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: www.phylosoft.org/forester
  26
  27 package org.forester.application;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.util.ArrayList;
  35 import java.util.Date;
  36 import java.util.HashMap;
  37 import java.util.HashSet;
  38 import java.util.List;
  39 import java.util.Map;
  40 import java.util.Map.Entry;
  41 import java.util.Set;
  42 import java.util.SortedMap;
  43 import java.util.SortedSet;
  44 import java.util.TreeMap;
  45 import java.util.TreeSet;
  46
  47 import org.forester.evoinference.distance.NeighborJoining;
  48 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  49 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  50 import org.forester.go.GoId;
  51 import org.forester.go.GoNameSpace;
  52 import org.forester.go.GoTerm;
  53 import org.forester.go.GoUtils;
  54 import org.forester.go.OBOparser;
  55 import org.forester.go.PfamToGoMapping;
  56 import org.forester.go.PfamToGoParser;
  57 import org.forester.io.parsers.HmmscanPerDomainTableParser;
  58 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
  59 import org.forester.io.parsers.util.ParserUtils;
  60 import org.forester.io.writers.PhylogenyWriter;
  61 import org.forester.phylogeny.Phylogeny;
  62 import org.forester.phylogeny.PhylogenyMethods;
  63 import org.forester.phylogeny.PhylogenyNode;
  64 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  65 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  66 import org.forester.surfacing.BasicDomainSimilarityCalculator;
  67 import org.forester.surfacing.BasicGenomeWideCombinableDomains;
  68 import org.forester.surfacing.BasicSpecies;
  69 import org.forester.surfacing.BinaryDomainCombination;
  70 import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
  71 import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
  72 import org.forester.surfacing.DomainCountsDifferenceUtil;
  73 import org.forester.surfacing.DomainId;
  74 import org.forester.surfacing.DomainLengthsTable;
  75 import org.forester.surfacing.DomainParsimonyCalculator;
  76 import org.forester.surfacing.DomainSimilarity;
  77 import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
  78 import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
  79 import org.forester.surfacing.DomainSimilarityCalculator;
  80 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  81 import org.forester.surfacing.GenomeWideCombinableDomains;
  82 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  83 import org.forester.surfacing.MappingResults;
  84 import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
  85 import org.forester.surfacing.PairwiseGenomeComparator;
  86 import org.forester.surfacing.PrintableDomainSimilarity;
  87 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  88 import org.forester.surfacing.Protein;
  89 import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
  90 import org.forester.surfacing.Species;
  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                               INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX                               = "_sd_nj.nh";
 229     final static private String                               INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX                              = "_sbc_nj.nh";
 230     final static private String                               FILTER_POSITIVE_OPTION                                                 = "pos_filter";
 231     final static private String                               FILTER_NEGATIVE_OPTION                                                 = "neg_filter";
 232     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                         = "neg_dom_filter";
 233     final static private String                               INPUT_FILES_FROM_FILE_OPTION                                           = "input";
 234     final static private String                               INPUT_SPECIES_TREE_OPTION                                              = "species_tree";
 235     final static private String                               SEQ_EXTRACT_OPTION                                                     = "prot_extract";
 236     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                             = '#';
 237     final static private String                               PRG_VERSION                                                            = "2.210";
 238     final static private String                               PRG_DATE                                                               = "2011.12.08";
 239     final static private String                               E_MAIL                                                                 = "czmasek@burnham.org";
 240     final static private String                               WWW                                                                    = "www.phylosoft.org/forester/applications/surfacing";
 241     final static private boolean                              IGNORE_DUFS_DEFAULT                                                    = true;
 242     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                  = false;
 243     final static private double                               MAX_E_VALUE_DEFAULT                                                    = -1;
 244     final static private int                                  MAX_ALLOWED_OVERLAP_DEFAULT                                            = -1;
 245     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                 = "random_seed";
 246     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                               = "consider_bdc_direction";
 247     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                 = "consider_bdc_adj";
 248     private static final String                               SEQ_EXTRACT_SUFFIX                                                     = ".prot";
 249     private static final String                               PLUS_MINUS_ANALYSIS_OPTION                                             = "plus_minus";
 250     private static final String                               PLUS_MINUS_DOM_SUFFIX                                                  = "_plus_minus_dom.txt";
 251     private static final String                               PLUS_MINUS_DOM_SUFFIX_HTML                                             = "_plus_minus_dom.html";
 252     private static final String                               PLUS_MINUS_DC_SUFFIX_HTML                                              = "_plus_minus_dc.html";
 253     private static final int                                  PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                   = 0;
 254     private static final double                               PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                     = 1.0;
 255     private static final String                               PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                       = "_plus_minus_go_ids_all.txt";
 256     private static final String                               PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                   = "_plus_minus_go_ids_passing.txt";
 257     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                    = "all_prot";
 258     private static final boolean                              VERBOSE                                                                = false;
 259     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX       = "_fitch_dc_gains_counts";
 260     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX         = "_fitch_dc_losses_counts";
 261     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                         = "_domain_lengths_analysis";
 262     private static final boolean                              PERFORM_DOMAIN_LENGTH_ANALYSIS                                         = true;
 263     public static final String                                ALL_PFAMS_ENCOUNTERED_SUFFIX                                           = "_all_encountered_pfams";
 264     public static final String                                ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX                        = "_all_encountered_pfams_with_go_annotation";
 265     public static final String                                ENCOUNTERED_PFAMS_SUMMARY_SUFFIX                                       = "_encountered_pfams_summary";
 266     public static final String                                ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX                                     = "_all_pfams_gained_as_domains";
 267     public static final String                                ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX                                       = "_all_pfams_lost_as_domains";
 268     public static final String                                ALL_PFAMS_GAINED_AS_DC_SUFFIX                                          = "_all_pfams_gained_as_dc";
 269     public static final String                                ALL_PFAMS_LOST_AS_DC_SUFFIX                                            = "_all_pfams_lost_as_dc";
 270     public static final String                                BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES                         = "PER_NODE_EVENTS";
 271     public static final String                                BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES                      = "PER_SUBTREE_EVENTS";
 272     public static final String                                D_PROMISCUITY_FILE_SUFFIX                                              = "_domain_promiscuities";
 273     private static final String                               LOG_FILE_SUFFIX                                                        = "_log.txt";
 274     private static final String                               DATA_FILE_SUFFIX                                                       = "_domain_combination_data.txt";
 275     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";
 276     private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                        = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
 277     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX                   = "_indep_dc_gains_fitch_counts.txt";
 278     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists.txt";
 279     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
 280     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";
 281
 282     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
 283                                                                  final String[][] input_file_properties,
 284                                                                  final String automated_pairwise_comparison_suffix,
 285                                                                  final File outdir ) {
 286         for( int i = 0; i < input_file_properties.length; ++i ) {
 287             for( int j = 0; j < i; ++j ) {
 288                 final String species_i = input_file_properties[ i ][ 1 ];
 289                 final String species_j = input_file_properties[ j ][ 1 ];
 290                 String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
 291                         + species_j + automated_pairwise_comparison_suffix;
 292                 switch ( domain_similarity_print_option ) {
 293                     case HTML:
 294                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 295                             pairwise_similarities_output_file_str += ".html";
 296                         }
 297                         break;
 298                 }
 299                 final String error = ForesterUtil
 300                         .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
 301                                 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 302                 if ( !ForesterUtil.isEmpty( error ) ) {
 303                     ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 304                 }
 305             }
 306         }
 307     }
 308
 309     private static StringBuilder createParametersAsString( final boolean ignore_dufs,
 310                                                            final double e_value_max,
 311                                                            final int max_allowed_overlap,
 312                                                            final boolean no_engulfing_overlaps,
 313                                                            final File cutoff_scores_file,
 314                                                            final BinaryDomainCombination.DomainCombinationType dc_type ) {
 315         final StringBuilder parameters_sb = new StringBuilder();
 316         parameters_sb.append( "E-value: " + e_value_max );
 317         if ( cutoff_scores_file != null ) {
 318             parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
 319         }
 320         else {
 321             parameters_sb.append( ", Cutoff-scores-file: not-set" );
 322         }
 323         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
 324             parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
 325         }
 326         else {
 327             parameters_sb.append( ", Max-overlap: not-set" );
 328         }
 329         if ( no_engulfing_overlaps ) {
 330             parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
 331         }
 332         else {
 333             parameters_sb.append( ", Engulfing-overlaps: allowed" );
 334         }
 335         if ( ignore_dufs ) {
 336             parameters_sb.append( ", Ignore-dufs: true" );
 337         }
 338         else {
 339             parameters_sb.append( ", Ignore-dufs: false" );
 340         }
 341         parameters_sb.append( ", DC type (if applicable): " + dc_type );
 342         return parameters_sb;
 343     }
 344
 345     /**
 346      * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
 347      *
 348      *
 349      * @param output_file
 350      * @param all_bin_domain_combinations_changed
 351      * @param sum_of_all_domains_encountered
 352      * @param all_bin_domain_combinations_encountered
 353      * @param is_gains_analysis
 354      * @throws IOException
 355      */
 356     private static void executeFitchGainsAnalysis( final File output_file,
 357                                                    final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
 358                                                    final int sum_of_all_domains_encountered,
 359                                                    final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
 360                                                    final boolean is_gains_analysis ) throws IOException {
 361         SurfacingUtil.checkForOutputFileWriteability( output_file );
 362         final Writer out = ForesterUtil.createBufferedWriter( output_file );
 363         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
 364                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
 365         final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
 366         final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
 367         int above_one = 0;
 368         int one = 0;
 369         for( final Object bdc_object : bdc_to_counts.keySet() ) {
 370             final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
 371             final int count = bdc_to_counts.get( bdc_object );
 372             if ( count < 1 ) {
 373                 ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
 374             }
 375             out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 376             if ( count > 1 ) {
 377                 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
 378                 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
 379                 above_one++;
 380             }
 381             else if ( count == 1 ) {
 382                 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
 383                 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
 384                 one++;
 385             }
 386         }
 387         final int all = all_bin_domain_combinations_encountered.size();
 388         int never_lost = -1;
 389         if ( !is_gains_analysis ) {
 390             all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
 391             never_lost = all_bin_domain_combinations_encountered.size();
 392             for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
 393                 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
 394             }
 395         }
 396         if ( is_gains_analysis ) {
 397             out.write( "Sum of all distinct domain combinations appearing once               : " + one
 398                     + ForesterUtil.LINE_SEPARATOR );
 399             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
 400                     + ForesterUtil.LINE_SEPARATOR );
 401             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
 402                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 403             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
 404                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 405         }
 406         else {
 407             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
 408                     + ForesterUtil.LINE_SEPARATOR );
 409             out.write( "Sum of all distinct domain combinations lost once                    : " + one
 410                     + ForesterUtil.LINE_SEPARATOR );
 411             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
 412                     + ForesterUtil.LINE_SEPARATOR );
 413             out.write( "Sum of all distinct domains in combinations lost only once           : "
 414                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 415             out.write( "Sum of all distinct domains in combinations lost more than once: "
 416                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 417         }
 418         out.write( "All binary combinations                                              : " + all
 419                 + ForesterUtil.LINE_SEPARATOR );
 420         out.write( "All domains                                                          : "
 421                 + sum_of_all_domains_encountered );
 422         out.close();
 423         ForesterUtil.programMessage( surfacing.PRG_NAME,
 424                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
 425                                              + "\"" );
 426     }
 427
 428     private static void executePlusMinusAnalysis( final File output_file,
 429                                                   final List<String> plus_minus_analysis_high_copy_base,
 430                                                   final List<String> plus_minus_analysis_high_copy_target,
 431                                                   final List<String> plus_minus_analysis_low_copy,
 432                                                   final List<GenomeWideCombinableDomains> gwcd_list,
 433                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species,
 434                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 435                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 436                                                   final List<Object> plus_minus_analysis_numbers ) {
 437         final Set<String> all_spec = new HashSet<String>();
 438         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 439             all_spec.add( gwcd.getSpecies().getSpeciesId() );
 440         }
 441         final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
 442         final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
 443         final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
 444         final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
 445         final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
 446         final File proteins_file_base = new File( output_file + "" );
 447         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
 448         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
 449         try {
 450             DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
 451                                                                        protein_lists_per_species,
 452                                                                        plus_minus_analysis_high_copy_base,
 453                                                                        plus_minus_analysis_high_copy_target,
 454                                                                        plus_minus_analysis_low_copy,
 455                                                                        min_diff,
 456                                                                        factor,
 457                                                                        plain_out_dom,
 458                                                                        html_out_dom,
 459                                                                        html_out_dc,
 460                                                                        domain_id_to_go_ids_map,
 461                                                                        go_id_to_term_map,
 462                                                                        all_domains_go_ids_out_dom,
 463                                                                        passing_domains_go_ids_out_dom,
 464                                                                        proteins_file_base );
 465         }
 466         catch ( final IOException e ) {
 467             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 468         }
 469         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 470                 + html_out_dom + "\"" );
 471         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
 472                 + plain_out_dom + "\"" );
 473         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
 474                 + "\"" );
 475         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
 476                 + passing_domains_go_ids_out_dom + "\"" );
 477         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
 478                 + all_domains_go_ids_out_dom + "\"" );
 479     }
 480
 481     private static Phylogeny[] getIntrees( final File[] intree_files,
 482                                            final int number_of_genomes,
 483                                            final String[][] input_file_properties ) {
 484         final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
 485         int i = 0;
 486         for( final File intree_file : intree_files ) {
 487             Phylogeny intree = null;
 488             final String error = ForesterUtil.isReadableFile( intree_file );
 489             if ( !ForesterUtil.isEmpty( error ) ) {
 490                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
 491                         + error );
 492             }
 493             try {
 494                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
 495                         .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
 496                 if ( p_array.length < 1 ) {
 497                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 498                             + "] does not contain any phylogeny in phyloXML format" );
 499                 }
 500                 else if ( p_array.length > 1 ) {
 501                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
 502                             + "] contains more than one phylogeny in phyloXML format" );
 503                 }
 504                 intree = p_array[ 0 ];
 505             }
 506             catch ( final Exception e ) {
 507                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
 508                         + "]: " + error );
 509             }
 510             if ( ( intree == null ) || intree.isEmpty() ) {
 511                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
 512             }
 513             if ( !intree.isRooted() ) {
 514                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
 515             }
 516             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
 517                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 518                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
 519                                                  + "] of input tree [" + intree_file
 520                                                  + "] is smaller than the number of genomes the be analyzed ["
 521                                                  + number_of_genomes + "]" );
 522             }
 523             final StringBuilder parent_names = new StringBuilder();
 524             final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
 525             if ( nodes_lacking_name > 0 ) {
 526                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
 527                         + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
 528             }
 529             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
 530             if ( !intree.isCompletelyBinary() ) {
 531                 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
 532                         + "] is not completely binary" );
 533             }
 534             intrees[ i++ ] = intree;
 535         }
 536         return intrees;
 537     }
 538
 539     private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
 540         final NeighborJoining nj = NeighborJoining.createInstance();
 541         final List<Phylogeny> phylogenies = nj.execute( distances_list );
 542         final PhylogenyWriter w = new PhylogenyWriter();
 543         try {
 544             w.toNewHampshire( phylogenies, true, true, outfile, ";" );
 545         }
 546         catch ( final IOException e ) {
 547             ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
 548         }
 549         return phylogenies;
 550     }
 551
 552     private static void log( final String msg, final Writer w ) {
 553         try {
 554             w.write( msg );
 555             w.write( ForesterUtil.LINE_SEPARATOR );
 556         }
 557         catch ( final IOException e ) {
 558             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 559         }
 560     }
 561
 562     public static void main( final String args[] ) {
 563         final long start_time = new Date().getTime();
 564         // final StringBuffer log = new StringBuffer();
 565         final StringBuilder html_desc = new StringBuilder();
 566         ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
 567                                               surfacing.PRG_VERSION,
 568                                               surfacing.PRG_DATE,
 569                                               surfacing.E_MAIL,
 570                                               surfacing.WWW );
 571         final String nl = ForesterUtil.LINE_SEPARATOR;
 572         html_desc.append( "<table>" + nl );
 573         html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
 574         html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
 575         html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
 576         html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
 577         html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
 578         CommandLineArguments cla = null;
 579         try {
 580             cla = new CommandLineArguments( args );
 581         }
 582         catch ( final Exception e ) {
 583             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 584         }
 585         if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
 586             surfacing.printHelp();
 587             System.exit( 0 );
 588         }
 589         if ( ( args.length < 1 ) ) {
 590             surfacing.printHelp();
 591             System.exit( -1 );
 592         }
 593         final List<String> allowed_options = new ArrayList<String>();
 594         allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
 595         allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
 596         allowed_options.add( surfacing.DETAILEDNESS_OPTION );
 597         allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
 598         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
 599         allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
 600         allowed_options.add( surfacing.SCORING_OPTION );
 601         allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 602         allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
 603         allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
 604         allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
 605         allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
 606         allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
 607         allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
 608         allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
 609         allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
 610         allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
 611         allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
 612         allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 613         allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
 614         allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
 615         allowed_options.add( JACKNIFE_OPTION );
 616         allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
 617         allowed_options.add( JACKNIFE_RATIO_OPTION );
 618         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
 619         //allowed_options.add( INFER_SPECIES_TREES_OPTION );
 620         allowed_options.add( FILTER_POSITIVE_OPTION );
 621         allowed_options.add( FILTER_NEGATIVE_OPTION );
 622         allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
 623         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 624         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
 625         allowed_options.add( IGNORE_VIRAL_IDS );
 626         allowed_options.add( SEQ_EXTRACT_OPTION );
 627         allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
 628         allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
 629         allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
 630         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
 631         allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
 632         boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
 633         boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
 634         double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
 635         int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
 636         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 637         if ( dissallowed_options.length() > 0 ) {
 638             ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
 639         }
 640         boolean output_binary_domain_combinationsfor_graph_analysis = false;
 641         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
 642             output_binary_domain_combinationsfor_graph_analysis = true;
 643         }
 644         if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
 645             try {
 646                 e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
 647             }
 648             catch ( final Exception e ) {
 649                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
 650             }
 651         }
 652         if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
 653             try {
 654                 max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
 655             }
 656             catch ( final Exception e ) {
 657                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
 658             }
 659         }
 660         boolean no_engulfing_overlaps = false;
 661         if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
 662             no_engulfing_overlaps = true;
 663         }
 664         boolean ignore_virus_like_ids = false;
 665         if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
 666             ignore_virus_like_ids = true;
 667         }
 668         if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
 669             ignore_dufs = false;
 670         }
 671         if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
 672             ignore_combination_with_same = true;
 673         }
 674         boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
 675         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
 676             ignore_domains_without_combs_in_all_spec = true;
 677         }
 678         boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
 679         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
 680             ignore_species_specific_domains = true;
 681         }
 682         File output_file = null;
 683         if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 684             if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
 685                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 686                                          "no value for domain combinations similarities output file: -"
 687                                                  + surfacing.OUTPUT_FILE_OPTION + "=<file>" );
 688             }
 689             output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
 690             SurfacingUtil.checkForOutputFileWriteability( output_file );
 691         }
 692         File cutoff_scores_file = null;
 693         Map<String, Double> individual_score_cutoffs = null;
 694         if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 695             if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
 696                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
 697                         + surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
 698             }
 699             cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
 700             final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
 701             if ( !ForesterUtil.isEmpty( error ) ) {
 702                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
 703                         + error );
 704             }
 705             try {
 706                 final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
 707                 individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
 708             }
 709             catch ( final IOException e ) {
 710                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
 711             }
 712         }
 713         BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
 714         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
 715             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
 716         }
 717         if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
 718             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
 719         }
 720         File out_dir = null;
 721         if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 722             if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
 723                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
 724                         + surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
 725             }
 726             out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
 727             if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
 728                 ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
 729             }
 730             if ( !out_dir.exists() ) {
 731                 final boolean success = out_dir.mkdir();
 732                 if ( !success || !out_dir.exists() ) {
 733                     ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
 734                 }
 735             }
 736             if ( !out_dir.canWrite() ) {
 737                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
 738             }
 739         }
 740         File positive_filter_file = null;
 741         File negative_filter_file = null;
 742         File negative_domains_filter_file = null;
 743         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 744             ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
 745         }
 746         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
 747                 && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
 748                         .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
 749             ForesterUtil
 750                     .fatalError( surfacing.PRG_NAME,
 751                                  "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
 752         }
 753         if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 754             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
 755                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
 756                         + surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
 757             }
 758             negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
 759             final String msg = ForesterUtil.isReadableFile( negative_filter_file );
 760             if ( !ForesterUtil.isEmpty( msg ) ) {
 761                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
 762                         + msg );
 763             }
 764         }
 765         else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 766             if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
 767                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
 768                         + surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
 769             }
 770             positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
 771             final String msg = ForesterUtil.isReadableFile( positive_filter_file );
 772             if ( !ForesterUtil.isEmpty( msg ) ) {
 773                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
 774                         + msg );
 775             }
 776         }
 777         else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 778             if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 779                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
 780                         + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
 781             }
 782             negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
 783             final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
 784             if ( !ForesterUtil.isEmpty( msg ) ) {
 785                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
 786                         + "\": " + msg );
 787             }
 788         }
 789         final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
 790         final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
 791         final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
 792         final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
 793         processPlusMinusAnalysisOption( cla,
 794                                         plus_minus_analysis_high_copy_base_species,
 795                                         plus_minus_analysis_high_copy_target_species,
 796                                         plus_minus_analysis_high_low_copy_species,
 797                                         plus_minus_analysis_numbers );
 798         File input_files_file = null;
 799         String[] input_file_names_from_file = null;
 800         if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
 801             if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
 802                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
 803                         + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 804             }
 805             input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
 806             final String msg = ForesterUtil.isReadableFile( input_files_file );
 807             if ( !ForesterUtil.isEmpty( msg ) ) {
 808                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
 809             }
 810             try {
 811                 input_file_names_from_file = ForesterUtil.file2array( input_files_file );
 812             }
 813             catch ( final IOException e ) {
 814                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
 815             }
 816         }
 817         if ( ( cla.getNumberOfNames() < 1 )
 818                 && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
 819             ForesterUtil.fatalError( surfacing.PRG_NAME,
 820                                      "No hmmpfam output file indicated is input: use comand line directly or "
 821                                              + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 822         }
 823         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
 824         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
 825             if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
 826                 ForesterUtil.fatalError( surfacing.PRG_NAME,
 827                                          "no value for scoring method for domain combinations similarity calculation: -"
 828                                                  + surfacing.SCORING_OPTION + "=<"
 829                                                  + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 830                                                  + surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
 831                                                  + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 832             }
 833             final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
 834             if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
 835                 scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
 836             }
 837             else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
 838                 scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 839             }
 840             else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
 841                 scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
 842             }
 843             else {
 844                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
 845                         + "\" for scoring method for domain combinations similarity calculation: \"-"
 846                         + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
 847                         + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
 848             }
 849         }
 850         boolean sort_by_species_count_first = false;
 851         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
 852             sort_by_species_count_first = true;
 853         }
 854         boolean species_matrix = false;
 855         if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
 856             species_matrix = true;
 857         }
 858         boolean output_protein_lists_for_all_domains = false;
 859         if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
 860             output_protein_lists_for_all_domains = true;
 861         }
 862         Detailedness detailedness = DETAILEDNESS_DEFAULT;
 863         if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
 864             if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
 865                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
 866                         + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
 867                         + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 868             }
 869             final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
 870             if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
 871                 detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
 872             }
 873             else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
 874                 detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
 875             }
 876             else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
 877                 detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 878             }
 879             else {
 880                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
 881                         + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
 882                         + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 883             }
 884         }
 885         String automated_pairwise_comparison_suffix = null;
 886         boolean perform_pwc = false;
 887         boolean write_pwc_files = false;
 888         if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 889             perform_pwc = true;
 890             if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 891                 write_pwc_files = false;
 892             }
 893             else {
 894                 write_pwc_files = true;
 895                 automated_pairwise_comparison_suffix = "_"
 896                         + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 897             }
 898         }
 899         String query_domain_ids = null;
 900         if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 901             if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
 902                 ForesterUtil
 903                         .fatalError( surfacing.PRG_NAME,
 904                                      "no domain ids given for sequences with given domains to be extracted : -"
 905                                              + surfacing.SEQ_EXTRACT_OPTION
 906                                              + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
 907             }
 908             query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
 909         }
 910         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
 911         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
 912         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 913             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 914                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
 915                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 916                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 917                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 918                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 919                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
 920                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 921                         + ">\"" );
 922             }
 923             final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
 924             if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
 925                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 926                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 927             }
 928             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
 929                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
 930                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 931             }
 932             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
 933                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
 934                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 935             }
 936             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
 937                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
 938                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
 939             }
 940             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
 941                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
 942                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 943             }
 944             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
 945                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
 946                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 947             }
 948             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
 949                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 950                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 951             }
 952             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
 953                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 954                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 955             }
 956             else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
 957                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 958                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 959             }
 960             else {
 961                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
 962                         + "\" for domain combinations similarities sorting: \"-"
 963                         + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 964                         + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
 965                         + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 966                         + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 967                         + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
 968                         + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
 969                         + ">\"" );
 970             }
 971         }
 972         PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
 973         if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 974             if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 975                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
 976                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 977                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 978                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 979             }
 980             final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
 981             if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
 982                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 983             }
 984             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
 985                 // domain_similarity_print_option =
 986                 // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
 987                 ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
 988             }
 989             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
 990                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
 991             }
 992             else {
 993                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
 994                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 995                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 996                         + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 997             }
 998         }
 999         GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
1000         if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1001             if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
1002                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
1003                         + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
1004                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1005                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1006                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1007             }
1008             final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
1009             if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
1010                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
1011             }
1012             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
1013                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
1014             }
1015             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
1016                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
1017             }
1018             else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
1019                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
1020             }
1021             else {
1022                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
1023                         + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
1024                         + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1025                         + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1026                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1027             }
1028         }
1029         String[][] input_file_properties = null;
1030         if ( input_file_names_from_file != null ) {
1031             input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
1032         }
1033         else {
1034             input_file_properties = surfacing.processInputFileNames( cla.getNames() );
1035         }
1036         final int number_of_genomes = input_file_properties.length;
1037         if ( number_of_genomes < 2 ) {
1038             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
1039         }
1040         if ( ( number_of_genomes < 3 ) && perform_pwc ) {
1041             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
1042                     + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1043                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
1044         }
1045         checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
1046                                                  input_file_properties,
1047                                                  automated_pairwise_comparison_suffix,
1048                                                  out_dir );
1049         for( int i = 0; i < number_of_genomes; i++ ) {
1050             File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
1051                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1052             if ( out_dir != null ) {
1053                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
1054             }
1055             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
1056         }
1057         File pfam_to_go_file = null;
1058         Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
1059         int domain_id_to_go_ids_count = 0;
1060         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1061             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1062                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
1063                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
1064             }
1065             pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
1066             final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
1067             if ( !ForesterUtil.isEmpty( error ) ) {
1068                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
1069             }
1070             try {
1071                 final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
1072                 final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
1073                 domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
1074                 if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
1075                     ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
1076                                                        "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
1077                 }
1078                 domain_id_to_go_ids_count = parser.getMappingCount();
1079             }
1080             catch ( final IOException e ) {
1081                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
1082             }
1083         }
1084         File go_obo_file = null;
1085         List<GoTerm> go_terms = null;
1086         if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1087             if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
1088                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
1089                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
1090             }
1091             if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
1092                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
1093                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
1094                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1095             }
1096             go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
1097             final String error = ForesterUtil.isReadableFile( go_obo_file );
1098             if ( !ForesterUtil.isEmpty( error ) ) {
1099                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
1100             }
1101             try {
1102                 final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
1103                 go_terms = parser.parse();
1104                 if ( parser.getGoTermCount() != go_terms.size() ) {
1105                     ForesterUtil
1106                             .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
1107                 }
1108             }
1109             catch ( final IOException e ) {
1110                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
1111             }
1112         }
1113         Map<GoId, GoTerm> go_id_to_term_map = null;
1114         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
1115                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
1116             go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
1117         }
1118         GoNameSpace go_namespace_limit = null;
1119         if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1120             if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1121                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
1122                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
1123                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
1124                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1125             }
1126             if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
1127                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
1128                         + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1129                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1130                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1131                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1132             }
1133             final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
1134                     .toLowerCase();
1135             if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
1136                 go_namespace_limit = GoNameSpace.createMolecularFunction();
1137             }
1138             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
1139                 go_namespace_limit = GoNameSpace.createBiologicalProcess();
1140             }
1141             else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
1142                 go_namespace_limit = GoNameSpace.createCellularComponent();
1143             }
1144             else {
1145                 ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
1146                         + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
1147                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1148                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1149                         + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1150             }
1151         }
1152         if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
1153                 && ( number_of_genomes > 2 ) ) {
1154             domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
1155         }
1156         boolean jacknifed_distances = false;
1157         int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
1158         double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
1159         long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
1160         if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) {
1161             if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
1162                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-"
1163                         + surfacing.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
1164                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1165                         + "=<suffix for pairwise comparison output files>)" );
1166             }
1167             jacknifed_distances = true;
1168             if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) {
1169                 try {
1170                     jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION );
1171                 }
1172                 catch ( final IOException e ) {
1173                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" );
1174                 }
1175                 if ( jacknife_resamplings < 2 ) {
1176                     ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" );
1177                 }
1178             }
1179             if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION )
1180                     && cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) {
1181                 try {
1182                     jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION );
1183                 }
1184                 catch ( final IOException e ) {
1185                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" );
1186                 }
1187                 if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
1188                     ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: "
1189                             + jacknife_ratio );
1190                 }
1191             }
1192             if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION )
1193                     && cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) {
1194                 try {
1195                     random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION );
1196                 }
1197                 catch ( final IOException e ) {
1198                     ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" );
1199                 }
1200             }
1201         }
1202         //        boolean infer_species_trees = false;
1203         //        if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
1204         //            if ( ( output_file == null ) || ( number_of_genomes < 3 )
1205         //                    || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
1206         //                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
1207         //                        + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
1208         //                        + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1209         //                        + "=<suffix for pairwise comparison output files>)" );
1210         //            }
1211         //            infer_species_trees = true;
1212         //        }
1213         File[] intree_files = null;
1214         Phylogeny[] intrees = null;
1215         if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1216             // TODO FIXME if jacknife.... maybe not
1217             if ( number_of_genomes < 3 ) {
1218                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
1219                         + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
1220                         + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1221                         + "=<suffix for pairwise comparison output files>)" );
1222             }
1223             if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
1224                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
1225                         + surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
1226             }
1227             final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
1228             if ( intrees_str.indexOf( "#" ) > 0 ) {
1229                 final String[] intrees_strs = intrees_str.split( "#" );
1230                 intree_files = new File[ intrees_strs.length ];
1231                 int i = 0;
1232                 for( final String s : intrees_strs ) {
1233                     intree_files[ i++ ] = new File( s.trim() );
1234                 }
1235             }
1236             else {
1237                 intree_files = new File[ 1 ];
1238                 intree_files[ 0 ] = new File( intrees_str );
1239             }
1240             intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
1241         }
1242         long random_number_seed_for_fitch_parsimony = 0l;
1243         boolean radomize_fitch_parsimony = false;
1244         if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1245             if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1246                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
1247                         + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
1248             }
1249             try {
1250                 random_number_seed_for_fitch_parsimony = cla
1251                         .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
1252             }
1253             catch ( final IOException e ) {
1254                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1255             }
1256             radomize_fitch_parsimony = true;
1257         }
1258         SortedSet<DomainId> filter = null;
1259         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1260                 || ( negative_domains_filter_file != null ) ) {
1261             filter = new TreeSet<DomainId>();
1262             if ( positive_filter_file != null ) {
1263                 processFilter( positive_filter_file, filter );
1264             }
1265             else if ( negative_filter_file != null ) {
1266                 processFilter( negative_filter_file, filter );
1267             }
1268             else if ( negative_domains_filter_file != null ) {
1269                 processFilter( negative_domains_filter_file, filter );
1270             }
1271         }
1272         Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
1273         File[] secondary_features_map_files = null;
1274         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1275                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
1276         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1277             SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
1278         }
1279         if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1280             if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1281                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
1282                         + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
1283             }
1284             final String[] secondary_features_map_files_strs = cla
1285                     .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
1286             secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
1287             domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
1288             int i = 0;
1289             for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
1290                 secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
1291                 final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
1292                 if ( !ForesterUtil.isEmpty( error ) ) {
1293                     ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
1294                 }
1295                 try {
1296                     domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
1297                             .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
1298                 }
1299                 catch ( final IOException e ) {
1300                     ForesterUtil.fatalError( surfacing.PRG_NAME,
1301                                              "cannot read secondary features map file: " + e.getMessage() );
1302                 }
1303                 catch ( final Exception e ) {
1304                     ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
1305                             + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
1306                 }
1307                 i++;
1308             }
1309         }
1310         if ( out_dir == null ) {
1311             ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
1312                     + surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
1313         }
1314         if ( output_file == null ) {
1315             ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
1316                     + surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
1317         }
1318         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
1319             ForesterUtil.fatalError( surfacing.PRG_NAME,
1320                                      "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
1321                                              + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1322         }
1323         if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1324             ForesterUtil.fatalError( surfacing.PRG_NAME,
1325                                      "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
1326                                              + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1327         }
1328         System.out.println( "Output directory            : " + out_dir );
1329         if ( input_file_names_from_file != null ) {
1330             System.out.println( "Input files names from      : " + input_files_file + " ["
1331                     + input_file_names_from_file.length + " input files]" );
1332             html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
1333                     + input_file_names_from_file.length + " input files]</td></tr>" + nl );
1334         }
1335         if ( positive_filter_file != null ) {
1336             final int filter_size = filter.size();
1337             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
1338                     + " domain ids]" );
1339             html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
1340                     + " domain ids]</td></tr>" + nl );
1341         }
1342         if ( negative_filter_file != null ) {
1343             final int filter_size = filter.size();
1344             System.out.println( "Negative protein filter     : " + negative_filter_file + " [" + filter_size
1345                     + " domain ids]" );
1346             html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
1347                     + " domain ids]</td></tr>" + nl );
1348         }
1349         if ( negative_domains_filter_file != null ) {
1350             final int filter_size = filter.size();
1351             System.out.println( "Negative domain filter      : " + negative_domains_filter_file + " [" + filter_size
1352                     + " domain ids]" );
1353             html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
1354                     + filter_size + " domain ids]</td></tr>" + nl );
1355         }
1356         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1357             String plus0 = "";
1358             for( final String s : plus_minus_analysis_high_copy_base_species ) {
1359                 plus0 += "+" + s + " ";
1360             }
1361             String plus1 = "";
1362             for( final String s : plus_minus_analysis_high_copy_target_species ) {
1363                 plus1 += "*" + s + " ";
1364             }
1365             String minus = "";
1366             for( final String s : plus_minus_analysis_high_low_copy_species ) {
1367                 minus += "-" + s + " ";
1368             }
1369             System.out.println( "Plus-minus analysis         : " + plus1 + "&& " + plus0 + "&& " + minus );
1370             html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
1371                     + "</td></tr>" + nl );
1372         }
1373         if ( cutoff_scores_file != null ) {
1374             System.out.println( "Cutoff scores file          : " + cutoff_scores_file );
1375             html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
1376         }
1377         if ( e_value_max >= 0.0 ) {
1378             System.out.println( "E-value maximum (inclusive) : " + e_value_max );
1379             html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
1380         }
1381         System.out.println( "Ignore DUFs                 : " + ignore_dufs );
1382         if ( ignore_virus_like_ids ) {
1383             System.out.println( "Ignore virus like ids       : " + ignore_virus_like_ids );
1384             html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
1385                     + ignore_virus_like_ids + "</td></tr>" + nl );
1386         }
1387         html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
1388         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1389             System.out.println( "Max allowed domain overlap  : " + max_allowed_overlap );
1390             html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
1391         }
1392         if ( no_engulfing_overlaps ) {
1393             System.out.println( "Ignore engulfed domains     : " + no_engulfing_overlaps );
1394             html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
1395                     + "</td></tr>" + nl );
1396         }
1397         System.out.println( "Ignore singlet domains      : " + ignore_domains_without_combs_in_all_spec );
1398         html_desc
1399                 .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1400                         + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
1401         System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
1402         html_desc
1403                 .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1404                         + ignore_species_specific_domains + "</td></tr>" + nl );
1405         System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
1406         html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
1407                 + ignore_combination_with_same + "</td></tr>" + nl );
1408         ;
1409         System.out.println( "Consider directedness       : "
1410                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
1411         html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
1412                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
1413         if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
1414             System.out.println( "Consider adjacency          : "
1415                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
1416             html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
1417                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
1418                     + nl );
1419         }
1420         System.out.print( "Domain counts sort order    : " );
1421         switch ( dc_sort_order ) {
1422             case ALPHABETICAL_KEY_ID:
1423                 System.out.println( "alphabetical" );
1424                 break;
1425             case KEY_DOMAIN_COUNT:
1426                 System.out.println( "domain count" );
1427                 break;
1428             case KEY_DOMAIN_PROTEINS_COUNT:
1429                 System.out.println( "domain proteins count" );
1430                 break;
1431             case COMBINATIONS_COUNT:
1432                 System.out.println( "domain combinations count" );
1433                 break;
1434             default:
1435                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
1436         }
1437         if ( domain_id_to_go_ids_map != null ) {
1438             System.out.println( "Pfam to GO mappings from    : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
1439                     + " mappings]" );
1440             html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
1441                     + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
1442         }
1443         if ( go_terms != null ) {
1444             System.out.println( "GO terms from               : " + go_obo_file + " [" + go_terms.size() + " terms]" );
1445             html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
1446                     + "</td></tr>" + nl );
1447         }
1448         if ( go_namespace_limit != null ) {
1449             System.out.println( "Limit GO terms to           : " + go_namespace_limit.toString() );
1450             html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
1451         }
1452         if ( perform_pwc ) {
1453             System.out.println( "Suffix for PWC files        : " + automated_pairwise_comparison_suffix );
1454             html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
1455                     + "</td></tr>" + nl );
1456         }
1457         if ( out_dir != null ) {
1458             System.out.println( "Output directory            : " + out_dir );
1459         }
1460         if ( query_domain_ids != null ) {
1461             System.out.println( "Query domains (ordered)     : " + query_domain_ids );
1462             html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
1463         }
1464         System.out.println( "Write similarities to       : " + output_file );
1465         System.out.print( "  Scoring method            : " );
1466         html_desc.append( "<tr><td>Scoring method:</td><td>" );
1467         switch ( scoring ) {
1468             case COMBINATIONS:
1469                 System.out.println( "domain combinations based" );
1470                 html_desc.append( "domain combinations based" + "</td></tr>" + nl );
1471                 break;
1472             case DOMAINS:
1473                 System.out.println( "domain counts based" );
1474                 html_desc.append( "domain counts based" + "</td></tr>" + nl );
1475                 break;
1476             case PROTEINS:
1477                 System.out.println( "domain proteins counts based" );
1478                 html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
1479                 break;
1480             default:
1481                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
1482         }
1483         System.out.print( "  Sort by                   : " );
1484         html_desc.append( "<tr><td>Sort by:</td><td>" );
1485         switch ( domain_similarity_sort_field ) {
1486             case MIN:
1487                 System.out.print( "score minimum" );
1488                 html_desc.append( "score minimum" );
1489                 break;
1490             case MAX:
1491                 System.out.print( "score maximum" );
1492                 html_desc.append( "score maximum" );
1493                 break;
1494             case MEAN:
1495                 System.out.print( "score mean" );
1496                 html_desc.append( "score mean" );
1497                 break;
1498             case SD:
1499                 System.out.print( "score standard deviation" );
1500                 html_desc.append( "score standard deviation" );
1501                 break;
1502             case SPECIES_COUNT:
1503                 System.out.print( "species number" );
1504                 html_desc.append( "species number" );
1505                 break;
1506             case DOMAIN_ID:
1507                 System.out.print( "alphabetical domain identifier" );
1508                 html_desc.append( "alphabetical domain identifier" );
1509                 break;
1510             case MAX_DIFFERENCE:
1511                 System.out.print( "(maximal) difference" );
1512                 html_desc.append( "(maximal) difference" );
1513                 break;
1514             case ABS_MAX_COUNTS_DIFFERENCE:
1515                 System.out.print( "absolute (maximal) counts difference" );
1516                 html_desc.append( "absolute (maximal) counts difference" );
1517                 break;
1518             case MAX_COUNTS_DIFFERENCE:
1519                 System.out.print( "(maximal) counts difference" );
1520                 html_desc.append( "(maximal) counts  difference" );
1521                 break;
1522             default:
1523                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1524         }
1525         if ( sort_by_species_count_first ) {
1526             System.out.println( " (sort by species count first)" );
1527             html_desc.append( " (sort by species count first)" );
1528         }
1529         else {
1530             System.out.println();
1531         }
1532         html_desc.append( "</td></tr>" + nl );
1533         System.out.print( "  Detailedness              : " );
1534         switch ( detailedness ) {
1535             case BASIC:
1536                 System.out.println( "basic" );
1537                 break;
1538             case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
1539                 System.out.println( "list combining domains for each species" );
1540                 break;
1541             case PUNCTILIOUS:
1542                 System.out.println( "punctilious" );
1543                 break;
1544             default:
1545                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" );
1546         }
1547         System.out.print( "  Print option              : " );
1548         switch ( domain_similarity_print_option ) {
1549             case HTML:
1550                 System.out.println( "HTML" );
1551                 break;
1552             case SIMPLE_TAB_DELIMITED:
1553                 System.out.println( "simple tab delimited" );
1554                 break;
1555             default:
1556                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
1557         }
1558         System.out.print( "  Species matrix            : " + species_matrix );
1559         System.out.println();
1560         final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
1561         System.out.println( "Domain comb data output     : " + dc_data_file );
1562         html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
1563         System.out.println();
1564         if ( perform_pwc ) {
1565             System.out.println( "Pairwise comparisons: " );
1566             html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
1567             System.out.print( "  Sort by                   : " );
1568             html_desc.append( "<tr><td>Sort by:</td><td>" );
1569             switch ( domain_similarity_sort_field_for_automated_pwc ) {
1570                 case MEAN:
1571                     System.out.print( "score mean" );
1572                     html_desc.append( "score mean" );
1573                     break;
1574                 case DOMAIN_ID:
1575                     System.out.print( "alphabetical domain identifier" );
1576                     html_desc.append( "alphabetical domain identifier" );
1577                     break;
1578                 case MAX_DIFFERENCE:
1579                     System.out.print( "difference" );
1580                     html_desc.append( "difference" );
1581                     break;
1582                 case ABS_MAX_COUNTS_DIFFERENCE:
1583                     System.out.print( "absolute counts difference" );
1584                     html_desc.append( "absolute counts difference" );
1585                     break;
1586                 case MAX_COUNTS_DIFFERENCE:
1587                     System.out.print( "counts difference" );
1588                     html_desc.append( "counts difference" );
1589                     break;
1590                 default:
1591                     ForesterUtil
1592                             .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
1593             }
1594             System.out.println();
1595             html_desc.append( "</td></tr>" + nl );
1596             if ( jacknifed_distances ) {
1597                 html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
1598                 html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
1599                         + "</td></tr>" + nl );
1600                 html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
1601                 System.out.println( "  Jacknife                  : " + jacknife_resamplings + " resamplings" );
1602                 System.out.println( "    Ratio                   : " + ForesterUtil.round( jacknife_ratio, 2 ) );
1603                 System.out.println( "    Random number seed      : " + random_seed );
1604             }
1605             //                if ( infer_species_trees ) {
1606             //                    html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
1607             //                    System.out.println( "  Infer species trees       : true" );
1608             //                }
1609             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
1610                 for( final File intree_file : intree_files ) {
1611                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
1612                             + "</td></tr>" + nl );
1613                     System.out.println( "  Intree for gain/loss pars.: " + intree_file );
1614                 }
1615             }
1616             if ( radomize_fitch_parsimony ) {
1617                 html_desc.append( "<tr><td>    Random number seed for Fitch parsimony analysis:</td><td>"
1618                         + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
1619                 System.out.println( "    Random number seed      : " + random_number_seed_for_fitch_parsimony );
1620             }
1621             if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1622                 for( int i = 0; i < secondary_features_map_files.length; i++ ) {
1623                     html_desc.append( "<tr><td>Secondary features map file:</td><td>"
1624                             + secondary_features_map_files[ i ] + "</td></tr>" + nl );
1625                     System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
1626                             + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
1627                     if ( VERBOSE ) {
1628                         System.out.println();
1629                         System.out.println( "Domain ids to secondary features map:" );
1630                         for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
1631                             System.out.print( domain_id.getId() );
1632                             System.out.print( " => " );
1633                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
1634                                 System.out.print( sec );
1635                                 System.out.print( " " );
1636                             }
1637                             System.out.println();
1638                         }
1639                     }
1640                 }
1641             }
1642         } // if ( perform_pwc ) {
1643         System.out.println();
1644         html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
1645         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
1646         BufferedWriter[] query_domains_writer_ary = null;
1647         List<DomainId>[] query_domain_ids_array = null;
1648         if ( query_domain_ids != null ) {
1649             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
1650             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
1651             query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
1652             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
1653                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
1654                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
1655                 final List<DomainId> query = new ArrayList<DomainId>();
1656                 for( final String element : query_domain_ids_str_ary ) {
1657                     query.add( new DomainId( element ) );
1658                 }
1659                 query_domain_ids_array[ i ] = query;
1660                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
1661                 String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX;
1662                 if ( out_dir != null ) {
1663                     protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
1664                 }
1665                 try {
1666                     query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
1667                 }
1668                 catch ( final IOException e ) {
1669                     ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
1670                             + e.getLocalizedMessage() );
1671                 }
1672             }
1673         }
1674         SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
1675         boolean need_protein_lists_per_species = false;
1676         if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
1677             need_protein_lists_per_species = true;
1678         }
1679         if ( need_protein_lists_per_species ) {
1680             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
1681         }
1682         final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
1683         final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
1684         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
1685         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
1686         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
1687         if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
1688             all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
1689             all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
1690         }
1691         final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
1692         final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
1693                 + output_file + D_PROMISCUITY_FILE_SUFFIX );
1694         BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
1695         try {
1696             per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
1697             per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
1698             per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
1699             per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
1700             per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
1701             per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
1702             per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
1703             per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
1704             per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
1705                     + ForesterUtil.LINE_SEPARATOR );
1706         }
1707         catch ( final IOException e2 ) {
1708             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1709         }
1710         final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
1711         BufferedWriter log_writer = null;
1712         try {
1713             log_writer = new BufferedWriter( new FileWriter( log_file ) );
1714         }
1715         catch ( final IOException e2 ) {
1716             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1717         }
1718         BufferedWriter dc_data_writer = null;
1719         try {
1720             dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
1721             dc_data_writer.write( DATA_FILE_DESC );
1722             dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
1723         }
1724         catch ( final IOException e2 ) {
1725             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
1726         }
1727         final DescriptiveStatistics protein_coverage_stats = new BasicDescriptiveStatistics();
1728         final DescriptiveStatistics all_genomes_domains_per_potein_stats = new BasicDescriptiveStatistics();
1729         final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo = new TreeMap<Integer, Integer>();
1730         final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
1731         final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
1732         final SortedSet<String> domains_which_never_single = new TreeSet<String>();
1733         BufferedWriter domains_per_potein_stats_writer = null;
1734         try {
1735             domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
1736                     + output_file + "__domains_per_potein_stats.txt" ) );
1737             domains_per_potein_stats_writer.write( "Genome" );
1738             domains_per_potein_stats_writer.write( "\t" );
1739             domains_per_potein_stats_writer.write( "Mean" );
1740             domains_per_potein_stats_writer.write( "\t" );
1741             domains_per_potein_stats_writer.write( "SD" );
1742             domains_per_potein_stats_writer.write( "\t" );
1743             domains_per_potein_stats_writer.write( "Median" );
1744             domains_per_potein_stats_writer.write( "\t" );
1745             domains_per_potein_stats_writer.write( "N" );
1746             domains_per_potein_stats_writer.write( "\t" );
1747             domains_per_potein_stats_writer.write( "Min" );
1748             domains_per_potein_stats_writer.write( "\t" );
1749             domains_per_potein_stats_writer.write( "Max" );
1750             domains_per_potein_stats_writer.write( "\n" );
1751         }
1752         catch ( final IOException e3 ) {
1753             e3.printStackTrace();
1754         }
1755         // Main loop:
1756         for( int i = 0; i < number_of_genomes; ++i ) {
1757             System.out.println();
1758             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
1759             log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
1760             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 0 ] );
1761             log( "Genome                                         : " + input_file_properties[ i ][ 0 ], log_writer );
1762             HmmscanPerDomainTableParser parser = null;
1763             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
1764             if ( individual_score_cutoffs != null ) {
1765                 ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
1766             }
1767             if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1768                     || ( negative_domains_filter_file != null ) ) {
1769                 HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
1770                 if ( positive_filter_file != null ) {
1771                     filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
1772                 }
1773                 else if ( negative_filter_file != null ) {
1774                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
1775                 }
1776                 else if ( negative_domains_filter_file != null ) {
1777                     filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
1778                 }
1779                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1780                                                           input_file_properties[ i ][ 1 ],
1781                                                           filter,
1782                                                           filter_type,
1783                                                           ind_score_cutoff,
1784                                                           true );
1785             }
1786             else {
1787                 parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
1788                                                           input_file_properties[ i ][ 1 ],
1789                                                           ind_score_cutoff,
1790                                                           true );
1791             }
1792             if ( e_value_max >= 0.0 ) {
1793                 parser.setEValueMaximum( e_value_max );
1794             }
1795             parser.setIgnoreDufs( ignore_dufs );
1796             parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
1797             parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
1798             if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1799                 parser.setMaxAllowedOverlap( max_allowed_overlap );
1800             }
1801             parser.setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
1802             if ( individual_score_cutoffs != null ) {
1803                 parser.setIndividualScoreCutoffs( individual_score_cutoffs );
1804             }
1805             List<Protein> protein_list = null;
1806             try {
1807                 protein_list = parser.parse();
1808             }
1809             catch ( final IOException e ) {
1810                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1811             }
1812             catch ( final Exception e ) {
1813                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
1814             }
1815             if ( VERBOSE ) {
1816                 System.out.println( "Domains ignored due to negative domain filter: " );
1817                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
1818                 System.out.println( "Domains ignored due to virus like id: " );
1819                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
1820             }
1821             final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
1822             protein_coverage_stats.addValue( coverage );
1823             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
1824             log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(), log_writer );
1825             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
1826             log( "Number of proteins stored                      : " + protein_list.size(), log_writer );
1827             System.out.println( "Coverage                                       : "
1828                     + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
1829             log( "Coverage                                       : " + ForesterUtil.roundToInt( 100.0 * coverage )
1830                     + "%", log_writer );
1831             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
1832             log( "Domains encountered                            : " + parser.getDomainsEncountered(), log_writer );
1833             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
1834             log( "Domains stored                                 : " + parser.getDomainsStored(), log_writer );
1835             System.out.println( "Distinct domains stored                        : "
1836                     + parser.getDomainsStoredSet().size() );
1837             log( "Distinct domains stored                        : " + parser.getDomainsStoredSet().size(), log_writer );
1838             System.out.println( "Domains ignored due to individual score cutoffs: "
1839                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
1840             log( "Domains ignored due to individual score cutoffs: "
1841                          + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
1842                  log_writer );
1843             System.out.println( "Domains ignored due to E-value                 : "
1844                     + parser.getDomainsIgnoredDueToEval() );
1845             log( "Domains ignored due to E-value                 : " + parser.getDomainsIgnoredDueToEval(), log_writer );
1846             System.out.println( "Domains ignored due to DUF designation         : "
1847                     + parser.getDomainsIgnoredDueToDuf() );
1848             log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
1849             if ( ignore_virus_like_ids ) {
1850                 System.out.println( "Domains ignored due virus like ids             : "
1851                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
1852                 log( "Domains ignored due virus like ids             : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
1853                      log_writer );
1854             }
1855             System.out.println( "Domains ignored due negative domain filter     : "
1856                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
1857             log( "Domains ignored due negative domain filter     : "
1858                          + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
1859                  log_writer );
1860             System.out.println( "Domains ignored due to overlap                 : "
1861                     + parser.getDomainsIgnoredDueToOverlap() );
1862             log( "Domains ignored due to overlap                 : " + parser.getDomainsIgnoredDueToOverlap(),
1863                  log_writer );
1864             if ( negative_filter_file != null ) {
1865                 System.out.println( "Proteins ignored due to negative filter        : "
1866                         + parser.getProteinsIgnoredDueToFilter() );
1867                 log( "Proteins ignored due to negative filter        : " + parser.getProteinsIgnoredDueToFilter(),
1868                      log_writer );
1869             }
1870             if ( positive_filter_file != null ) {
1871                 System.out.println( "Proteins ignored due to positive filter        : "
1872                         + parser.getProteinsIgnoredDueToFilter() );
1873                 log( "Proteins ignored due to positive filter        : " + parser.getProteinsIgnoredDueToFilter(),
1874                      log_writer );
1875             }
1876             System.out.println( "Time for processing                            : " + parser.getTime() + "ms" );
1877             log( "", log_writer );
1878             html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
1879                     + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
1880                     + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
1881                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
1882                     + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
1883                     + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
1884                     + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
1885                     + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
1886             if ( negative_filter_file != null ) {
1887                 html_desc.append( "; proteins ignored due to negative filter: "
1888                         + parser.getProteinsIgnoredDueToFilter() );
1889             }
1890             if ( positive_filter_file != null ) {
1891                 html_desc.append( "; proteins ignored due to positive filter: "
1892                         + parser.getProteinsIgnoredDueToFilter() );
1893             }
1894             html_desc.append( "</td></tr>" + nl );
1895             // domain_partner_counts_array[ i ] =
1896             // Methods.getDomainPartnerCounts( protein_domain_collections_array[
1897             // i ],
1898             // false, input_file_properties[ i ][ 1 ] );
1899             try {
1900                 int count = 0;
1901                 for( final Protein protein : protein_list ) {
1902                     dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
1903                             .toString() );
1904                     ++count;
1905                 }
1906             }
1907             catch ( final IOException e ) {
1908                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
1909             }
1910             SurfacingUtil.domainsPerProteinsStatistics( input_file_properties[ i ][ 1 ],
1911                                                         protein_list,
1912                                                         all_genomes_domains_per_potein_stats,
1913                                                         all_genomes_domains_per_potein_histo,
1914                                                         domains_which_are_always_single,
1915                                                         domains_which_are_sometimes_single_sometimes_not,
1916                                                         domains_which_never_single,
1917                                                         domains_per_potein_stats_writer );
1918             gwcd_list.add( BasicGenomeWideCombinableDomains
1919                     .createInstance( protein_list,
1920                                      ignore_combination_with_same,
1921                                      new BasicSpecies( input_file_properties[ i ][ 1 ] ),
1922                                      domain_id_to_go_ids_map,
1923                                      dc_type ) );
1924             domain_lengths_table.addLengths( protein_list );
1925             if ( gwcd_list.get( i ).getSize() > 0 ) {
1926                 SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
1927                                                                  out_dir,
1928                                                                  per_genome_domain_promiscuity_statistics_writer,
1929                                                                  gwcd_list.get( i ),
1930                                                                  i,
1931                                                                  dc_sort_order );
1932                 if ( output_binary_domain_combinationsfor_graph_analysis ) {
1933                     SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
1934                                                                                      out_dir,
1935                                                                                      gwcd_list.get( i ),
1936                                                                                      i,
1937                                                                                      dc_sort_order );
1938                 }
1939                 SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
1940                 SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
1941                                                                   all_bin_domain_combinations_encountered );
1942             }
1943             if ( query_domains_writer_ary != null ) {
1944                 for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1945                     try {
1946                         SurfacingUtil.extractProteinNames( protein_list,
1947                                                            query_domain_ids_array[ j ],
1948                                                            query_domains_writer_ary[ j ],
1949                                                            "\t" );
1950                         query_domains_writer_ary[ j ].flush();
1951                     }
1952                     catch ( final IOException e ) {
1953                         e.printStackTrace();
1954                     }
1955                 }
1956             }
1957             if ( need_protein_lists_per_species ) {
1958                 protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
1959             }
1960             try {
1961                 log_writer.flush();
1962             }
1963             catch ( final IOException e2 ) {
1964                 ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
1965             }
1966             System.gc();
1967         } // for( int i = 0; i < number_of_genomes; ++i ) {
1968         ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
1969                 + per_genome_domain_promiscuity_statistics_file );
1970         //
1971         try {
1972             domains_per_potein_stats_writer.write( "ALL" );
1973             domains_per_potein_stats_writer.write( "\t" );
1974             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.arithmeticMean() + "" );
1975             domains_per_potein_stats_writer.write( "\t" );
1976             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.sampleStandardDeviation() + "" );
1977             domains_per_potein_stats_writer.write( "\t" );
1978             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.median() + "" );
1979             domains_per_potein_stats_writer.write( "\t" );
1980             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getN() + "" );
1981             domains_per_potein_stats_writer.write( "\t" );
1982             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMin() + "" );
1983             domains_per_potein_stats_writer.write( "\t" );
1984             domains_per_potein_stats_writer.write( all_genomes_domains_per_potein_stats.getMax() + "" );
1985             domains_per_potein_stats_writer.write( "\n" );
1986             domains_per_potein_stats_writer.close();
1987             printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer );
1988             ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1989                     + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
1990             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1991                     + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
1992             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1993                     + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
1994             ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1995                     + "__domains_always_combined.txt" ), domains_which_never_single, "\n" );
1996             ForesterUtil.programMessage( PRG_NAME,
1997                                          "Average of proteins with a least one domain assigned: "
1998                                                  + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
1999                                                  + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)" );
2000             ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: " + 100
2001                     * protein_coverage_stats.getMin() + "%-" + 100 * protein_coverage_stats.getMax() + "%" );
2002             log( "Average of prot with a least one dom assigned  : " + ( 100 * protein_coverage_stats.arithmeticMean() )
2003                     + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
2004             log( "Range of prot with a least one dom assigned    : " + 100 * protein_coverage_stats.getMin() + "%-"
2005                     + 100 * protein_coverage_stats.getMax() + "%", log_writer );
2006         }
2007         catch ( final IOException e2 ) {
2008             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2009         }
2010         if ( query_domains_writer_ary != null ) {
2011             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
2012                 try {
2013                     query_domains_writer_ary[ j ].close();
2014                 }
2015                 catch ( final IOException e ) {
2016                     ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
2017                 }
2018             }
2019         }
2020         try {
2021             per_genome_domain_promiscuity_statistics_writer.close();
2022             dc_data_writer.close();
2023             log_writer.close();
2024         }
2025         catch ( final IOException e2 ) {
2026             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
2027         }
2028         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
2029             try {
2030                 SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
2031                                                            number_of_genomes,
2032                                                            domain_lengths_table,
2033                                                            domain_lengths_analysis_outfile );
2034             }
2035             catch ( final IOException e1 ) {
2036                 ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
2037             }
2038             System.out.println();
2039             ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
2040             System.out.println();
2041         }
2042         final long analysis_start_time = new Date().getTime();
2043         PairwiseDomainSimilarityCalculator pw_calc = null;
2044         // double[] values_for_all_scores_histogram = null;
2045         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
2046                                                                                      sort_by_species_count_first,
2047                                                                                      number_of_genomes == 2 );
2048         switch ( scoring ) {
2049             case COMBINATIONS:
2050                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
2051                 break;
2052             case DOMAINS:
2053                 pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
2054                 break;
2055             case PROTEINS:
2056                 pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
2057                 break;
2058             default:
2059                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
2060         }
2061         DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
2062         if ( domain_id_to_go_ids_map != null ) {
2063             go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
2064         }
2065         final SortedSet<DomainSimilarity> similarities = calc
2066                 .calculateSimilarities( pw_calc,
2067                                         gwcd_list,
2068                                         ignore_domains_without_combs_in_all_spec,
2069                                         ignore_species_specific_domains );
2070         SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
2071                                                            detailedness,
2072                                                            go_annotation_output,
2073                                                            go_id_to_term_map,
2074                                                            go_namespace_limit );
2075         DescriptiveStatistics pw_stats = null;
2076         try {
2077             String my_outfile = output_file.toString();
2078             Map<Character, Writer> split_writers = null;
2079             Writer writer = null;
2080             if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
2081                 if ( my_outfile.endsWith( ".html" ) ) {
2082                     my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
2083                 }
2084                 split_writers = new HashMap<Character, Writer>();
2085                 createSplitWriters( out_dir, my_outfile, split_writers );
2086             }
2087             else if ( !my_outfile.endsWith( ".html" ) ) {
2088                 my_outfile += ".html";
2089                 writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
2090             }
2091             List<Species> species_order = null;
2092             if ( species_matrix ) {
2093                 species_order = new ArrayList<Species>();
2094                 for( int i = 0; i < number_of_genomes; i++ ) {
2095                     species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
2096                 }
2097             }
2098             html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
2099                     + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
2100             html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
2101                     + "</td></tr>" + nl );
2102             html_desc.append( "<tr><td>Analysis date/time:</td><td>"
2103                     + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
2104                     + "</td></tr>" + nl );
2105             html_desc.append( "</table>" + nl );
2106             pw_stats = SurfacingUtil
2107                     .writeDomainSimilaritiesToFile( html_desc,
2108                                                     new StringBuilder( number_of_genomes + " genomes" ),
2109                                                     writer,
2110                                                     split_writers,
2111                                                     similarities,
2112                                                     number_of_genomes == 2,
2113                                                     species_order,
2114                                                     domain_similarity_print_option,
2115                                                     domain_similarity_sort_field,
2116                                                     scoring,
2117                                                     true );
2118             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
2119                     + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
2120         }
2121         catch ( final IOException e ) {
2122             ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
2123                     + e.getMessage() + "]" );
2124         }
2125         System.out.println();
2126         // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
2127         final Species[] species = new Species[ number_of_genomes ];
2128         for( int i = 0; i < number_of_genomes; ++i ) {
2129             species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
2130         }
2131         List<Phylogeny> inferred_trees = null;
2132         if ( ( number_of_genomes > 2 ) && perform_pwc ) {
2133             final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
2134             pwgc.performPairwiseComparisons( html_desc,
2135                                              sort_by_species_count_first,
2136                                              detailedness,
2137                                              ignore_domains_without_combs_in_all_spec,
2138                                              ignore_species_specific_domains,
2139                                              domain_similarity_sort_field_for_automated_pwc,
2140                                              domain_similarity_print_option,
2141                                              scoring,
2142                                              domain_id_to_go_ids_map,
2143                                              go_id_to_term_map,
2144                                              go_namespace_limit,
2145                                              species,
2146                                              number_of_genomes,
2147                                              gwcd_list,
2148                                              pw_calc,
2149                                              automated_pairwise_comparison_suffix,
2150                                              true,
2151                                              surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
2152                                              surfacing.PRG_NAME,
2153                                              out_dir,
2154                                              write_pwc_files );
2155             String matrix_output_file = new String( output_file.toString() );
2156             if ( matrix_output_file.indexOf( '.' ) > 1 ) {
2157                 matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
2158             }
2159             if ( out_dir != null ) {
2160                 matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
2161                 output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2162             }
2163             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2164                     + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
2165             SurfacingUtil
2166                     .writeMatrixToFile( new File( matrix_output_file
2167                                                 + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2168                                         pwgc.getSharedBinaryCombinationsBasedDistances() );
2169             SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
2170                                                      + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2171                                              pwgc.getSharedDomainsBasedDistances() );
2172             final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2173                     + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
2174                     .get( 0 ) );
2175             final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2176                     + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2177                     .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
2178             final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2179                     + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2180                     .getSharedDomainsBasedDistances().get( 0 ) );
2181             inferred_trees = new ArrayList<Phylogeny>();
2182             inferred_trees.add( nj_gd );
2183             inferred_trees.add( nj_bc );
2184             inferred_trees.add( nj_d );
2185             if ( jacknifed_distances ) {
2186                 pwgc.performPairwiseComparisonsJacknifed( species,
2187                                                           number_of_genomes,
2188                                                           gwcd_list,
2189                                                           true,
2190                                                           jacknife_resamplings,
2191                                                           jacknife_ratio,
2192                                                           random_seed );
2193                 SurfacingUtil
2194                         .writeMatrixToFile( new File( matrix_output_file
2195                                                     + "_"
2196                                                     + ForesterUtil.round( jacknife_ratio, 2 )
2197                                                     + "_"
2198                                                     + jacknife_resamplings
2199                                                     + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2200                                             pwgc.getSharedBinaryCombinationsBasedDistances() );
2201                 SurfacingUtil
2202                         .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 )
2203                                                     + "_" + jacknife_resamplings
2204                                                     + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2205                                             pwgc.getSharedDomainsBasedDistances() );
2206                 //                if ( infer_species_trees ) {
2207                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2208                 //                            + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
2209                 //                            .getSharedBinaryCombinationsBasedDistances() );
2210                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2211                 //                            + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
2212                 //                }
2213             }
2214         } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
2215         if ( ( out_dir != null ) && ( !perform_pwc ) ) {
2216             output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2217         }
2218         writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
2219         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
2220             final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2221                                                                           e_value_max,
2222                                                                           max_allowed_overlap,
2223                                                                           no_engulfing_overlaps,
2224                                                                           cutoff_scores_file,
2225                                                                           dc_type );
2226             String s = "_";
2227             if ( radomize_fitch_parsimony ) {
2228                 s += random_number_seed_for_fitch_parsimony + "_";
2229             }
2230             int i = 0;
2231             for( final Phylogeny intree : intrees ) {
2232                 final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
2233                         + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
2234                 final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
2235                                                                                                              gwcd_list );
2236                 SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2237                                                         radomize_fitch_parsimony,
2238                                                         outfile_name,
2239                                                         domain_parsimony,
2240                                                         intree,
2241                                                         domain_id_to_go_ids_map,
2242                                                         go_id_to_term_map,
2243                                                         go_namespace_limit,
2244                                                         parameters_sb.toString(),
2245                                                         domain_id_to_secondary_features_maps,
2246                                                         positive_filter_file == null ? null : filter,
2247                                                         output_binary_domain_combinationsfor_graph_analysis,
2248                                                         all_bin_domain_combinations_gained_fitch,
2249                                                         all_bin_domain_combinations_lost_fitch,
2250                                                         dc_type );
2251                 // Listing of all domain combinations gained is only done if only one input tree is used.
2252                 if ( ( domain_id_to_secondary_features_maps != null )
2253                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
2254                     int j = 0;
2255                     for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
2256                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
2257                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
2258                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
2259                         SurfacingUtil
2260                                 .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
2261                                                                                        + "_"
2262                                                                                        + secondary_features_map_files[ j++ ],
2263                                                                                secondary_features_parsimony,
2264                                                                                intree,
2265                                                                                parameters_sb.toString(),
2266                                                                                mapping_results_map );
2267                         if ( i == 0 ) {
2268                             System.out.println();
2269                             System.out.println( "Mapping to secondary features:" );
2270                             for( final Species spec : mapping_results_map.keySet() ) {
2271                                 final MappingResults mapping_results = mapping_results_map.get( spec );
2272                                 final int total_domains = mapping_results.getSumOfFailures()
2273                                         + mapping_results.getSumOfSuccesses();
2274                                 System.out.print( spec + ":" );
2275                                 System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
2276                                 System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
2277                                 if ( total_domains > 0 ) {
2278                                     System.out.println( ", mapped ratio = "
2279                                             + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" );
2280                                 }
2281                                 else {
2282                                     System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
2283                                 }
2284                             }
2285                         }
2286                     }
2287                 }
2288                 i++;
2289             } // for( final Phylogeny intree : intrees ) {
2290         }
2291         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
2292             executePlusMinusAnalysis( output_file,
2293                                       plus_minus_analysis_high_copy_base_species,
2294                                       plus_minus_analysis_high_copy_target_species,
2295                                       plus_minus_analysis_high_low_copy_species,
2296                                       gwcd_list,
2297                                       protein_lists_per_species,
2298                                       domain_id_to_go_ids_map,
2299                                       go_id_to_term_map,
2300                                       plus_minus_analysis_numbers );
2301         }
2302         if ( output_protein_lists_for_all_domains ) {
2303             writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list );
2304         }
2305         //        if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) {
2306         //            final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2307         //                                                                          e_value_max,
2308         //                                                                          max_allowed_overlap,
2309         //                                                                          no_engulfing_overlaps,
2310         //                                                                          cutoff_scores_file );
2311         //            String s = "_";
2312         //            if ( radomize_fitch_parsimony ) {
2313         //                s += random_number_seed_for_fitch_parsimony + "_";
2314         //            }
2315         //            int i = 0;
2316         //            for( final Phylogeny inferred_tree : inferred_trees ) {
2317         //                if ( !inferred_tree.isRooted() ) {
2318         //                    intrees[ 0 ].getRoot().getName();
2319         //                    inferred_tree.r
2320         //                }
2321         //                final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s;
2322         //                final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator
2323         //                        .createInstance( inferred_tree, gwcd_list );
2324         //                SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2325         //                                                        radomize_fitch_parsimony,
2326         //                                                        outfile_name,
2327         //                                                        domain_parsimony,
2328         //                                                        inferred_tree,
2329         //                                                        domain_id_to_go_ids_map,
2330         //                                                        go_id_to_term_map,
2331         //                                                        go_namespace_limit,
2332         //                                                        parameters_sb.toString() );
2333         //                i++;
2334         //            }
2335         //        }
2336         if ( all_bin_domain_combinations_gained_fitch != null ) {
2337             try {
2338                 executeFitchGainsAnalysis( new File( output_file
2339                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2340                                            all_bin_domain_combinations_gained_fitch,
2341                                            all_domains_encountered.size(),
2342                                            all_bin_domain_combinations_encountered,
2343                                            true );
2344             }
2345             catch ( final IOException e ) {
2346                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2347             }
2348         }
2349         if ( all_bin_domain_combinations_lost_fitch != null ) {
2350             try {
2351                 executeFitchGainsAnalysis( new File( output_file
2352                                                    + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2353                                            all_bin_domain_combinations_lost_fitch,
2354                                            all_domains_encountered.size(),
2355                                            all_bin_domain_combinations_encountered,
2356                                            false );
2357             }
2358             catch ( final IOException e ) {
2359                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2360             }
2361         }
2362         final Runtime rt = java.lang.Runtime.getRuntime();
2363         final long free_memory = rt.freeMemory() / 1000000;
2364         final long total_memory = rt.totalMemory() / 1000000;
2365         System.out.println();
2366         System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
2367         System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
2368         System.out.println( "Free memory       : " + free_memory + "MB, total memory: " + total_memory + "MB" );
2369         System.out.println();
2370         System.out.println( "If this application is useful to you, please cite:" );
2371         System.out.println( surfacing.WWW );
2372         System.out.println();
2373         ForesterUtil.programMessage( PRG_NAME, "OK" );
2374         System.out.println();
2375     }
2376
2377     private static void createSplitWriters( final File out_dir,
2378                                             final String my_outfile,
2379                                             final Map<Character, Writer> split_writers ) throws IOException {
2380         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2381                 + "_domains_A.html" ) ) );
2382         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2383                 + "_domains_B.html" ) ) );
2384         split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2385                 + "_domains_C.html" ) ) );
2386         split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2387                 + "_domains_D.html" ) ) );
2388         split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2389                 + "_domains_E.html" ) ) );
2390         split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2391                 + "_domains_F.html" ) ) );
2392         split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2393                 + "_domains_G.html" ) ) );
2394         split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2395                 + "_domains_H.html" ) ) );
2396         split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2397                 + "_domains_I.html" ) ) );
2398         split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2399                 + "_domains_J.html" ) ) );
2400         split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2401                 + "_domains_K.html" ) ) );
2402         split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2403                 + "_domains_L.html" ) ) );
2404         split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2405                 + "_domains_M.html" ) ) );
2406         split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2407                 + "_domains_N.html" ) ) );
2408         split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2409                 + "_domains_O.html" ) ) );
2410         split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2411                 + "_domains_P.html" ) ) );
2412         split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2413                 + "_domains_Q.html" ) ) );
2414         split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2415                 + "_domains_R.html" ) ) );
2416         split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2417                 + "_domains_S.html" ) ) );
2418         split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2419                 + "_domains_T.html" ) ) );
2420         split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2421                 + "_domains_U.html" ) ) );
2422         split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2423                 + "_domains_V.html" ) ) );
2424         split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2425                 + "_domains_W.html" ) ) );
2426         split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2427                 + "_domains_X.html" ) ) );
2428         split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2429                 + "_domains_Y.html" ) ) );
2430         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2431                 + "_domains_Z.html" ) ) );
2432         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
2433                 + "_domains_0.html" ) ) );
2434     }
2435
2436     private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2437                                                                  final Writer log_writer ) {
2438         int sum = 0;
2439         for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
2440             sum += entry.getValue();
2441         }
2442         final double percentage = 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) / sum;
2443         ForesterUtil.programMessage( PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
2444         log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
2445     }
2446
2447     private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
2448                                                               final String[][] input_file_properties ) {
2449         final String[] genomes = new String[ input_file_properties.length ];
2450         for( int i = 0; i < input_file_properties.length; ++i ) {
2451             if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
2452                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2453                         + "] is not unique in input tree " + intree.getName() );
2454             }
2455             genomes[ i ] = input_file_properties[ i ][ 1 ];
2456         }
2457         //
2458         final PhylogenyNodeIterator it = intree.iteratorPostorder();
2459         while ( it.hasNext() ) {
2460             final PhylogenyNode n = it.next();
2461             if ( ForesterUtil.isEmpty( n.getName() ) ) {
2462                 if ( n.getNodeData().isHasTaxonomy()
2463                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
2464                     n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
2465                 }
2466                 else if ( n.getNodeData().isHasTaxonomy()
2467                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
2468                     n.setName( n.getNodeData().getTaxonomy().getScientificName() );
2469                 }
2470                 else if ( n.getNodeData().isHasTaxonomy()
2471                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
2472                     n.setName( n.getNodeData().getTaxonomy().getCommonName() );
2473                 }
2474                 else {
2475                     ForesterUtil
2476                             .fatalError( surfacing.PRG_NAME,
2477                                          "node with no name, scientific name, common name, or taxonomy code present" );
2478                 }
2479             }
2480         }
2481         //
2482         final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
2483         if ( igns.size() > 0 ) {
2484             System.out.println( "Not using the following " + igns.size() + " nodes:" );
2485             for( int i = 0; i < igns.size(); ++i ) {
2486                 System.out.println( " " + i + ": " + igns.get( i ) );
2487             }
2488             System.out.println( "--" );
2489         }
2490         for( int i = 0; i < input_file_properties.length; ++i ) {
2491             try {
2492                 intree.getNode( input_file_properties[ i ][ 1 ] );
2493             }
2494             catch ( final IllegalArgumentException e ) {
2495                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2496                         + "] not present/not unique in input tree" );
2497             }
2498         }
2499     }
2500
2501     // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
2502     // final SortedMap<String, CombinableDomains> map ) {
2503     // final StringBuffer sb = new StringBuffer();
2504     // for( final Iterator<String> iter = map.keySet().iterator();
2505     // iter.hasNext(); ) {
2506     // final Object key = iter.next();
2507     // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ',
2508     // false ) );
2509     // final CombinableDomains domain_combination = map.get( key );
2510     // sb.append( ForesterUtil.pad( new StringBuffer( "" +
2511     // domain_combination.getNumberOfCombiningDomains() ), 8,
2512     // ' ', false ) );
2513     // sb.append( domain_combination.toStringBuffer() );
2514     // sb.append( ForesterUtil.getLineSeparator() );
2515     // }
2516     // return sb;
2517     // }
2518     private static void printHelp() {
2519         System.out.println();
2520         System.out.println( "Usage:" );
2521         System.out.println();
2522         System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME
2523                 + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
2524         System.out.println();
2525         System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
2526         System.out
2527                 .println( "       hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
2528         System.out.println();
2529         System.out.println( " Options: " );
2530         System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
2531                 + DETAILEDNESS_DEFAULT + ")" );
2532         System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
2533                 + ": to ignore combinations with self (default: not to ignore)" );
2534         System.out
2535                 .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
2536                         + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2537         System.out
2538                 .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
2539                         + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2540         System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
2541                 + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
2542         System.out
2543                 .println( surfacing.IGNORE_VIRAL_IDS
2544                         + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
2545         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
2546                 + DOMAIN_SORT_FILD_DEFAULT + ")" );
2547         System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
2548         System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
2549         System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
2550         System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
2551         System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
2552         System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
2553         System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
2554                 + DOMAINS_SORT_ORDER_DEFAULT + ")" );
2555         System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
2556                 + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
2557         System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
2558         System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
2559                 + ": sort by species count first" );
2560         System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
2561         System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
2562         System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
2563         System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
2564         System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
2565                 + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
2566         System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
2567                 + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
2568         System.out
2569                 .println( JACKNIFE_OPTION
2570                         + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
2571                         + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
2572         System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
2573                 + JACKNIFE_RATIO_DEFAULT + "]" );
2574         System.out.println( JACKNIFE_RANDOM_SEED_OPTION
2575                 + ": seed for random number generator for jacknife resampling [default: "
2576                 + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
2577         //        System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
2578         //                + ": to infer NJ species trees based on shared domains/binary domain combinations" );
2579         System.out
2580                 .println( surfacing.INPUT_SPECIES_TREE_OPTION
2581                         + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
2582         System.out.println( surfacing.FILTER_POSITIVE_OPTION
2583                 + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
2584         System.out.println( surfacing.FILTER_NEGATIVE_OPTION
2585                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
2586         System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
2587                 + "=<file>: to filter out (ignore) domains listed in <file>" );
2588         System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
2589         System.out
2590                 .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
2591                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
2592         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
2593                 + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
2594         System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
2595                 + ": to consider directedness and adjacency in binary combinations" );
2596         System.out
2597                 .println( surfacing.SEQ_EXTRACT_OPTION
2598                         + "=<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')" );
2599         System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
2600                 + "=<file>: to perfom parsimony analysis on secondary features" );
2601         System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
2602         System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
2603                 + ": to output binary domain combinations for (downstream) graph analysis" );
2604         System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
2605         System.out.println();
2606         System.out.println();
2607         System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2608                 + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
2609                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
2610                 + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
2611                 + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
2612                 + "=50 human mouse brafl strpu" );
2613         System.out.println();
2614     }
2615
2616     private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
2617         SortedSet<String> filter_str = null;
2618         try {
2619             filter_str = ForesterUtil.file2set( filter_file );
2620         }
2621         catch ( final IOException e ) {
2622             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2623         }
2624         if ( filter_str != null ) {
2625             for( final String string : filter_str ) {
2626                 filter.add( new DomainId( string ) );
2627             }
2628         }
2629         if ( VERBOSE ) {
2630             System.out.println( "Filter:" );
2631             for( final DomainId domainId : filter ) {
2632                 System.out.println( domainId.getId() );
2633             }
2634         }
2635     }
2636
2637     private static String[][] processInputFileNames( final String[] names ) {
2638         final String[][] input_file_properties = new String[ names.length ][];
2639         for( int i = 0; i < names.length; ++i ) {
2640             if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
2641                 input_file_properties[ i ] = new String[ 2 ];
2642                 input_file_properties[ i ][ 0 ] = names[ i ];
2643                 input_file_properties[ i ][ 1 ] = names[ i ];
2644             }
2645             else {
2646                 input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
2647                 if ( input_file_properties[ i ].length != 3 ) {
2648                     ForesterUtil
2649                             .fatalError( surfacing.PRG_NAME,
2650                                          "properties for the input files (hmmpfam output) are expected "
2651                                                  + "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 \""
2652                                                  + names[ i ] + "\"" );
2653                 }
2654             }
2655             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
2656             if ( !ForesterUtil.isEmpty( error ) ) {
2657                 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
2658             }
2659         }
2660         return input_file_properties;
2661     }
2662
2663     private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
2664                                                         final List<String> high_copy_base,
2665                                                         final List<String> high_copy_target,
2666                                                         final List<String> low_copy,
2667                                                         final List<Object> numbers ) {
2668         if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2669             if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2670                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
2671                         + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
2672             }
2673             final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
2674             final String msg = ForesterUtil.isReadableFile( plus_minus_file );
2675             if ( !ForesterUtil.isEmpty( msg ) ) {
2676                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
2677             }
2678             processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
2679         }
2680     }
2681
2682     // First numbers is minimal difference, second is factor.
2683     private static void processPlusMinusFile( final File plus_minus_file,
2684                                               final List<String> high_copy_base,
2685                                               final List<String> high_copy_target,
2686                                               final List<String> low_copy,
2687                                               final List<Object> numbers ) {
2688         Set<String> species_set = null;
2689         int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
2690         double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
2691         try {
2692             species_set = ForesterUtil.file2set( plus_minus_file );
2693         }
2694         catch ( final IOException e ) {
2695             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2696         }
2697         if ( species_set != null ) {
2698             for( final String species : species_set ) {
2699                 final String species_trimmed = species.substring( 1 );
2700                 if ( species.startsWith( "+" ) ) {
2701                     if ( low_copy.contains( species_trimmed ) ) {
2702                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2703                                                  "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
2704                                                          + species_trimmed + "\"" );
2705                     }
2706                     high_copy_base.add( species_trimmed );
2707                 }
2708                 else if ( species.startsWith( "*" ) ) {
2709                     if ( low_copy.contains( species_trimmed ) ) {
2710                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2711                                                  "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
2712                                                          + species_trimmed + "\"" );
2713                     }
2714                     high_copy_target.add( species_trimmed );
2715                 }
2716                 else if ( species.startsWith( "-" ) ) {
2717                     if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
2718                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2719                                                  "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
2720                                                          + species_trimmed + "\"" );
2721                     }
2722                     low_copy.add( species_trimmed );
2723                 }
2724                 else if ( species.startsWith( "$D" ) ) {
2725                     try {
2726                         min_diff = Integer.parseInt( species.substring( 3 ) );
2727                     }
2728                     catch ( final NumberFormatException e ) {
2729                         ForesterUtil.fatalError( surfacing.PRG_NAME,
2730                                                  "could not parse integer value for minimal difference from: \""
2731                                                          + species.substring( 3 ) + "\"" );
2732                     }
2733                 }
2734                 else if ( species.startsWith( "$F" ) ) {
2735                     try {
2736                         factor = Double.parseDouble( species.substring( 3 ) );
2737                     }
2738                     catch ( final NumberFormatException e ) {
2739                         ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
2740                                 + species.substring( 3 ) + "\"" );
2741                     }
2742                 }
2743                 else if ( species.startsWith( "#" ) ) {
2744                     // Comment, ignore.
2745                 }
2746                 else {
2747                     ForesterUtil
2748                             .fatalError( surfacing.PRG_NAME,
2749                                          "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
2750                                                  + species + "\"" );
2751                 }
2752                 numbers.add( new Integer( min_diff + "" ) );
2753                 numbers.add( new Double( factor + "" ) );
2754             }
2755         }
2756         else {
2757             ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
2758         }
2759     }
2760
2761     private static void writePresentToNexus( final File output_file,
2762                                              final File positive_filter_file,
2763                                              final SortedSet<DomainId> filter,
2764                                              final List<GenomeWideCombinableDomains> gwcd_list ) {
2765         try {
2766             SurfacingUtil
2767                     .writeMatrixToFile( DomainParsimonyCalculator
2768                             .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
2769                                     : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
2770             SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
2771                     .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
2772                     + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
2773         }
2774         catch ( final Exception e ) {
2775             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2776         }
2777     }
2778
2779     private static void writeProteinListsForAllSpecies( final File output_dir,
2780                                                         final SortedMap<Species, List<Protein>> protein_lists_per_species,
2781                                                         final List<GenomeWideCombinableDomains> gwcd_list ) {
2782         final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
2783         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2784             all_domains.addAll( gwcd.getAllDomainIds() );
2785         }
2786         for( final DomainId domain : all_domains ) {
2787             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
2788             SurfacingUtil.checkForOutputFileWriteability( out );
2789             try {
2790                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2791                 SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
2792                 proteins_file_writer.close();
2793             }
2794             catch ( final IOException e ) {
2795                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2796             }
2797             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2798         }
2799     }
2800 }