Architectures:" );
2434         System.out.println( unique_das );
2435         System.out.println();
2436         System.out.println();
2437     }
2438
2439     private static int storeDomainArchitectures( final String genome,
2440                                                  final SortedMap<String, Set<String>> domain_architecutures,
2441                                                  final List<Protein> protein_list,
2442                                                  final Map<String, Integer> distinct_domain_architecuture_counts ) {
2443         final Set<String> da = new HashSet<String>();
2444         domain_architecutures.put( genome, da );
2445         for( final Protein protein : protein_list ) {
2446             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~" );
2447             if ( !da.contains( da_str ) ) {
2448                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
2449                     distinct_domain_architecuture_counts.put( da_str, 1 );
2450                 }
2451                 else {
2452                     distinct_domain_architecuture_counts.put( da_str,
2453                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
2454                 }
2455                 da.add( da_str );
2456             }
2457         }
2458         return da.size();
2459     }
2460
2461     private static void createSplitWriters( final File out_dir,
2462                                             final String my_outfile,
2463                                             final Map<Character, Writer> split_writers ) throws IOException {
2464         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2465                 + "_domains_A.html" ) ) );
2466         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2467                 + "_domains_B.html" ) ) );
2468         split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2469                 + "_domains_C.html" ) ) );
2470         split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2471                 + "_domains_D.html" ) ) );
2472         split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2473                 + "_domains_E.html" ) ) );
2474         split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2475                 + "_domains_F.html" ) ) );
2476         split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2477                 + "_domains_G.html" ) ) );
2478         split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2479                 + "_domains_H.html" ) ) );
2480         split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2481                 + "_domains_I.html" ) ) );
2482         split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2483                 + "_domains_J.html" ) ) );
2484         split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2485                 + "_domains_K.html" ) ) );
2486         split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2487                 + "_domains_L.html" ) ) );
2488         split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2489                 + "_domains_M.html" ) ) );
2490         split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2491                 + "_domains_N.html" ) ) );
2492         split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2493                 + "_domains_O.html" ) ) );
2494         split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2495                 + "_domains_P.html" ) ) );
2496         split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2497                 + "_domains_Q.html" ) ) );
2498         split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2499                 + "_domains_R.html" ) ) );
2500         split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2501                 + "_domains_S.html" ) ) );
2502         split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2503                 + "_domains_T.html" ) ) );
2504         split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2505                 + "_domains_U.html" ) ) );
2506         split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2507                 + "_domains_V.html" ) ) );
2508         split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2509                 + "_domains_W.html" ) ) );
2510         split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2511                 + "_domains_X.html" ) ) );
2512         split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2513                 + "_domains_Y.html" ) ) );
2514         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2515                 + "_domains_Z.html" ) ) );
2516         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2517                 + "_domains_0.html" ) ) );
2518     }
2519
2520     private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2521                                                                  final Writer log_writer ) {
2522         int sum = 0;
2523         for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
2524             sum += entry.getValue();
2525         }
2526         final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
2527         ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
2528         log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
2529     }
2530
2531     private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
2532                                                               final String[][] input_file_properties ) {
2533         final String[] genomes = new String[ input_file_properties.length ];
2534         for( int i = 0; i < input_file_properties.length; ++i ) {
2535             if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
2536                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2537                         + "] is not unique in input tree " + intree.getName() );
2538             }
2539             genomes[ i ] = input_file_properties[ i ][ 1 ];
2540         }
2541         //
2542         final PhylogenyNodeIterator it = intree.iteratorPostorder();
2543         while ( it.hasNext() ) {
2544             final PhylogenyNode n = it.next();
2545             if ( ForesterUtil.isEmpty( n.getName() ) ) {
2546                 if ( n.getNodeData().isHasTaxonomy()
2547                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
2548                     n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
2549                 }
2550                 else if ( n.getNodeData().isHasTaxonomy()
2551                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
2552                     n.setName( n.getNodeData().getTaxonomy().getScientificName() );
2553                 }
2554                 else if ( n.getNodeData().isHasTaxonomy()
2555                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
2556                     n.setName( n.getNodeData().getTaxonomy().getCommonName() );
2557                 }
2558                 else {
2559                     ForesterUtil
2560                             .fatalError( surfacing.PRG_NAME,
2561                                          "node with no name, scientific name, common name, or taxonomy code present" );
2562                 }
2563             }
2564         }
2565         //
2566         final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
2567         if ( igns.size() > 0 ) {
2568             System.out.println( "Not using the following " + igns.size() + " nodes:" );
2569             for( int i = 0; i < igns.size(); ++i ) {
2570                 System.out.println( " " + i + ": " + igns.get( i ) );
2571             }
2572             System.out.println( "--" );
2573         }
2574         for( final String[] input_file_propertie : input_file_properties ) {
2575             try {
2576                 intree.getNode( input_file_propertie[ 1 ] );
2577             }
2578             catch ( final IllegalArgumentException e ) {
2579                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
2580                         + "] not present/not unique in input tree" );
2581             }
2582         }
2583     }
2584
2585     private static void printHelp() {
2586         System.out.println();
2587         System.out.println( "Usage:" );
2588         System.out.println();
2589         System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME
2590                 + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
2591         System.out.println();
2592         System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
2593         System.out
2594                 .println( "       hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
2595         System.out.println();
2596         System.out.println( " Options: " );
2597         System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
2598                 + DETAILEDNESS_DEFAULT + ")" );
2599         System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
2600                 + ": to ignore combinations with self (default: not to ignore)" );
2601         System.out
2602                 .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
2603                         + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2604         System.out
2605                 .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
2606                         + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2607         System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
2608                 + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
2609         System.out
2610                 .println( surfacing.IGNORE_VIRAL_IDS
2611                         + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
2612         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
2613                 + DOMAIN_SORT_FILD_DEFAULT + ")" );
2614         System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
2615         System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
2616         System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
2617         System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
2618         System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
2619         System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
2620         System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
2621                 + DOMAINS_SORT_ORDER_DEFAULT + ")" );
2622         System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
2623                 + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
2624         System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
2625         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
2626                 + ": sort by species count first" );
2627         System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
2628         System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
2629         System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
2630         System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
2631         System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
2632                 + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
2633         System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
2634                 + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
2635         System.out
2636                 .println( JACKNIFE_OPTION
2637                         + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
2638                         + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
2639         System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
2640                 + JACKNIFE_RATIO_DEFAULT + "]" );
2641         System.out.println( JACKNIFE_RANDOM_SEED_OPTION
2642                 + ": seed for random number generator for jacknife resampling [default: "
2643                 + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
2644         //        System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
2645         //                + ": to infer NJ species trees based on shared domains/binary domain combinations" );
2646         System.out
2647                 .println( surfacing.INPUT_SPECIES_TREE_OPTION
2648                         + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
2649         System.out.println( surfacing.FILTER_POSITIVE_OPTION
2650                 + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
2651         System.out.println( surfacing.FILTER_NEGATIVE_OPTION
2652                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
2653         System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
2654                 + "=<file>: to filter out (ignore) domains listed in <file>" );
2655         System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
2656         System.out
2657                 .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
2658                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
2659         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
2660                 + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
2661         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
2662                 + ": to consider directedness and adjacency in binary combinations" );
2663         System.out
2664                 .println( surfacing.SEQ_EXTRACT_OPTION
2665                         + "=<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')" );
2666         System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
2667                 + "=<file>: to perfom parsimony analysis on secondary features" );
2668         System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
2669         System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
2670                 + ": to output binary domain combinations for (downstream) graph analysis" );
2671         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
2672         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
2673                 + ": e value max per domain for output of all proteins per domain" );
2674         System.out.println();
2675         System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2676                 + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
2677                 + " -no_eo -mo=0 -input=genomes_limited.txt -out_dir=out -o=o "
2678                 + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
2679         System.out.println();
2680         System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2681                 + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
2682                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
2683                 + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
2684                 + "-ds_output=detailed_html -scoring=domains -sort=alpha human mouse brafl strpu" );
2685         System.out.println();
2686     }
2687
2688     private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
2689         SortedSet<String> filter_str = null;
2690         try {
2691             filter_str = ForesterUtil.file2set( filter_file );
2692         }
2693         catch ( final IOException e ) {
2694             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2695         }
2696         if ( filter_str != null ) {
2697             for( final String string : filter_str ) {
2698                 filter.add( new DomainId( string ) );
2699             }
2700         }
2701         if ( VERBOSE ) {
2702             System.out.println( "Filter:" );
2703             for( final DomainId domainId : filter ) {
2704                 System.out.println( domainId.getId() );
2705             }
2706         }
2707     }
2708
2709     private static String[][] processInputFileNames( final String[] names ) {
2710         final String[][] input_file_properties = new String[ names.length ][];
2711         for( int i = 0; i < names.length; ++i ) {
2712             if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
2713                 input_file_properties[ i ] = new String[ 2 ];
2714                 input_file_properties[ i ][ 0 ] = names[ i ];
2715                 input_file_properties[ i ][ 1 ] = names[ i ];
2716             }
2717             else {
2718                 input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
2719                 if ( input_file_properties[ i ].length != 3 ) {
2720                     ForesterUtil
2721                             .fatalError( surfacing.PRG_NAME,
2722                                          "properties for the input files (hmmpfam output) are expected "
2723                                                  + "to be in the following format \"<hmmpfam output file>#<species>\" (or just one word, which is both the filename and the species id), instead received \""
2724                                                  + names[ i ] + "\"" );
2725                 }
2726             }
2727             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
2728             if ( !ForesterUtil.isEmpty( error ) ) {
2729                 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
2730             }
2731         }
2732         return input_file_properties;
2733     }
2734
2735     private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
2736                                                         final List<String> high_copy_base,
2737                                                         final List<String> high_copy_target,
2738                                                         final List<String> low_copy,
2739                                                         final List<Object> numbers ) {
2740         if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2741             if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2742                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
2743                         + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
2744             }
2745             final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
2746             final String msg = ForesterUtil.isReadableFile( plus_minus_file );
2747             if ( !ForesterUtil.isEmpty( msg ) ) {
2748                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
2749             }
2750             processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
2751         }
2752     }
2753
2754     // First numbers is minimal difference, second is factor.
2755     private static void processPlusMinusFile( final File plus_minus_file,
2756                                               final List<String> high_copy_base,
2757                                               final List<String> high_copy_target,
2758                                               final List<String> low_copy,
2759                                               final List<Object> numbers ) {
2760         Set<String> species_set = null;
2761         int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
2762         double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
2763         try {
2764             species_set = ForesterUtil.file2set( plus_minus_file );
2765         }
2766         catch ( final IOException e ) {
2767             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2768         }
2769         if ( species_set != null ) {
2770             for( final String species : species_set ) {
2771                 final String species_trimmed = species.substring( 1 );
2772                 if ( species.startsWith( "+" ) ) {
2773                     if ( low_copy.contains( species_trimmed ) ) {
2774                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2775                                                  "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
2776                                                          + species_trimmed + "\"" );
2777                     }
2778                     high_copy_base.add( species_trimmed );
2779                 }
2780                 else if ( species.startsWith( "*" ) ) {
2781                     if ( low_copy.contains( species_trimmed ) ) {
2782                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2783                                                  "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
2784                                                          + species_trimmed + "\"" );
2785                     }
2786                     high_copy_target.add( species_trimmed );
2787                 }
2788                 else if ( species.startsWith( "-" ) ) {
2789                     if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
2790                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2791                                                  "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
2792                                                          + species_trimmed + "\"" );
2793                     }
2794                     low_copy.add( species_trimmed );
2795                 }
2796                 else if ( species.startsWith( "$D" ) ) {
2797                     try {
2798                         min_diff = Integer.parseInt( species.substring( 3 ) );
2799                     }
2800                     catch ( final NumberFormatException e ) {
2801                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2802                                                  "could not parse integer value for minimal difference from: \""
2803                                                          + species.substring( 3 ) + "\"" );
2804                     }
2805                 }
2806                 else if ( species.startsWith( "$F" ) ) {
2807                     try {
2808                         factor = Double.parseDouble( species.substring( 3 ) );
2809                     }
2810                     catch ( final NumberFormatException e ) {
2811                         ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
2812                                 + species.substring( 3 ) + "\"" );
2813                     }
2814                 }
2815                 else if ( species.startsWith( "#" ) ) {
2816                     // Comment, ignore.
2817                 }
2818                 else {
2819                     ForesterUtil
2820                             .fatalError( surfacing.PRG_NAME,
2821                                          "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
2822                                                  + species + "\"" );
2823                 }
2824                 numbers.add( new Integer( min_diff + "" ) );
2825                 numbers.add( new Double( factor + "" ) );
2826             }
2827         }
2828         else {
2829             ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
2830         }
2831     }
2832
2833     private static void writePresentToNexus( final File output_file,
2834                                              final File positive_filter_file,
2835                                              final SortedSet<DomainId> filter,
2836                                              final List<GenomeWideCombinableDomains> gwcd_list ) {
2837         try {
2838             SurfacingUtil
2839                     .writeMatrixToFile( DomainParsimonyCalculator
2840                             .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
2841                                     : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
2842             SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
2843                     .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
2844                     + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
2845         }
2846         catch ( final Exception e ) {
2847             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2848         }
2849     }
2850
2851     private static void writeProteinListsForAllSpecies( final File output_dir,
2852                                                         final SortedMap<Species, List<Protein>> protein_lists_per_species,
2853                                                         final List<GenomeWideCombinableDomains> gwcd_list,
2854                                                         final double domain_e_cutoff ) {
2855         final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
2856         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2857             all_domains.addAll( gwcd.getAllDomainIds() );
2858         }
2859         for( final DomainId domain : all_domains ) {
2860             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
2861             SurfacingUtil.checkForOutputFileWriteability( out );
2862             try {
2863                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2864                 SurfacingUtil.extractProteinNames( protein_lists_per_species,
2865                                                    domain,
2866                                                    proteins_file_writer,
2867                                                    "\t",
2868                                                    LIMIT_SPEC_FOR_PROT_EX,
2869                                                    domain_e_cutoff );
2870                 proteins_file_writer.close();
2871             }
2872             catch ( final IOException e ) {
2873                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2874             }
2875             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2876         }
2877     }
2878 }