forester/java/src/org/forester/application/surfacing_hmmpfam.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.HashSet;
  37 import java.util.List;
  38 import java.util.Map;
  39 import java.util.Set;
  40 import java.util.SortedMap;
  41 import java.util.SortedSet;
  42 import java.util.TreeMap;
  43 import java.util.TreeSet;
  44
  45 import org.forester.evoinference.distance.NeighborJoining;
  46 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  47 import org.forester.go.GoId;
  48 import org.forester.go.GoNameSpace;
  49 import org.forester.go.GoTerm;
  50 import org.forester.go.GoUtils;
  51 import org.forester.go.OBOparser;
  52 import org.forester.go.PfamToGoMapping;
  53 import org.forester.go.PfamToGoParser;
  54 import org.forester.io.parsers.HmmPfamOutputParser;
  55 import org.forester.io.writers.PhylogenyWriter;
  56 import org.forester.phylogeny.Phylogeny;
  57 import org.forester.phylogeny.PhylogenyMethods;
  58 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  59 import org.forester.surfacing.BasicDomainSimilarityCalculator;
  60 import org.forester.surfacing.BasicGenomeWideCombinableDomains;
  61 import org.forester.surfacing.BasicSpecies;
  62 import org.forester.surfacing.BinaryDomainCombination;
  63 import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
  64 import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
  65 import org.forester.surfacing.DomainCountsDifferenceUtil;
  66 import org.forester.surfacing.DomainId;
  67 import org.forester.surfacing.DomainLengthsTable;
  68 import org.forester.surfacing.DomainParsimonyCalculator;
  69 import org.forester.surfacing.DomainSimilarity;
  70 import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
  71 import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
  72 import org.forester.surfacing.DomainSimilarityCalculator;
  73 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  74 import org.forester.surfacing.GenomeWideCombinableDomains;
  75 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  76 import org.forester.surfacing.MappingResults;
  77 import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
  78 import org.forester.surfacing.PairwiseGenomeComparator;
  79 import org.forester.surfacing.PrintableDomainSimilarity;
  80 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  81 import org.forester.surfacing.Protein;
  82 import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
  83 import org.forester.surfacing.Species;
  84 import org.forester.surfacing.SurfacingUtil;
  85 import org.forester.util.BasicTable;
  86 import org.forester.util.BasicTableParser;
  87 import org.forester.util.CommandLineArguments;
  88 import org.forester.util.DescriptiveStatistics;
  89 import org.forester.util.ForesterConstants;
  90 import org.forester.util.ForesterUtil;
  91
  92 public class surfacing_hmmpfam {
  93
  94     public final static String                                DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS                    = "graph_analysis_out";
  95     public final static String                                DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS                = "_dc.dot";
  96     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
  97     public final static String                                DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX                             = ".dcc";
  98     // gain/loss:
  99     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS                               = "_dollo_gl_d";
 100     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS                   = "_dollo_gl_dc";
 101     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS                               = "_fitch_gl_d";
 102     public final static String                                PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS                   = "_fitch_gl_dc";
 103     // gain/loss counts:
 104     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS                        = "_dollo_glc_d";
 105     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS            = "_dollo_glc_dc";
 106     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS                        = "_fitch_glc_d";
 107     public final static String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS            = "_fitch_glc_dc";
 108     // tables:
 109     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_BC                                        = "_fitch_gains_dc";
 110     public final static String                                PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC                                   = "_fitch_gains_dc.html";
 111     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_BC                                       = "_fitch_losses_dc";
 112     public final static String                                PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC                                  = "_fitch_losses_dc.html";
 113     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_BC                                      = "_fitch_present_dc";
 114     public final static String                                PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC                                 = "_fitch_present_dc.html";
 115     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_D                                         = "_dollo_gains_d";
 116     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D                                    = "_dollo_gains_goid_d";
 117     public final static String                                PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D                                    = "_dollo_gains_d.html";
 118     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_D                                        = "_dollo_losses_d";
 119     public final static String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D                                   = "_dollo_losses_d.html";
 120     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_D                                       = "_dollo_present_d";
 121     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D                                  = "_dollo_present_goid_d";
 122     public final static String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D                                  = "_dollo_present_d.html";
 123     public final static String                                DOMAINS_PRESENT_NEXUS                                                  = "_dom.nex";
 124     public final static String                                BDC_PRESENT_NEXUS                                                      = "_dc.nex";
 125     // ---
 126     public final static String                                PRG_NAME                                                               = "surfacing";
 127     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                             = "_d_dollo"
 128                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 129     public static final String                                DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH                             = "_d_fitch"
 130                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 131     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO          = "_dc_dollo"
 132                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 133     public static final String                                BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH          = "_dc_fitch"
 134                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 135     public static final String                                NEXUS_EXTERNAL_DOMAINS                                                 = "_dom.nex";
 136     public static final String                                NEXUS_EXTERNAL_DOMAIN_COMBINATIONS                                     = "_dc.nex";
 137     public static final String                                NEXUS_SECONDARY_FEATURES                                               = "_secondary_features.nex";
 138     public static final String                                PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES                    = "_dollo_gl_secondary_features";
 139     public static final String                                PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES             = "_dollo_glc_secondary_features";
 140     public static final String                                PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES                        = "_dollo_gains_secondary_features";
 141     public static final String                                PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES                       = "_dollo_losses_secondary_features";
 142     public static final String                                PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES                      = "_dollo_present_secondary_features";
 143     public static final String                                SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO                  = "_secondary_features_dollo"
 144                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 145     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS                   = "_dollo_biol_proc_goid_d";
 146     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT                   = "_dollo_cell_comp_goid_d";
 147     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION                   = "_dollo_mol_funct_goid_d";
 148     public static final String                                PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES                       = "_dollo_goid_d";
 149     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS                  = "_fitch_biol_proc_goid_dc";
 150     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT                  = "_fitch_cell_comp_goid_dc";
 151     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION                  = "_fitch_mol_funct_goid_dc";
 152     public static final String                                PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES                      = "_fitch_goid_dc";
 153     final static private String                               HELP_OPTION_1                                                          = "help";
 154     final static private String                               HELP_OPTION_2                                                          = "h";
 155     final static private String                               OUTPUT_DIR_OPTION                                                      = "out_dir";
 156     final static private String                               SCORING_OPTION                                                         = "scoring";
 157     private static final DomainSimilarityScoring              SCORING_DEFAULT                                                        = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 158     final static private String                               SCORING_DOMAIN_COUNT_BASED                                             = "domains";
 159     final static private String                               SCORING_PROTEIN_COUNT_BASED                                            = "proteins";
 160     final static private String                               SCORING_COMBINATION_BASED                                              = "combinations";
 161     final static private String                               DETAILEDNESS_OPTION                                                    = "detail";
 162     private final static Detailedness                         DETAILEDNESS_DEFAULT                                                   = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 163     final static private String                               SPECIES_MATRIX_OPTION                                                  = "smatrix";
 164     final static private String                               DETAILEDNESS_BASIC                                                     = "basic";
 165     final static private String                               DETAILEDNESS_LIST_IDS                                                  = "list_ids";
 166     final static private String                               DETAILEDNESS_PUNCTILIOUS                                               = "punctilious";
 167     final static private String                               DOMAIN_SIMILARITY_SORT_OPTION                                          = "sort";
 168     private static final DomainSimilaritySortField            DOMAIN_SORT_FILD_DEFAULT                                               = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 169     final static private String                               DOMAIN_SIMILARITY_SORT_MIN                                             = "min";
 170     final static private String                               DOMAIN_SIMILARITY_SORT_MAX                                             = "max";
 171     final static private String                               DOMAIN_SIMILARITY_SORT_SD                                              = "sd";
 172     final static private String                               DOMAIN_SIMILARITY_SORT_MEAN                                            = "mean";
 173     final static private String                               DOMAIN_SIMILARITY_SORT_DIFF                                            = "diff";
 174     final static private String                               DOMAIN_SIMILARITY_SORT_COUNTS_DIFF                                     = "count_diff";
 175     final static private String                               DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF                                 = "abs_count_diff";
 176     final static private String                               DOMAIN_SIMILARITY_SORT_SPECIES_COUNT                                   = "species";
 177     final static private String                               DOMAIN_SIMILARITY_SORT_ALPHA                                           = "alpha";
 178     final static private String                               DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION                   = "species_first";
 179     final static private String                               DOMAIN_COUNT_SORT_OPTION                                               = "dc_sort";
 180     private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT                                             = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
 181     final static private String                               DOMAIN_COUNT_SORT_ALPHA                                                = "alpha";
 182     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT                                     = "dom";
 183     final static private String                               DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT                            = "prot";
 184     final static private String                               DOMAIN_COUNT_SORT_COMBINATIONS_COUNT                                   = "comb";
 185     final static private String                               CUTOFF_SCORE_FILE_OPTION                                               = "cos";
 186     final static private String                               NOT_IGNORE_DUFS_OPTION                                                 = "dufs";
 187     final static private String                               MAX_E_VALUE_OPTION                                                     = "e";
 188     final static private String                               MAX_ALLOWED_OVERLAP_OPTION                                             = "mo";
 189     final static private String                               NO_ENGULFING_OVERLAP_OPTION                                            = "no_eo";
 190     final static private String                               IGNORE_COMBINATION_WITH_SAME_OPTION                                    = "ignore_self_comb";
 191     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                     = "pwc_";
 192     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_OPTION                                     = "pwc";
 193     final static private String                               OUTPUT_FILE_OPTION                                                     = "o";
 194     final static private String                               PFAM_TO_GO_FILE_USE_OPTION                                             = "p2g";
 195     final static private String                               GO_OBO_FILE_USE_OPTION                                                 = "obo";
 196     final static private String                               GO_NAMESPACE_LIMIT_OPTION                                              = "go_namespace";
 197     final static private String                               GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION                           = "molecular_function";
 198     final static private String                               GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS                           = "biological_process";
 199     final static private String                               GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT                           = "cellular_component";
 200     final static private String                               SECONDARY_FEATURES_PARSIMONY_MAP_FILE                                  = "secondary";
 201     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED                    = "simple_tab";
 202     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML                             = "simple_html";
 203     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML                           = "detailed_html";
 204     final static private String                               DOMAIN_SIMILARITY_PRINT_OPTION                                         = "ds_output";
 205     private static final PRINT_OPTION                         DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT                                 = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 206     final static private String                               IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION              = "ignore_singlet_domains";
 207     final static private String                               IGNORE_VIRAL_IDS                                                       = "ignore_viral_ids";
 208     final static private boolean                              IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT             = false;
 209     final static private String                               IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION                          = "ignore_species_specific_domains";
 210     final static private boolean                              IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT                  = false;
 211     final static private String                               MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                         = "_mean_score.pwd";
 212     final static private String                               MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                     = "_domains.pwd";
 213     final static private String                               MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX            = "_bin_combinations.pwd";
 214     final static private String                               NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX                        = "_mean_score_NJ"
 215                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 216     final static private String                               NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX                    = "_domains_NJ"
 217                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 218     final static private String                               NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX           = "_bin_combinations_NJ"
 219                                                                                                                                              + ForesterConstants.PHYLO_XML_SUFFIX;
 220     final static private String                               DISPLAY_M_HISTOGRAMS_OPTION                                            = "mhisto";
 221     //  final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT                                    = false;
 222     final static private String                               JACKNIFE_OPTION                                                        = "jack";
 223     final static private String                               JACKNIFE_RANDOM_SEED_OPTION                                            = "seed";
 224     final static private String                               JACKNIFE_RATIO_OPTION                                                  = "jack_ratio";
 225     private static final int                                  JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT                                 = 100;
 226     final static private long                                 JACKNIFE_RANDOM_SEED_DEFAULT                                           = 19;
 227     final static private double                               JACKNIFE_RATIO_DEFAULT                                                 = 0.5;
 228     //final static private String  INFER_SPECIES_TREES_OPTION                                             = "species_tree_inference";
 229     final static private String                               INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX                               = "_sd_nj.nh";
 230     final static private String                               INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX                              = "_sbc_nj.nh";
 231     final static private String                               FILTER_POSITIVE_OPTION                                                 = "pos_filter";
 232     final static private String                               FILTER_NEGATIVE_OPTION                                                 = "neg_filter";
 233     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                         = "neg_dom_filter";
 234     final static private String                               INPUT_FILES_FROM_FILE_OPTION                                           = "input";
 235     final static private String                               INPUT_SPECIES_TREE_OPTION                                              = "species_tree";
 236     final static private String                               SEQ_EXTRACT_OPTION                                                     = "prot_extract";
 237     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                             = '#';
 238     final static private String                               PRG_VERSION                                                            = "1.00";
 239     final static private String                               PRG_DATE                                                               = "2009.07.06";
 240     final static private String                               E_MAIL                                                                 = "czmasek@burnham.org";
 241     final static private String                               WWW                                                                    = "www.phylosoft.org/forester/applications/surfacing";
 242     final static private boolean                              IGNORE_DUFS_DEFAULT                                                    = true;
 243     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                  = false;
 244     final static private double                               MAX_E_VALUE_DEFAULT                                                    = -1;
 245     final static private int                                  MAX_ALLOWED_OVERLAP_DEFAULT                                            = -1;
 246     final static private String                               DEFAULT_SEARCH_PARAMETER                                               = "ls";
 247     final private static boolean                              ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT                       = true;
 248     final private static boolean                              VERBOSE_DEFAULT                                                        = true;
 249     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                 = "random_seed";
 250     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                               = "consider_bdc_direction";
 251     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                 = "consider_bdc_adj";
 252     private static final String                               SEQ_EXTRACT_SUFFIX                                                     = ".prot";
 253     private static final String                               PLUS_MINUS_ANALYSIS_OPTION                                             = "plus_minus";
 254     private static final String                               PLUS_MINUS_DOM_SUFFIX                                                  = "_plus_minus_dom.txt";
 255     private static final String                               PLUS_MINUS_DOM_SUFFIX_HTML                                             = "_plus_minus_dom.html";
 256     private static final String                               PLUS_MINUS_DC_SUFFIX_HTML                                              = "_plus_minus_dc.html";
 257     private static final int                                  PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                   = 0;
 258     private static final double                               PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                     = 1.0;
 259     private static final String                               PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                       = "_plus_minus_go_ids_all.txt";
 260     private static final String                               PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                   = "_plus_minus_go_ids_passing.txt";
 261     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                    = "all_prot";
 262     private static final boolean                              VERBOSE                                                                = false;
 263     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX       = "_fitch_dc_gains_counts";
 264     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX         = "_fitch_dc_losses_counts";
 265     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                         = "_domain_lengths_analysis";
 266     private static final boolean                              PERFORM_DOMAIN_LENGTH_ANALYSIS                                         = true;
 267     public static final String                                ALL_PFAMS_ENCOUNTERED_SUFFIX                                           = "_all_encountered_pfams";
 268     public static final String                                ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX                        = "_all_encountered_pfams_with_go_annotation";
 269     public static final String                                ENCOUNTERED_PFAMS_SUMMARY_SUFFIX                                       = "_encountered_pfams_summary";
 270     public static final String                                ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX                                     = "_all_pfams_gained_as_domains";
 271     public static final String                                ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX                                       = "_all_pfams_lost_as_domains";
 272     public static final String                                ALL_PFAMS_GAINED_AS_DC_SUFFIX                                          = "_all_pfams_gained_as_dc";
 273     public static final String                                ALL_PFAMS_LOST_AS_DC_SUFFIX                                            = "_all_pfams_lost_as_dc";
 274     public static final String                                BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES                         = "PER_NODE_EVENTS";
 275     public static final String                                BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES                      = "PER_SUBTREE_EVENTS";
 276     public static final String                                D_PROMISCUITY_FILE_SUFFIX                                              = "_domain_promiscuities";
 277
 278     // final String error = ForesterUtil.isReadableFile( new File(
 279     // input_file_properties[ i ][ 0 ] ) );
 280     // if ( !ForesterUtil.isEmpty( error ) ) {
 281     // ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 282     // }
 283     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
 284                                                                  final String[][] input_file_properties,
 285                                                                  final String automated_pairwise_comparison_suffix,
 286                                                                  final File outdir ) {
 287         for( int i = 0; i < input_file_properties.length; ++i ) {
 288             for( int j = 0; j < i; ++j ) {
 289                 final String species_i = input_file_properties[ i ][ 1 ];
 290                 final String species_j = input_file_properties[ j ][ 1 ];
 291                 String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
 292                         + species_j + automated_pairwise_comparison_suffix;
 293                 switch ( domain_similarity_print_option ) {
 294                     case HTML:
 295                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 296                             pairwise_similarities_output_file_str += ".html";
 297                         }
 298                         break;
 299                 }
 300                 final String error = ForesterUtil
 301                         .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
 302                                 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 303                 if ( !ForesterUtil.isEmpty( error ) ) {
 304                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, error );
 305                 }
 306             }
 307         }
 308     }
 309
 310     private static StringBuilder createParametersAsString( final boolean ignore_dufs,
 311                                                            final double e_value_max,
 312                                                            final int max_allowed_overlap,
 313                                                            final boolean no_engulfing_overlaps,
 314                                                            final File cutoff_scores_file,
 315                                                            final BinaryDomainCombination.DomainCombinationType dc_type ) {
 316         final StringBuilder parameters_sb = new StringBuilder();
 317         parameters_sb.append( "E-value: " + e_value_max );
 318         if ( cutoff_scores_file != null ) {
 319             parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
 320         }
 321         else {
 322             parameters_sb.append( ", Cutoff-scores-file: not-set" );
 323         }
 324         if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
 325             parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
 326         }
 327         else {
 328             parameters_sb.append( ", Max-overlap: not-set" );
 329         }
 330         if ( no_engulfing_overlaps ) {
 331             parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
 332         }
 333         else {
 334             parameters_sb.append( ", Engulfing-overlaps: allowed" );
 335         }
 336         if ( ignore_dufs ) {
 337             parameters_sb.append( ", Ignore-dufs: true" );
 338         }
 339         else {
 340             parameters_sb.append( ", Ignore-dufs: false" );
 341         }
 342         parameters_sb.append( ", DC type (if applicable): " + dc_type );
 343         return parameters_sb;
 344     }
 345
 346     /**
 347      * Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
 348      *
 349      *
 350      * @param output_file
 351      * @param all_bin_domain_combinations_changed
 352      * @param sum_of_all_domains_encountered
 353      * @param all_bin_domain_combinations_encountered
 354      * @param is_gains_analysis
 355      * @throws IOException
 356      */
 357     private static void executeFitchGainsAnalysis( final File output_file,
 358                                                    final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
 359                                                    final int sum_of_all_domains_encountered,
 360                                                    final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
 361                                                    final boolean is_gains_analysis ) throws IOException {
 362         SurfacingUtil.checkForOutputFileWriteability( output_file );
 363         final Writer out = ForesterUtil.createBufferedWriter( output_file );
 364         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
 365                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
 366         final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
 367         final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
 368         int above_one = 0;
 369         int one = 0;
 370         for( final Object bdc_object : bdc_to_counts.keySet() ) {
 371             final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
 372             final int count = bdc_to_counts.get( bdc_object );
 373             if ( count < 1 ) {
 374                 ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
 375             }
 376             out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 377             if ( count > 1 ) {
 378                 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
 379                 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
 380                 above_one++;
 381             }
 382             else if ( count == 1 ) {
 383                 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
 384                 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
 385                 one++;
 386             }
 387         }
 388         final int all = all_bin_domain_combinations_encountered.size();
 389         int never_lost = -1;
 390         if ( !is_gains_analysis ) {
 391             all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
 392             never_lost = all_bin_domain_combinations_encountered.size();
 393             for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
 394                 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
 395             }
 396         }
 397         if ( is_gains_analysis ) {
 398             out.write( "Sum of all distinct domain combinations appearing once               : " + one
 399                     + ForesterUtil.LINE_SEPARATOR );
 400             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
 401                     + ForesterUtil.LINE_SEPARATOR );
 402             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
 403                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 404             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
 405                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 406         }
 407         else {
 408             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
 409                     + ForesterUtil.LINE_SEPARATOR );
 410             out.write( "Sum of all distinct domain combinations lost once                    : " + one
 411                     + ForesterUtil.LINE_SEPARATOR );
 412             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
 413                     + ForesterUtil.LINE_SEPARATOR );
 414             out.write( "Sum of all distinct domains in combinations lost only once           : "
 415                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 416             out.write( "Sum of all distinct domains in combinations lost more than once: "
 417                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 418         }
 419         out.write( "All binary combinations                                              : " + all
 420                 + ForesterUtil.LINE_SEPARATOR );
 421         out.write( "All domains                                                          : "
 422                 + sum_of_all_domains_encountered );
 423         out.close();
 424         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
 425                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
 426                                              + "\"" );
 427     }
 428
 429     private static void executePlusMinusAnalysis( final File output_file,
 430                                                   final List<String> plus_minus_analysis_high_copy_base,
 431                                                   final List<String> plus_minus_analysis_high_copy_target,
 432                                                   final List<String> plus_minus_analysis_low_copy,
 433                                                   final List<GenomeWideCombinableDomains> gwcd_list,
 434                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species,
 435                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 436                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 437                                                   final List<Object> plus_minus_analysis_numbers ) {
 438         final Set<String> all_spec = new HashSet<String>();
 439         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 440             all_spec.add( gwcd.getSpecies().getSpeciesId() );
 441         }
 442         final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
 443         final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
 444         final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
 445         final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
 446         final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
 447         final File proteins_file_base = new File( output_file + "" );
 448         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
 449         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
 450         try {
 451             DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
 452                                                                        protein_lists_per_species,
 453                                                                        plus_minus_analysis_high_copy_base,
 454                                                                        plus_minus_analysis_high_copy_target,
 455                                                                        plus_minus_analysis_low_copy,
 456                                                                        min_diff,
 457                                                                        factor,
 458                                                                        plain_out_dom,
 459                                                                        html_out_dom,
 460                                                                        html_out_dc,
 461                                                                        domain_id_to_go_ids_map,
 462                                                                        go_id_to_term_map,
 463                                                                        all_domains_go_ids_out_dom,
 464                                                                        passing_domains_go_ids_out_dom,
 465                                                                        proteins_file_base );
 466         }
 467         catch ( final IOException e ) {
 468             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getLocalizedMessage() );
 469         }
 470         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
 471                 + html_out_dom + "\"" );
 472         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
 473                 + plain_out_dom + "\"" );
 474         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
 475                 + html_out_dc + "\"" );
 476         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
 477                                      "Wrote plus minus domain analysis based passing GO ids to \""
 478                                              + passing_domains_go_ids_out_dom + "\"" );
 479         ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
 480                                      "Wrote plus minus domain analysis based all GO ids to \""
 481                                              + all_domains_go_ids_out_dom + "\"" );
 482     }
 483
 484     private static Phylogeny[] getIntrees( final File[] intree_files,
 485                                            final int number_of_genomes,
 486                                            final String[][] input_file_properties ) {
 487         final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
 488         int i = 0;
 489         for( final File intree_file : intree_files ) {
 490             Phylogeny intree = null;
 491             final String error = ForesterUtil.isReadableFile( intree_file );
 492             if ( !ForesterUtil.isEmpty( error ) ) {
 493                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read input tree file [" + intree_file
 494                         + "]: " + error );
 495             }
 496             try {
 497                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
 498                         .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
 499                 if ( p_array.length < 1 ) {
 500                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
 501                             + "] does not contain any phylogeny in phyloXML format" );
 502                 }
 503                 else if ( p_array.length > 1 ) {
 504                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
 505                             + "] contains more than one phylogeny in phyloXML format" );
 506                 }
 507                 intree = p_array[ 0 ];
 508             }
 509             catch ( final Exception e ) {
 510                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to read input tree from file ["
 511                         + intree_file + "]: " + error );
 512             }
 513             if ( ( intree == null ) || intree.isEmpty() ) {
 514                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] is empty" );
 515             }
 516             if ( !intree.isRooted() ) {
 517                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
 518             }
 519             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
 520                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 521                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
 522                                                  + "] of input tree [" + intree_file
 523                                                  + "] is smaller than the number of genomes the be analyzed ["
 524                                                  + number_of_genomes + "]" );
 525             }
 526             final StringBuilder parent_names = new StringBuilder();
 527             final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
 528             if ( nodes_lacking_name > 0 ) {
 529                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] has "
 530                         + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
 531             }
 532             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
 533             if ( !intree.isCompletelyBinary() ) {
 534                 ForesterUtil.printWarningMessage( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file
 535                         + "] is not completely binary" );
 536             }
 537             intrees[ i++ ] = intree;
 538         }
 539         return intrees;
 540     }
 541
 542     private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
 543         final NeighborJoining nj = NeighborJoining.createInstance();
 544         final List<Phylogeny> phylogenies = nj.execute( distances_list );
 545         final PhylogenyWriter w = new PhylogenyWriter();
 546         try {
 547             w.toNewHampshire( phylogenies, true, true, outfile, ";" );
 548         }
 549         catch ( final IOException e ) {
 550             ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
 551         }
 552         return phylogenies;
 553     }
 554
 555     public static void main( final String args[] ) {
 556         final long start_time = new Date().getTime();
 557         // final StringBuffer log = new StringBuffer();
 558         final StringBuilder html_desc = new StringBuilder();
 559         ForesterUtil.printProgramInformation( surfacing_hmmpfam.PRG_NAME,
 560                                               surfacing_hmmpfam.PRG_VERSION,
 561                                               surfacing_hmmpfam.PRG_DATE,
 562                                               surfacing_hmmpfam.E_MAIL,
 563                                               surfacing_hmmpfam.WWW );
 564         final String nl = ForesterUtil.LINE_SEPARATOR;
 565         html_desc.append( "<table>" + nl );
 566         html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing_hmmpfam.PRG_NAME + "</td></tr>" + nl );
 567         html_desc.append( "<tr><td>Version:</td><td>" + surfacing_hmmpfam.PRG_VERSION + "</td></tr>" + nl );
 568         html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing_hmmpfam.PRG_DATE + "</td></tr>" + nl );
 569         html_desc.append( "<tr><td>Contact:</td><td>" + surfacing_hmmpfam.E_MAIL + "</td></tr>" + nl );
 570         html_desc.append( "<tr><td>WWW:</td><td>" + surfacing_hmmpfam.WWW + "</td></tr>" + nl );
 571         CommandLineArguments cla = null;
 572         try {
 573             cla = new CommandLineArguments( args );
 574         }
 575         catch ( final Exception e ) {
 576             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
 577         }
 578         if ( cla.isOptionSet( surfacing_hmmpfam.HELP_OPTION_1 ) || cla.isOptionSet( surfacing_hmmpfam.HELP_OPTION_2 ) ) {
 579             surfacing_hmmpfam.printHelp();
 580             System.exit( 0 );
 581         }
 582         if ( ( args.length < 1 ) ) {
 583             surfacing_hmmpfam.printHelp();
 584             System.exit( -1 );
 585         }
 586         final List<String> allowed_options = new ArrayList<String>();
 587         allowed_options.add( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION );
 588         allowed_options.add( surfacing_hmmpfam.MAX_E_VALUE_OPTION );
 589         allowed_options.add( surfacing_hmmpfam.DETAILEDNESS_OPTION );
 590         allowed_options.add( surfacing_hmmpfam.OUTPUT_FILE_OPTION );
 591         allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION );
 592         allowed_options.add( surfacing_hmmpfam.SPECIES_MATRIX_OPTION );
 593         allowed_options.add( surfacing_hmmpfam.SCORING_OPTION );
 594         allowed_options.add( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION );
 595         allowed_options.add( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION );
 596         allowed_options.add( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION );
 597         allowed_options.add( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION );
 598         allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
 599         allowed_options.add( surfacing_hmmpfam.OUTPUT_DIR_OPTION );
 600         allowed_options.add( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION );
 601         allowed_options.add( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION );
 602         allowed_options.add( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION );
 603         allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION );
 604         allowed_options.add( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION );
 605         allowed_options.add( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 606         allowed_options.add( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
 607         allowed_options.add( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION );
 608         allowed_options.add( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
 609         allowed_options.add( JACKNIFE_OPTION );
 610         allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
 611         allowed_options.add( JACKNIFE_RATIO_OPTION );
 612         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
 613         //allowed_options.add( INFER_SPECIES_TREES_OPTION );
 614         allowed_options.add( FILTER_POSITIVE_OPTION );
 615         allowed_options.add( FILTER_NEGATIVE_OPTION );
 616         allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
 617         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
 618         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
 619         allowed_options.add( IGNORE_VIRAL_IDS );
 620         allowed_options.add( SEQ_EXTRACT_OPTION );
 621         allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
 622         allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
 623         allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
 624         allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
 625         allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
 626         boolean ignore_dufs = surfacing_hmmpfam.IGNORE_DUFS_DEFAULT;
 627         boolean ignore_combination_with_same = surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
 628         double e_value_max = surfacing_hmmpfam.MAX_E_VALUE_DEFAULT;
 629         int max_allowed_overlap = surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT;
 630         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 631         if ( dissallowed_options.length() > 0 ) {
 632             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown option(s): " + dissallowed_options );
 633         }
 634         boolean output_binary_domain_combinationsfor_graph_analysis = false;
 635         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
 636             output_binary_domain_combinationsfor_graph_analysis = true;
 637         }
 638         if ( cla.isOptionSet( surfacing_hmmpfam.MAX_E_VALUE_OPTION ) ) {
 639             try {
 640                 e_value_max = cla.getOptionValueAsDouble( surfacing_hmmpfam.MAX_E_VALUE_OPTION );
 641             }
 642             catch ( final Exception e ) {
 643                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no acceptable value for E-value maximum" );
 644             }
 645         }
 646         if ( cla.isOptionSet( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION ) ) {
 647             try {
 648                 max_allowed_overlap = cla.getOptionValueAsInt( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION );
 649             }
 650             catch ( final Exception e ) {
 651                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 652                                          "no acceptable value for maximal allowed domain overlap" );
 653             }
 654         }
 655         boolean no_engulfing_overlaps = false;
 656         if ( cla.isOptionSet( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION ) ) {
 657             no_engulfing_overlaps = true;
 658         }
 659         boolean ignore_virus_like_ids = false;
 660         if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_VIRAL_IDS ) ) {
 661             ignore_virus_like_ids = true;
 662         }
 663         if ( cla.isOptionSet( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION ) ) {
 664             ignore_dufs = false;
 665         }
 666         if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
 667             ignore_combination_with_same = true;
 668         }
 669         boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
 670         if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
 671             ignore_domains_without_combs_in_all_spec = true;
 672         }
 673         boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
 674         if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
 675             ignore_species_specific_domains = true;
 676         }
 677         File output_file = null;
 678         if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) ) {
 679             if ( !cla.isOptionValueSet( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) ) {
 680                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 681                                          "no value for domain combinations similarities output file: -"
 682                                                  + surfacing_hmmpfam.OUTPUT_FILE_OPTION + "=<file>" );
 683             }
 684             output_file = new File( cla.getOptionValue( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) );
 685             SurfacingUtil.checkForOutputFileWriteability( output_file );
 686         }
 687         File cutoff_scores_file = null;
 688         Map<String, String> individual_domain_score_cutoffs = null;
 689         if ( cla.isOptionSet( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) ) {
 690             if ( !cla.isOptionValueSet( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) ) {
 691                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 692                                          "no value for individual domain score cutoffs file: -"
 693                                                  + surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
 694             }
 695             cutoff_scores_file = new File( cla.getOptionValue( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) );
 696             final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
 697             if ( !ForesterUtil.isEmpty( error ) ) {
 698                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 699                                          "cannot read individual domain score cutoffs file: " + error );
 700             }
 701             try {
 702                 final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
 703                 individual_domain_score_cutoffs = scores_table.getColumnsAsMap( 0, 1 );
 704             }
 705             catch ( final IOException e ) {
 706                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 707                                          "cannot read from individual domain score cutoffs file: " + e );
 708             }
 709         }
 710         BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
 711         if ( cla.isOptionSet( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
 712             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
 713         }
 714         if ( cla.isOptionSet( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
 715             dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
 716         }
 717         File out_dir = null;
 718         if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) ) {
 719             if ( !cla.isOptionValueSet( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) ) {
 720                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for output directory: -"
 721                         + surfacing_hmmpfam.OUTPUT_DIR_OPTION + "=<dir>" );
 722             }
 723             out_dir = new File( cla.getOptionValue( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) );
 724             if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
 725                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "\"" + out_dir
 726                         + "\" aready exists and is not empty" );
 727             }
 728             if ( !out_dir.exists() ) {
 729                 final boolean success = out_dir.mkdir();
 730                 if ( !success || !out_dir.exists() ) {
 731                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to create \"" + out_dir + "\"" );
 732                 }
 733             }
 734             if ( !out_dir.canWrite() ) {
 735                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
 736             }
 737         }
 738         File positive_filter_file = null;
 739         File negative_filter_file = null;
 740         File negative_domains_filter_file = null;
 741         if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION )
 742                 && cla.isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
 743             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 744                                      "attempt to use both negative and positive protein filter" );
 745         }
 746         if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION )
 747                 && ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) || cla
 748                         .isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) ) {
 749             ForesterUtil
 750                     .fatalError( surfacing_hmmpfam.PRG_NAME,
 751                                  "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
 752         }
 753         if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) ) {
 754             if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) ) {
 755                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for negative filter: -"
 756                         + surfacing_hmmpfam.FILTER_NEGATIVE_OPTION + "=<file>" );
 757             }
 758             negative_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) );
 759             final String msg = ForesterUtil.isReadableFile( negative_filter_file );
 760             if ( !ForesterUtil.isEmpty( msg ) ) {
 761                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + negative_filter_file
 762                         + "\": " + msg );
 763             }
 764         }
 765         else if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
 766             if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
 767                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for positive filter: -"
 768                         + surfacing_hmmpfam.FILTER_POSITIVE_OPTION + "=<file>" );
 769             }
 770             positive_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) );
 771             final String msg = ForesterUtil.isReadableFile( positive_filter_file );
 772             if ( !ForesterUtil.isEmpty( msg ) ) {
 773                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + positive_filter_file
 774                         + "\": " + msg );
 775             }
 776         }
 777         else if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 778             if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
 779                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for negative domains filter: -"
 780                         + surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
 781             }
 782             negative_domains_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) );
 783             final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
 784             if ( !ForesterUtil.isEmpty( msg ) ) {
 785                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \""
 786                         + negative_domains_filter_file + "\": " + 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_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) ) {
 801             if ( !cla.isOptionValueSet( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) ) {
 802                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for input files file: -"
 803                         + surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 804             }
 805             input_files_file = new File( cla.getOptionValue( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) );
 806             final String msg = ForesterUtil.isReadableFile( input_files_file );
 807             if ( !ForesterUtil.isEmpty( msg ) ) {
 808                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + input_files_file + "\": "
 809                         + msg );
 810             }
 811             try {
 812                 input_file_names_from_file = ForesterUtil.file2array( input_files_file );
 813             }
 814             catch ( final IOException e ) {
 815                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to read from \"" + input_files_file
 816                         + "\": " + e );
 817             }
 818         }
 819         if ( ( cla.getNumberOfNames() < 1 )
 820                 && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
 821             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 822                                      "No hmmpfam output file indicated is input: use comand line directly or "
 823                                              + surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
 824         }
 825         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
 826         if ( cla.isOptionSet( surfacing_hmmpfam.SCORING_OPTION ) ) {
 827             if ( !cla.isOptionValueSet( surfacing_hmmpfam.SCORING_OPTION ) ) {
 828                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 829                                          "no value for scoring method for domain combinations similarity calculation: -"
 830                                                  + surfacing_hmmpfam.SCORING_OPTION + "=<"
 831                                                  + surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED + "|"
 832                                                  + surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED + "|"
 833                                                  + surfacing_hmmpfam.SCORING_COMBINATION_BASED + ">\"" );
 834             }
 835             final String scoring_str = cla.getOptionValue( surfacing_hmmpfam.SCORING_OPTION );
 836             if ( scoring_str.equals( surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED ) ) {
 837                 scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
 838             }
 839             else if ( scoring_str.equals( surfacing_hmmpfam.SCORING_COMBINATION_BASED ) ) {
 840                 scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
 841             }
 842             else if ( scoring_str.equals( surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED ) ) {
 843                 scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
 844             }
 845             else {
 846                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + scoring_str
 847                         + "\" for scoring method for domain combinations similarity calculation: \"-"
 848                         + surfacing_hmmpfam.SCORING_OPTION + "=<" + surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED + "|"
 849                         + surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED + "|"
 850                         + surfacing_hmmpfam.SCORING_COMBINATION_BASED + ">\"" );
 851             }
 852         }
 853         boolean sort_by_species_count_first = false;
 854         if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
 855             sort_by_species_count_first = true;
 856         }
 857         boolean species_matrix = false;
 858         if ( cla.isOptionSet( surfacing_hmmpfam.SPECIES_MATRIX_OPTION ) ) {
 859             species_matrix = true;
 860         }
 861         boolean output_protein_lists_for_all_domains = false;
 862         if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
 863             output_protein_lists_for_all_domains = true;
 864         }
 865         Detailedness detailedness = DETAILEDNESS_DEFAULT;
 866         if ( cla.isOptionSet( surfacing_hmmpfam.DETAILEDNESS_OPTION ) ) {
 867             if ( !cla.isOptionValueSet( surfacing_hmmpfam.DETAILEDNESS_OPTION ) ) {
 868                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for -"
 869                         + surfacing_hmmpfam.DETAILEDNESS_OPTION + "=<" + surfacing_hmmpfam.DETAILEDNESS_BASIC + "|"
 870                         + surfacing_hmmpfam.DETAILEDNESS_LIST_IDS + "|" + surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS
 871                         + ">\"" );
 872             }
 873             final String detness = cla.getOptionValue( surfacing_hmmpfam.DETAILEDNESS_OPTION ).toLowerCase();
 874             if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_BASIC ) ) {
 875                 detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
 876             }
 877             else if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_LIST_IDS ) ) {
 878                 detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
 879             }
 880             else if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS ) ) {
 881                 detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 882             }
 883             else {
 884                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + detness
 885                         + "\" for detailedness: \"-" + surfacing_hmmpfam.DETAILEDNESS_OPTION + "=<"
 886                         + surfacing_hmmpfam.DETAILEDNESS_BASIC + "|" + surfacing_hmmpfam.DETAILEDNESS_LIST_IDS + "|"
 887                         + surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS + ">\"" );
 888             }
 889         }
 890         String automated_pairwise_comparison_suffix = null;
 891         boolean perform_pwc = false;
 892         boolean write_pwc_files = false;
 893         if ( cla.isOptionSet( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 894             perform_pwc = true;
 895             if ( !cla.isOptionValueSet( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
 896                 write_pwc_files = false;
 897             }
 898             else {
 899                 write_pwc_files = true;
 900                 automated_pairwise_comparison_suffix = "_"
 901                         + cla.getOptionValue( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
 902             }
 903         }
 904         String query_domain_ids = null;
 905         if ( cla.isOptionSet( surfacing_hmmpfam.SEQ_EXTRACT_OPTION ) ) {
 906             if ( !cla.isOptionValueSet( surfacing_hmmpfam.SEQ_EXTRACT_OPTION ) ) {
 907                 ForesterUtil
 908                         .fatalError( surfacing_hmmpfam.PRG_NAME,
 909                                      "no domain ids given for sequences with given domains to be extracted : -"
 910                                              + surfacing_hmmpfam.SEQ_EXTRACT_OPTION
 911                                              + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
 912             }
 913             query_domain_ids = cla.getOptionValue( surfacing_hmmpfam.SEQ_EXTRACT_OPTION );
 914         }
 915         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
 916         DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
 917         if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 918             if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
 919                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
 920                                          "no value for domain combinations similarities sorting: -"
 921                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
 922                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 923                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX + "|"
 924                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN + "|"
 925                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN + "|"
 926                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 927                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 928                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
 929                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
 930                                                  + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
 931             }
 932             final String sort_str = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
 933             if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
 934                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 935                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 936             }
 937             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX ) ) {
 938                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
 939                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 940             }
 941             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN ) ) {
 942                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
 943                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 944             }
 945             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
 946                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
 947                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
 948             }
 949             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
 950                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
 951                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 952             }
 953             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD ) ) {
 954                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
 955                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
 956             }
 957             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
 958                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 959                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
 960             }
 961             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
 962                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 963                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
 964             }
 965             else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
 966                 domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 967                 domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
 968             }
 969             else {
 970                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort_str
 971                         + "\" for domain combinations similarities sorting: \"-"
 972                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
 973                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
 974                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX + "|"
 975                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN + "|"
 976                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN + "|"
 977                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF + "|"
 978                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
 979                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
 980                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
 981                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
 982             }
 983         }
 984         PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
 985         if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 986             if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
 987                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for print option: -"
 988                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
 989                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
 990                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
 991             }
 992             final String sort = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
 993             if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
 994                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
 995             }
 996             else if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
 997                 // domain_similarity_print_option =
 998                 // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
 999                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "simple HTML output not implemented yet :(" );
1000             }
1001             else if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
1002                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
1003             }
1004             else {
1005                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort
1006                         + "\" for print option: -" + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML
1007                         + "|" + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
1008                         + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
1009             }
1010         }
1011         GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
1012         if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ) ) {
1013             if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ) ) {
1014                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for sorting of domain counts: -"
1015                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA
1016                         + "|" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1017                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1018                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1019             }
1020             final String sort = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
1021             if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA ) ) {
1022                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
1023             }
1024             else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
1025                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
1026             }
1027             else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
1028                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
1029             }
1030             else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
1031                 dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
1032             }
1033             else {
1034                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort
1035                         + "\" for sorting of domain counts: \"-" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + "=<"
1036                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA + "|"
1037                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
1038                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
1039                         + surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
1040             }
1041         }
1042         String[][] input_file_properties = null;
1043         if ( input_file_names_from_file != null ) {
1044             input_file_properties = surfacing_hmmpfam.processInputFileNames( input_file_names_from_file );
1045         }
1046         else {
1047             input_file_properties = surfacing_hmmpfam.processInputFileNames( cla.getNames() );
1048         }
1049         final int number_of_genomes = input_file_properties.length;
1050         if ( number_of_genomes < 2 ) {
1051             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot analyze less than two files" );
1052         }
1053         if ( ( number_of_genomes < 3 ) && perform_pwc ) {
1054             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use : -"
1055                     + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1056                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
1057         }
1058         checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
1059                                                  input_file_properties,
1060                                                  automated_pairwise_comparison_suffix,
1061                                                  out_dir );
1062         for( int i = 0; i < number_of_genomes; i++ ) {
1063             File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
1064                     + surfacing_hmmpfam.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1065             if ( out_dir != null ) {
1066                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
1067             }
1068             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
1069         }
1070         File pfam_to_go_file = null;
1071         Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
1072         int domain_id_to_go_ids_count = 0;
1073         if ( cla.isOptionSet( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1074             if ( !cla.isOptionValueSet( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) ) {
1075                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for Pfam to GO mapping file: -"
1076                         + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
1077             }
1078             pfam_to_go_file = new File( cla.getOptionValue( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) );
1079             final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
1080             if ( !ForesterUtil.isEmpty( error ) ) {
1081                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
1082             }
1083             try {
1084                 final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
1085                 final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
1086                 domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
1087                 if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
1088                     ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
1089                                                        "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
1090                 }
1091                 domain_id_to_go_ids_count = parser.getMappingCount();
1092             }
1093             catch ( final IOException e ) {
1094                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
1095             }
1096         }
1097         File go_obo_file = null;
1098         List<GoTerm> go_terms = null;
1099         if ( cla.isOptionSet( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) ) {
1100             if ( !cla.isOptionValueSet( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) ) {
1101                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for GO OBO file: -"
1102                         + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>" );
1103             }
1104             if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
1105                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use GO OBO file (-"
1106                         + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
1107                         + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1108             }
1109             go_obo_file = new File( cla.getOptionValue( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) );
1110             final String error = ForesterUtil.isReadableFile( go_obo_file );
1111             if ( !ForesterUtil.isEmpty( error ) ) {
1112                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read GO OBO file: " + error );
1113             }
1114             try {
1115                 final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
1116                 go_terms = parser.parse();
1117                 if ( parser.getGoTermCount() != go_terms.size() ) {
1118                     ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
1119                                                        "parser.getGoTermCount() != go_terms.size()" );
1120                 }
1121             }
1122             catch ( final IOException e ) {
1123                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
1124                                          "cannot read from GO OBO file: " + e.getLocalizedMessage() );
1125             }
1126         }
1127         Map<GoId, GoTerm> go_id_to_term_map = null;
1128         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
1129                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
1130             go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
1131         }
1132         GoNameSpace go_namespace_limit = null;
1133         if ( cla.isOptionSet( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION ) ) {
1134             if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1135                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use GO namespace limit (-"
1136                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION
1137                         + "=<namespace>) without Pfam to GO mapping file ("
1138                         + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
1139                         + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1140             }
1141             if ( !cla.isOptionValueSet( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION ) ) {
1142                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for GO namespace limit: \"-"
1143                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + "=<"
1144                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1145                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1146                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1147             }
1148             final String go_namespace_limit_str = cla.getOptionValue( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION )
1149                     .toLowerCase();
1150             if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
1151                 go_namespace_limit = GoNameSpace.createMolecularFunction();
1152             }
1153             else if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
1154                 go_namespace_limit = GoNameSpace.createBiologicalProcess();
1155             }
1156             else if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
1157                 go_namespace_limit = GoNameSpace.createCellularComponent();
1158             }
1159             else {
1160                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + go_namespace_limit_str
1161                         + "\" for GO namespace limit: \"-" + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + "=<"
1162                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
1163                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
1164                         + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
1165             }
1166         }
1167         if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
1168                 && ( number_of_genomes > 2 ) ) {
1169             domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
1170         }
1171         boolean jacknifed_distances = false;
1172         int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
1173         double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
1174         long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
1175         if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_OPTION ) ) {
1176             if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
1177                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use jacknife resampling analysis (-"
1178                         + surfacing_hmmpfam.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
1179                         + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1180                         + "=<suffix for pairwise comparison output files>)" );
1181             }
1182             jacknifed_distances = true;
1183             if ( cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_OPTION ) ) {
1184                 try {
1185                     jacknife_resamplings = cla.getOptionValueAsInt( surfacing_hmmpfam.JACKNIFE_OPTION );
1186                 }
1187                 catch ( final IOException e ) {
1188                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for number of resamplings" );
1189                 }
1190                 if ( jacknife_resamplings < 2 ) {
1191                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "attempt to use less than 2 resamplings" );
1192                 }
1193             }
1194             if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION )
1195                     && cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION ) ) {
1196                 try {
1197                     jacknife_ratio = cla.getOptionValueAsDouble( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION );
1198                 }
1199                 catch ( final IOException e ) {
1200                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for jacknife ratio" );
1201                 }
1202                 if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
1203                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
1204                                              "attempt to use illegal value for jacknife ratio: " + jacknife_ratio );
1205                 }
1206             }
1207             if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION )
1208                     && cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION ) ) {
1209                 try {
1210                     random_seed = cla.getOptionValueAsLong( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION );
1211                 }
1212                 catch ( final IOException e ) {
1213                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for random generator seed" );
1214                 }
1215             }
1216         }
1217         //        boolean infer_species_trees = false;
1218         //        if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
1219         //            if ( ( output_file == null ) || ( number_of_genomes < 3 )
1220         //                    || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
1221         //                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
1222         //                        + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
1223         //                        + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1224         //                        + "=<suffix for pairwise comparison output files>)" );
1225         //            }
1226         //            infer_species_trees = true;
1227         //        }
1228         File[] intree_files = null;
1229         Phylogeny[] intrees = null;
1230         if ( cla.isOptionSet( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION ) ) {
1231             // TODO FIXME if jacknife.... maybe not
1232             if ( number_of_genomes < 3 ) {
1233                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
1234                                          "cannot infer gains and losses on input species trees (-"
1235                                                  + surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
1236                                                  + " without pairwise analyses ("
1237                                                  + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
1238                                                  + "=<suffix for pairwise comparison output files>)" );
1239             }
1240             if ( !cla.isOptionValueSet( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION ) ) {
1241                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for input tree: -"
1242                         + surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
1243             }
1244             final String intrees_str = cla.getOptionValue( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION );
1245             if ( intrees_str.indexOf( "#" ) > 0 ) {
1246                 final String[] intrees_strs = intrees_str.split( "#" );
1247                 intree_files = new File[ intrees_strs.length ];
1248                 int i = 0;
1249                 for( final String s : intrees_strs ) {
1250                     intree_files[ i++ ] = new File( s.trim() );
1251                 }
1252             }
1253             else {
1254                 intree_files = new File[ 1 ];
1255                 intree_files[ 0 ] = new File( intrees_str );
1256             }
1257             intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
1258         }
1259         long random_number_seed_for_fitch_parsimony = 0l;
1260         boolean radomize_fitch_parsimony = false;
1261         if ( cla.isOptionSet( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1262             if ( !cla.isOptionValueSet( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
1263                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for random number seed: -"
1264                         + surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
1265             }
1266             try {
1267                 random_number_seed_for_fitch_parsimony = cla
1268                         .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
1269             }
1270             catch ( final IOException e ) {
1271                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
1272             }
1273             radomize_fitch_parsimony = true;
1274         }
1275         SortedSet<DomainId> filter = null;
1276         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1277                 || ( negative_domains_filter_file != null ) ) {
1278             filter = new TreeSet<DomainId>();
1279             if ( positive_filter_file != null ) {
1280                 processFilter( positive_filter_file, filter );
1281             }
1282             else if ( negative_filter_file != null ) {
1283                 processFilter( negative_filter_file, filter );
1284             }
1285             else if ( negative_domains_filter_file != null ) {
1286                 processFilter( negative_domains_filter_file, filter );
1287             }
1288         }
1289         Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
1290         File[] secondary_features_map_files = null;
1291         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
1292                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
1293         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1294             SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
1295         }
1296         if ( cla.isOptionSet( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1297             if ( !cla.isOptionValueSet( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
1298                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for secondary features map file: -"
1299                         + surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
1300             }
1301             final String[] secondary_features_map_files_strs = cla
1302                     .getOptionValue( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
1303             secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
1304             domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
1305             int i = 0;
1306             for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
1307                 secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
1308                 final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
1309                 if ( !ForesterUtil.isEmpty( error ) ) {
1310                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read secondary features map file: "
1311                             + error );
1312                 }
1313                 try {
1314                     domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
1315                             .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
1316                 }
1317                 catch ( final IOException e ) {
1318                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read secondary features map file: "
1319                             + e.getMessage() );
1320                 }
1321                 catch ( final Exception e ) {
1322                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "problem with contents of features map file ["
1323                             + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
1324                 }
1325                 i++;
1326             }
1327         }
1328         if ( out_dir == null ) {
1329             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no output directory indicated (-"
1330                     + surfacing_hmmpfam.OUTPUT_DIR_OPTION + "=<dir>)" );
1331         }
1332         if ( output_file == null ) {
1333             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no name for (main) output file indicated (-"
1334                     + surfacing_hmmpfam.OUTPUT_FILE_OPTION + "=<file>)" );
1335         }
1336         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
1337             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
1338                                      "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
1339                                              + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
1340         }
1341         if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
1342             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
1343                                      "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
1344                                              + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>)" );
1345         }
1346         boolean display_histograms = false;
1347         if ( cla.isOptionSet( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
1348             display_histograms = true;
1349         }
1350         System.out.println( "Output directory            : " + out_dir );
1351         if ( input_file_names_from_file != null ) {
1352             System.out.println( "Input files names from      : " + input_files_file + " ["
1353                     + input_file_names_from_file.length + " input files]" );
1354             html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
1355                     + input_file_names_from_file.length + " input files]</td></tr>" + nl );
1356         }
1357         if ( positive_filter_file != null ) {
1358             final int filter_size = filter.size();
1359             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
1360                     + " domain ids]" );
1361             html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
1362                     + " domain ids]</td></tr>" + nl );
1363         }
1364         if ( negative_filter_file != null ) {
1365             final int filter_size = filter.size();
1366             System.out.println( "Negative protein filter     : " + negative_filter_file + " [" + filter_size
1367                     + " domain ids]" );
1368             html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
1369                     + " domain ids]</td></tr>" + nl );
1370         }
1371         if ( negative_domains_filter_file != null ) {
1372             final int filter_size = filter.size();
1373             System.out.println( "Negative domain filter      : " + negative_domains_filter_file + " [" + filter_size
1374                     + " domain ids]" );
1375             html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
1376                     + filter_size + " domain ids]</td></tr>" + nl );
1377         }
1378         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
1379             String plus0 = "";
1380             for( final String s : plus_minus_analysis_high_copy_base_species ) {
1381                 plus0 += "+" + s + " ";
1382             }
1383             String plus1 = "";
1384             for( final String s : plus_minus_analysis_high_copy_target_species ) {
1385                 plus1 += "*" + s + " ";
1386             }
1387             String minus = "";
1388             for( final String s : plus_minus_analysis_high_low_copy_species ) {
1389                 minus += "-" + s + " ";
1390             }
1391             System.out.println( "Plus-minus analysis         : " + plus1 + "&& " + plus0 + "&& " + minus );
1392             html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
1393                     + "</td></tr>" + nl );
1394         }
1395         if ( cutoff_scores_file != null ) {
1396             System.out.println( "Cutoff scores file          : " + cutoff_scores_file );
1397             html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
1398         }
1399         if ( e_value_max >= 0.0 ) {
1400             System.out.println( "E-value maximum (inclusive) : " + e_value_max );
1401             html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
1402         }
1403         System.out.println( "Ignore DUFs                 : " + ignore_dufs );
1404         if ( ignore_virus_like_ids ) {
1405             System.out.println( "Ignore virus like ids       : " + ignore_virus_like_ids );
1406             html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
1407                     + ignore_virus_like_ids + "</td></tr>" + nl );
1408         }
1409         html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
1410         if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1411             System.out.println( "Max allowed domain overlap  : " + max_allowed_overlap );
1412             html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
1413         }
1414         if ( no_engulfing_overlaps ) {
1415             System.out.println( "Ignore engulfed domains     : " + no_engulfing_overlaps );
1416             html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
1417                     + "</td></tr>" + nl );
1418         }
1419         System.out.println( "Ignore singlet domains      : " + ignore_domains_without_combs_in_all_spec );
1420         html_desc
1421                 .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1422                         + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
1423         System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
1424         html_desc
1425                 .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
1426                         + ignore_species_specific_domains + "</td></tr>" + nl );
1427         System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
1428         html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
1429                 + ignore_combination_with_same + "</td></tr>" + nl );
1430         ;
1431         System.out.println( "Consider directedness       : "
1432                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
1433         html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
1434                 + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
1435         if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
1436             System.out.println( "Consider adjacency          : "
1437                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
1438             html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
1439                     + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
1440                     + nl );
1441         }
1442         System.out.print( "Domain counts sort order    : " );
1443         switch ( dc_sort_order ) {
1444             case ALPHABETICAL_KEY_ID:
1445                 System.out.println( "alphabetical" );
1446                 break;
1447             case KEY_DOMAIN_COUNT:
1448                 System.out.println( "domain count" );
1449                 break;
1450             case KEY_DOMAIN_PROTEINS_COUNT:
1451                 System.out.println( "domain proteins count" );
1452                 break;
1453             case COMBINATIONS_COUNT:
1454                 System.out.println( "domain combinations count" );
1455                 break;
1456             default:
1457                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for dc sort order" );
1458         }
1459         if ( domain_id_to_go_ids_map != null ) {
1460             System.out.println( "Pfam to GO mappings from    : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
1461                     + " mappings]" );
1462             html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
1463                     + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
1464         }
1465         if ( go_terms != null ) {
1466             System.out.println( "GO terms from               : " + go_obo_file + " [" + go_terms.size() + " terms]" );
1467             html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
1468                     + "</td></tr>" + nl );
1469         }
1470         if ( go_namespace_limit != null ) {
1471             System.out.println( "Limit GO terms to           : " + go_namespace_limit.toString() );
1472             html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
1473         }
1474         if ( perform_pwc ) {
1475             System.out.println( "Suffix for PWC files        : " + automated_pairwise_comparison_suffix );
1476             html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
1477                     + "</td></tr>" + nl );
1478         }
1479         if ( out_dir != null ) {
1480             System.out.println( "Output directory            : " + out_dir );
1481         }
1482         if ( query_domain_ids != null ) {
1483             System.out.println( "Query domains (ordered)     : " + query_domain_ids );
1484             html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
1485         }
1486         System.out.println( "Write similarities to       : " + output_file );
1487         System.out.print( "  Scoring method            : " );
1488         html_desc.append( "<tr><td>Scoring method:</td><td>" );
1489         switch ( scoring ) {
1490             case COMBINATIONS:
1491                 System.out.println( "domain combinations based" );
1492                 html_desc.append( "domain combinations based" + "</td></tr>" + nl );
1493                 break;
1494             case DOMAINS:
1495                 System.out.println( "domain counts based" );
1496                 html_desc.append( "domain counts based" + "</td></tr>" + nl );
1497                 break;
1498             case PROTEINS:
1499                 System.out.println( "domain proteins counts based" );
1500                 html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
1501                 break;
1502             default:
1503                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for sorting for scoring" );
1504         }
1505         System.out.print( "  Sort by                   : " );
1506         html_desc.append( "<tr><td>Sort by:</td><td>" );
1507         switch ( domain_similarity_sort_field ) {
1508             case MIN:
1509                 System.out.print( "score minimum" );
1510                 html_desc.append( "score minimum" );
1511                 break;
1512             case MAX:
1513                 System.out.print( "score maximum" );
1514                 html_desc.append( "score maximum" );
1515                 break;
1516             case MEAN:
1517                 System.out.print( "score mean" );
1518                 html_desc.append( "score mean" );
1519                 break;
1520             case SD:
1521                 System.out.print( "score standard deviation" );
1522                 html_desc.append( "score standard deviation" );
1523                 break;
1524             case SPECIES_COUNT:
1525                 System.out.print( "species number" );
1526                 html_desc.append( "species number" );
1527                 break;
1528             case DOMAIN_ID:
1529                 System.out.print( "alphabetical domain identifier" );
1530                 html_desc.append( "alphabetical domain identifier" );
1531                 break;
1532             case MAX_DIFFERENCE:
1533                 System.out.print( "(maximal) difference" );
1534                 html_desc.append( "(maximal) difference" );
1535                 break;
1536             case ABS_MAX_COUNTS_DIFFERENCE:
1537                 System.out.print( "absolute (maximal) counts difference" );
1538                 html_desc.append( "absolute (maximal) counts difference" );
1539                 break;
1540             case MAX_COUNTS_DIFFERENCE:
1541                 System.out.print( "(maximal) counts difference" );
1542                 html_desc.append( "(maximal) counts  difference" );
1543                 break;
1544             default:
1545                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
1546                                                    "unknown value for sorting for similarities" );
1547         }
1548         if ( sort_by_species_count_first ) {
1549             System.out.println( " (sort by species count first)" );
1550             html_desc.append( " (sort by species count first)" );
1551         }
1552         else {
1553             System.out.println();
1554         }
1555         html_desc.append( "</td></tr>" + nl );
1556         System.out.print( "  Detailedness              : " );
1557         switch ( detailedness ) {
1558             case BASIC:
1559                 System.out.println( "basic" );
1560                 break;
1561             case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
1562                 System.out.println( "list combining domains for each species" );
1563                 break;
1564             case PUNCTILIOUS:
1565                 System.out.println( "punctilious" );
1566                 break;
1567             default:
1568                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
1569                                                    "unknown value for sorting for detailedness" );
1570         }
1571         System.out.print( "  Print option              : " );
1572         switch ( domain_similarity_print_option ) {
1573             case HTML:
1574                 System.out.println( "HTML" );
1575                 break;
1576             case SIMPLE_TAB_DELIMITED:
1577                 System.out.println( "simple tab delimited" );
1578                 break;
1579             default:
1580                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for print option" );
1581         }
1582         System.out.print( "  Species matrix            : " + species_matrix );
1583         System.out.println();
1584         if ( perform_pwc ) {
1585             System.out.println( "Pairwise comparisons: " );
1586             html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
1587             System.out.print( "  Sort by                   : " );
1588             html_desc.append( "<tr><td>Sort by:</td><td>" );
1589             switch ( domain_similarity_sort_field_for_automated_pwc ) {
1590                 case MEAN:
1591                     System.out.print( "score mean" );
1592                     html_desc.append( "score mean" );
1593                     break;
1594                 case DOMAIN_ID:
1595                     System.out.print( "alphabetical domain identifier" );
1596                     html_desc.append( "alphabetical domain identifier" );
1597                     break;
1598                 case MAX_DIFFERENCE:
1599                     System.out.print( "difference" );
1600                     html_desc.append( "difference" );
1601                     break;
1602                 case ABS_MAX_COUNTS_DIFFERENCE:
1603                     System.out.print( "absolute counts difference" );
1604                     html_desc.append( "absolute counts difference" );
1605                     break;
1606                 case MAX_COUNTS_DIFFERENCE:
1607                     System.out.print( "counts difference" );
1608                     html_desc.append( "counts difference" );
1609                     break;
1610                 default:
1611                     ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
1612                                                        "unknown value for sorting for similarities" );
1613             }
1614             System.out.println();
1615             html_desc.append( "</td></tr>" + nl );
1616             if ( jacknifed_distances ) {
1617                 html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
1618                 html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
1619                         + "</td></tr>" + nl );
1620                 html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
1621                 System.out.println( "  Jacknife                  : " + jacknife_resamplings + " resamplings" );
1622                 System.out.println( "    Ratio                   : " + ForesterUtil.round( jacknife_ratio, 2 ) );
1623                 System.out.println( "    Random number seed      : " + random_seed );
1624             }
1625             //                if ( infer_species_trees ) {
1626             //                    html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
1627             //                    System.out.println( "  Infer species trees       : true" );
1628             //                }
1629             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
1630                 for( final File intree_file : intree_files ) {
1631                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
1632                             + "</td></tr>" + nl );
1633                     System.out.println( "  Intree for gain/loss pars.: " + intree_file );
1634                 }
1635             }
1636             if ( radomize_fitch_parsimony ) {
1637                 html_desc.append( "<tr><td>    Random number seed for Fitch parsimony analysis:</td><td>"
1638                         + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
1639                 System.out.println( "    Random number seed      : " + random_number_seed_for_fitch_parsimony );
1640             }
1641             if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1642                 for( int i = 0; i < secondary_features_map_files.length; i++ ) {
1643                     html_desc.append( "<tr><td>Secondary features map file:</td><td>"
1644                             + secondary_features_map_files[ i ] + "</td></tr>" + nl );
1645                     System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
1646                             + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
1647                     if ( VERBOSE ) {
1648                         System.out.println();
1649                         System.out.println( "Domain ids to secondary features map:" );
1650                         for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
1651                             System.out.print( domain_id.getId() );
1652                             System.out.print( " => " );
1653                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
1654                                 System.out.print( sec );
1655                                 System.out.print( " " );
1656                             }
1657                             System.out.println();
1658                         }
1659                     }
1660                 }
1661             }
1662         } // if ( perform_pwc ) {
1663         System.out.println();
1664         html_desc.append( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
1665         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
1666         BufferedWriter[] query_domains_writer_ary = null;
1667         List<DomainId>[] query_domain_ids_array = null;
1668         if ( query_domain_ids != null ) {
1669             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
1670             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
1671             query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
1672             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
1673                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
1674                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
1675                 final List<DomainId> query = new ArrayList<DomainId>();
1676                 for( final String element : query_domain_ids_str_ary ) {
1677                     query.add( new DomainId( element ) );
1678                 }
1679                 query_domain_ids_array[ i ] = query;
1680                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
1681                 String protein_names_writer_str = query_domain_ids_str + surfacing_hmmpfam.SEQ_EXTRACT_SUFFIX;
1682                 if ( out_dir != null ) {
1683                     protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
1684                 }
1685                 try {
1686                     query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
1687                 }
1688                 catch ( final IOException e ) {
1689                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "Could not open [" + protein_names_writer_str
1690                             + "]: " + e.getLocalizedMessage() );
1691                 }
1692             }
1693         }
1694         SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
1695         boolean need_protein_lists_per_species = false;
1696         if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
1697             need_protein_lists_per_species = true;
1698         }
1699         if ( need_protein_lists_per_species ) {
1700             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
1701         }
1702         final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
1703         final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
1704         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
1705         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
1706         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
1707         if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
1708             all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
1709             all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
1710         }
1711         final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
1712         final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
1713                 + output_file + D_PROMISCUITY_FILE_SUFFIX );
1714         BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
1715         try {
1716             per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
1717             per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
1718             per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
1719             per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
1720             per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
1721             per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
1722             per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
1723             per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
1724             per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
1725                     + ForesterUtil.LINE_SEPARATOR );
1726         }
1727         catch ( final IOException e2 ) {
1728             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e2.getMessage() );
1729         }
1730         for( int i = 0; i < number_of_genomes; ++i ) {
1731             System.out.println();
1732             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
1733             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 0 ] );
1734             HmmPfamOutputParser parser = null;
1735             if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
1736                     || ( negative_domains_filter_file != null ) ) {
1737                 HmmPfamOutputParser.FilterType filter_type = HmmPfamOutputParser.FilterType.NONE;
1738                 if ( positive_filter_file != null ) {
1739                     filter_type = HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN;
1740                 }
1741                 else if ( negative_filter_file != null ) {
1742                     filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN;
1743                 }
1744                 else if ( negative_domains_filter_file != null ) {
1745                     filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN;
1746                 }
1747                 parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
1748                                                   input_file_properties[ i ][ 1 ],
1749                                                   input_file_properties[ i ][ 2 ],
1750                                                   filter,
1751                                                   filter_type );
1752             }
1753             else {
1754                 parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
1755                                                   input_file_properties[ i ][ 1 ],
1756                                                   input_file_properties[ i ][ 2 ] );
1757             }
1758             if ( e_value_max >= 0.0 ) {
1759                 parser.setEValueMaximum( e_value_max );
1760             }
1761             parser.setIgnoreDufs( ignore_dufs );
1762             parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
1763             parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
1764             if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
1765                 parser.setMaxAllowedOverlap( max_allowed_overlap );
1766             }
1767             parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
1768             if ( individual_domain_score_cutoffs != null ) {
1769                 parser.setIndividualDomainScoreCutoffs( individual_domain_score_cutoffs );
1770             }
1771             parser.setAllowNonUniqueQuery( ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT );
1772             parser.setVerbose( VERBOSE_DEFAULT );
1773             List<Protein> protein_list = null;
1774             try {
1775                 protein_list = parser.parse();
1776             }
1777             catch ( final IOException e ) {
1778                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
1779             }
1780             catch ( final Exception e ) {
1781                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage(), e );
1782             }
1783             if ( VERBOSE ) {
1784                 System.out.println( "Domains ignored due to negative domain filter: " );
1785                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
1786                 System.out.println( "Domains ignored due to virus like id: " );
1787                 ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
1788             }
1789             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
1790             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
1791             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
1792             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
1793             System.out.println( "Distinct domains stored                        : "
1794                     + parser.getDomainsStoredSet().size() );
1795             System.out.println( "Domains ignored due to individual score cutoffs: "
1796                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
1797             System.out.println( "Domains ignored due to E-value                 : "
1798                     + parser.getDomainsIgnoredDueToEval() );
1799             System.out.println( "Domains ignored due to DUF designation         : "
1800                     + parser.getDomainsIgnoredDueToDuf() );
1801             if ( ignore_virus_like_ids ) {
1802                 System.out.println( "Domains ignored due virus like ids             : "
1803                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
1804             }
1805             System.out.println( "Domains ignored due negative domain filter     : "
1806                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
1807             System.out.println( "Domains ignored due to overlap                 : "
1808                     + parser.getDomainsIgnoredDueToOverlap() );
1809             if ( negative_filter_file != null ) {
1810                 System.out.println( "Proteins ignored due to negative filter        : "
1811                         + parser.getProteinsIgnoredDueToFilter() );
1812             }
1813             if ( positive_filter_file != null ) {
1814                 System.out.println( "Proteins ignored due to positive filter        : "
1815                         + parser.getProteinsIgnoredDueToFilter() );
1816             }
1817             System.out.println( "Time for processing                            : " + parser.getTime() + "ms" );
1818             html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
1819                     + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
1820                     + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
1821                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
1822                     + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
1823                     + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
1824                     + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
1825                     + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
1826             if ( negative_filter_file != null ) {
1827                 html_desc.append( "; proteins ignored due to negative filter: "
1828                         + parser.getProteinsIgnoredDueToFilter() );
1829             }
1830             if ( positive_filter_file != null ) {
1831                 html_desc.append( "; proteins ignored due to positive filter: "
1832                         + parser.getProteinsIgnoredDueToFilter() );
1833             }
1834             html_desc.append( "</td></tr>" + nl );
1835             // domain_partner_counts_array[ i ] =
1836             // Methods.getDomainPartnerCounts( protein_domain_collections_array[
1837             // i ],
1838             // false, input_file_properties[ i ][ 1 ] );
1839             gwcd_list.add( BasicGenomeWideCombinableDomains
1840                     .createInstance( protein_list,
1841                                      ignore_combination_with_same,
1842                                      new BasicSpecies( input_file_properties[ i ][ 1 ] ),
1843                                      domain_id_to_go_ids_map,
1844                                      dc_type ) );
1845             domain_lengths_table.addLengths( protein_list );
1846             if ( gwcd_list.get( i ).getSize() > 0 ) {
1847                 SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
1848                                                                  out_dir,
1849                                                                  per_genome_domain_promiscuity_statistics_writer,
1850                                                                  gwcd_list.get( i ),
1851                                                                  i,
1852                                                                  dc_sort_order );
1853                 if ( output_binary_domain_combinationsfor_graph_analysis ) {
1854                     SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
1855                                                                                      out_dir,
1856                                                                                      gwcd_list.get( i ),
1857                                                                                      i,
1858                                                                                      dc_sort_order );
1859                 }
1860                 SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
1861                 SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
1862                                                                   all_bin_domain_combinations_encountered );
1863             }
1864             if ( query_domains_writer_ary != null ) {
1865                 for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1866                     try {
1867                         SurfacingUtil.extractProteinNames( protein_list,
1868                                                            query_domain_ids_array[ j ],
1869                                                            query_domains_writer_ary[ j ],
1870                                                            "\t" );
1871                         query_domains_writer_ary[ j ].flush();
1872                     }
1873                     catch ( final IOException e ) {
1874                         e.printStackTrace();
1875                     }
1876                 }
1877             }
1878             if ( need_protein_lists_per_species ) {
1879                 protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
1880             }
1881             System.gc();
1882         } // for( int i = 0; i < number_of_hmmpfam_files_to_analyze; ++i ) {
1883         try {
1884             per_genome_domain_promiscuity_statistics_writer.flush();
1885             per_genome_domain_promiscuity_statistics_writer.close();
1886         }
1887         catch ( final IOException e2 ) {
1888             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e2.toString() );
1889         }
1890         ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
1891                 + per_genome_domain_promiscuity_statistics_file );
1892         if ( query_domains_writer_ary != null ) {
1893             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
1894                 try {
1895                     query_domains_writer_ary[ j ].close();
1896                 }
1897                 catch ( final IOException e ) {
1898                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.toString() );
1899                 }
1900             }
1901         }
1902         if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
1903             try {
1904                 SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
1905                                                            number_of_genomes,
1906                                                            domain_lengths_table,
1907                                                            domain_lengths_analysis_outfile );
1908             }
1909             catch ( final IOException e1 ) {
1910                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e1.toString() );
1911             }
1912             System.out.println();
1913             ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
1914             System.out.println();
1915         }
1916         final long analysis_start_time = new Date().getTime();
1917         PairwiseDomainSimilarityCalculator pw_calc = null;
1918         // double[] values_for_all_scores_histogram = null;
1919         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
1920                                                                                      sort_by_species_count_first,
1921                                                                                      number_of_genomes == 2 );
1922         switch ( scoring ) {
1923             case COMBINATIONS:
1924                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
1925                 break;
1926             case DOMAINS:
1927                 pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
1928                 break;
1929             case PROTEINS:
1930                 pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
1931                 break;
1932             default:
1933                 ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for sorting for scoring" );
1934         }
1935         DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
1936         if ( domain_id_to_go_ids_map != null ) {
1937             go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
1938         }
1939         final SortedSet<DomainSimilarity> similarities = calc
1940                 .calculateSimilarities( pw_calc,
1941                                         gwcd_list,
1942                                         ignore_domains_without_combs_in_all_spec,
1943                                         ignore_species_specific_domains );
1944         SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
1945                                                            detailedness,
1946                                                            go_annotation_output,
1947                                                            go_id_to_term_map,
1948                                                            go_namespace_limit );
1949         DescriptiveStatistics pw_stats = null;
1950         try {
1951             String my_outfile = output_file.toString();
1952             if ( !my_outfile.endsWith( ".html" ) ) {
1953                 my_outfile += ".html";
1954             }
1955             final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir
1956                     + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
1957             List<Species> species_order = null;
1958             if ( species_matrix ) {
1959                 species_order = new ArrayList<Species>();
1960                 for( int i = 0; i < number_of_genomes; i++ ) {
1961                     species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
1962                 }
1963             }
1964             html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
1965                     + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
1966             html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
1967                     + "</td></tr>" + nl );
1968             html_desc.append( "<tr><td>Analysis date/time:</td><td>"
1969                     + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
1970                     + "</td></tr>" + nl );
1971             html_desc.append( "</table>" + nl );
1972             pw_stats = SurfacingUtil
1973                     .writeDomainSimilaritiesToFile( html_desc,
1974                                                     new StringBuilder( number_of_genomes + " genomes" ),
1975                                                     writer,
1976                                                     similarities,
1977                                                     number_of_genomes == 2,
1978                                                     species_order,
1979                                                     domain_similarity_print_option,
1980                                                     domain_similarity_sort_field,
1981                                                     scoring,
1982                                                     true );
1983             ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
1984                                          "Wrote main output (includes domain similarities) to: \""
1985                                                  + ( out_dir == null ? my_outfile : out_dir
1986                                                          + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
1987         }
1988         catch ( final IOException e ) {
1989             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "Failed to write similarites to: \"" + output_file
1990                     + "\" [" + e.getMessage() + "]" );
1991         }
1992         System.out.println();
1993         // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
1994         final Species[] species = new Species[ number_of_genomes ];
1995         for( int i = 0; i < number_of_genomes; ++i ) {
1996             species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
1997         }
1998         List<Phylogeny> inferred_trees = null;
1999         if ( ( number_of_genomes > 2 ) && perform_pwc ) {
2000             final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
2001             pwgc.performPairwiseComparisons( html_desc,
2002                                              sort_by_species_count_first,
2003                                              detailedness,
2004                                              ignore_domains_without_combs_in_all_spec,
2005                                              ignore_species_specific_domains,
2006                                              domain_similarity_sort_field_for_automated_pwc,
2007                                              domain_similarity_print_option,
2008                                              scoring,
2009                                              domain_id_to_go_ids_map,
2010                                              go_id_to_term_map,
2011                                              go_namespace_limit,
2012                                              species,
2013                                              number_of_genomes,
2014                                              gwcd_list,
2015                                              pw_calc,
2016                                              automated_pairwise_comparison_suffix,
2017                                              true,
2018                                              surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
2019                                              surfacing_hmmpfam.PRG_NAME,
2020                                              out_dir,
2021                                              write_pwc_files );
2022             String matrix_output_file = new String( output_file.toString() );
2023             if ( matrix_output_file.indexOf( '.' ) > 1 ) {
2024                 matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
2025             }
2026             if ( out_dir != null ) {
2027                 matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
2028                 output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2029             }
2030             SurfacingUtil
2031                     .writeMatrixToFile( new File( matrix_output_file
2032                                                 + surfacing_hmmpfam.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ),
2033                                         pwgc.getDomainDistanceScoresMeans() );
2034             SurfacingUtil
2035                     .writeMatrixToFile( new File( matrix_output_file
2036                                                 + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2037                                         pwgc.getSharedBinaryCombinationsBasedDistances() );
2038             SurfacingUtil
2039                     .writeMatrixToFile( new File( matrix_output_file
2040                                                 + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2041                                         pwgc.getSharedDomainsBasedDistances() );
2042             final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2043                     + surfacing_hmmpfam.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2044                     .getDomainDistanceScoresMeans().get( 0 ) );
2045             final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2046                     + surfacing_hmmpfam.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2047                     .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
2048             final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
2049                     + surfacing_hmmpfam.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
2050                     .getSharedDomainsBasedDistances().get( 0 ) );
2051             inferred_trees = new ArrayList<Phylogeny>();
2052             inferred_trees.add( nj_gd );
2053             inferred_trees.add( nj_bc );
2054             inferred_trees.add( nj_d );
2055             // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
2056             //            if ( infer_species_trees ) {
2057             //                inferred_trees = new ArrayList<Phylogeny>();
2058             //                final List<Phylogeny> inferred_trees_bc =  inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
2059             //                        .getSharedBinaryCombinationsBasedDistances() );
2060             //                final List<Phylogeny> inferred_trees_d =  inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
2061             //                        .getSharedDomainsBasedDistances() );
2062             //                inferred_trees.addAll( inferred_trees_bc );
2063             //                inferred_trees.addAll( inferred_trees_d );
2064             //            }
2065             if ( jacknifed_distances ) {
2066                 pwgc.performPairwiseComparisonsJacknifed( species,
2067                                                           number_of_genomes,
2068                                                           gwcd_list,
2069                                                           true,
2070                                                           jacknife_resamplings,
2071                                                           jacknife_ratio,
2072                                                           random_seed );
2073                 SurfacingUtil
2074                         .writeMatrixToFile( new File( matrix_output_file
2075                                                     + "_"
2076                                                     + ForesterUtil.round( jacknife_ratio, 2 )
2077                                                     + "_"
2078                                                     + jacknife_resamplings
2079                                                     + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
2080                                             pwgc.getSharedBinaryCombinationsBasedDistances() );
2081                 SurfacingUtil
2082                         .writeMatrixToFile( new File( matrix_output_file
2083                                                     + "_"
2084                                                     + ForesterUtil.round( jacknife_ratio, 2 )
2085                                                     + "_"
2086                                                     + jacknife_resamplings
2087                                                     + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
2088                                             pwgc.getSharedDomainsBasedDistances() );
2089                 //                if ( infer_species_trees ) {
2090                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2091                 //                            + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
2092                 //                            .getSharedBinaryCombinationsBasedDistances() );
2093                 //                    inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
2094                 //                            + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
2095                 //                }
2096             }
2097             if ( display_histograms ) {
2098                 //                final List<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
2099                 //                histogram_datas_all.add( new HistogramData( "all",
2100                 //                                                            values_for_all_scores_histogram,
2101                 //                                                            null,
2102                 //                                                            20 ) );
2103                 //                final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all );
2104                 //                final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
2105                 //                hf_all.setVisible( true );
2106                 //                hf.setVisible( true );
2107             }
2108         } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
2109         if ( ( out_dir != null ) && ( !perform_pwc ) ) {
2110             output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
2111         }
2112         //    writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
2113         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
2114             final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2115                                                                           e_value_max,
2116                                                                           max_allowed_overlap,
2117                                                                           no_engulfing_overlaps,
2118                                                                           cutoff_scores_file,
2119                                                                           dc_type );
2120             String s = "_";
2121             if ( radomize_fitch_parsimony ) {
2122                 s += random_number_seed_for_fitch_parsimony + "_";
2123             }
2124             int i = 0;
2125             for( final Phylogeny intree : intrees ) {
2126                 final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
2127                         + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
2128                 final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
2129                                                                                                              gwcd_list );
2130                 SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2131                                                         radomize_fitch_parsimony,
2132                                                         outfile_name,
2133                                                         domain_parsimony,
2134                                                         intree,
2135                                                         domain_id_to_go_ids_map,
2136                                                         go_id_to_term_map,
2137                                                         go_namespace_limit,
2138                                                         parameters_sb.toString(),
2139                                                         domain_id_to_secondary_features_maps,
2140                                                         positive_filter_file == null ? null : filter,
2141                                                         output_binary_domain_combinationsfor_graph_analysis,
2142                                                         all_bin_domain_combinations_gained_fitch,
2143                                                         all_bin_domain_combinations_lost_fitch,
2144                                                         dc_type );
2145                 // Listing of all domain combinations gained is only done if only one input tree is used.
2146                 if ( ( domain_id_to_secondary_features_maps != null )
2147                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
2148                     int j = 0;
2149                     for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
2150                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
2151                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
2152                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
2153                         SurfacingUtil
2154                                 .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
2155                                                                                        + "_"
2156                                                                                        + secondary_features_map_files[ j++ ],
2157                                                                                secondary_features_parsimony,
2158                                                                                intree,
2159                                                                                parameters_sb.toString(),
2160                                                                                mapping_results_map );
2161                         if ( i == 0 ) {
2162                             System.out.println();
2163                             System.out.println( "Mapping to secondary features:" );
2164                             for( final Species spec : mapping_results_map.keySet() ) {
2165                                 final MappingResults mapping_results = mapping_results_map.get( spec );
2166                                 final int total_domains = mapping_results.getSumOfFailures()
2167                                         + mapping_results.getSumOfSuccesses();
2168                                 System.out.print( spec + ":" );
2169                                 System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
2170                                 System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
2171                                 if ( total_domains > 0 ) {
2172                                     System.out.println( ", mapped ratio = "
2173                                             + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" );
2174                                 }
2175                                 else {
2176                                     System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
2177                                 }
2178                             }
2179                         }
2180                     }
2181                 }
2182                 i++;
2183             } // for( final Phylogeny intree : intrees ) {
2184         }
2185         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
2186             executePlusMinusAnalysis( output_file,
2187                                       plus_minus_analysis_high_copy_base_species,
2188                                       plus_minus_analysis_high_copy_target_species,
2189                                       plus_minus_analysis_high_low_copy_species,
2190                                       gwcd_list,
2191                                       protein_lists_per_species,
2192                                       domain_id_to_go_ids_map,
2193                                       go_id_to_term_map,
2194                                       plus_minus_analysis_numbers );
2195         }
2196         if ( output_protein_lists_for_all_domains ) {
2197             writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list );
2198         }
2199         //        if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) {
2200         //            final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
2201         //                                                                          e_value_max,
2202         //                                                                          max_allowed_overlap,
2203         //                                                                          no_engulfing_overlaps,
2204         //                                                                          cutoff_scores_file );
2205         //            String s = "_";
2206         //            if ( radomize_fitch_parsimony ) {
2207         //                s += random_number_seed_for_fitch_parsimony + "_";
2208         //            }
2209         //            int i = 0;
2210         //            for( final Phylogeny inferred_tree : inferred_trees ) {
2211         //                if ( !inferred_tree.isRooted() ) {
2212         //                    intrees[ 0 ].getRoot().getName();
2213         //                    inferred_tree.r
2214         //                }
2215         //                final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s;
2216         //                final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator
2217         //                        .createInstance( inferred_tree, gwcd_list );
2218         //                SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
2219         //                                                        radomize_fitch_parsimony,
2220         //                                                        outfile_name,
2221         //                                                        domain_parsimony,
2222         //                                                        inferred_tree,
2223         //                                                        domain_id_to_go_ids_map,
2224         //                                                        go_id_to_term_map,
2225         //                                                        go_namespace_limit,
2226         //                                                        parameters_sb.toString() );
2227         //                i++;
2228         //            }
2229         //        }
2230         if ( all_bin_domain_combinations_gained_fitch != null ) {
2231             try {
2232                 executeFitchGainsAnalysis( new File( output_file
2233                                                    + surfacing_hmmpfam.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2234                                            all_bin_domain_combinations_gained_fitch,
2235                                            all_domains_encountered.size(),
2236                                            all_bin_domain_combinations_encountered,
2237                                            true );
2238             }
2239             catch ( final IOException e ) {
2240                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2241             }
2242         }
2243         if ( all_bin_domain_combinations_lost_fitch != null ) {
2244             try {
2245                 executeFitchGainsAnalysis( new File( output_file
2246                                                    + surfacing_hmmpfam.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
2247                                            all_bin_domain_combinations_lost_fitch,
2248                                            all_domains_encountered.size(),
2249                                            all_bin_domain_combinations_encountered,
2250                                            false );
2251             }
2252             catch ( final IOException e ) {
2253                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
2254             }
2255         }
2256         final Runtime rt = java.lang.Runtime.getRuntime();
2257         final long free_memory = rt.freeMemory() / 1000000;
2258         final long total_memory = rt.totalMemory() / 1000000;
2259         System.out.println();
2260         System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
2261         System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
2262         System.out.println( "Free memory       : " + free_memory + "MB, total memory: " + total_memory + "MB" );
2263         System.out.println();
2264         System.out.println( "If this application is useful to you, please cite:" );
2265         System.out.println( surfacing_hmmpfam.WWW );
2266         System.out.println();
2267         ForesterUtil.programMessage( PRG_NAME, "OK" );
2268         System.out.println();
2269     }
2270
2271     private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
2272                                                               final String[][] input_file_properties ) {
2273         final String[] genomes = new String[ input_file_properties.length ];
2274         for( int i = 0; i < input_file_properties.length; ++i ) {
2275             if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
2276                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2277                         + "] is not unique in input tree " + intree.getName() );
2278             }
2279             genomes[ i ] = input_file_properties[ i ][ 1 ];
2280         }
2281         PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
2282         for( int i = 0; i < input_file_properties.length; ++i ) {
2283             try {
2284                 intree.getNode( input_file_properties[ i ][ 1 ] );
2285             }
2286             catch ( final IllegalArgumentException e ) {
2287                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
2288                         + "] not present/not unique in input tree" );
2289             }
2290         }
2291     }
2292
2293     // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
2294     // final SortedMap<String, CombinableDomains> map ) {
2295     // final StringBuffer sb = new StringBuffer();
2296     // for( final Iterator<String> iter = map.keySet().iterator();
2297     // iter.hasNext(); ) {
2298     // final Object key = iter.next();
2299     // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ',
2300     // false ) );
2301     // final CombinableDomains domain_combination = map.get( key );
2302     // sb.append( ForesterUtil.pad( new StringBuffer( "" +
2303     // domain_combination.getNumberOfCombiningDomains() ), 8,
2304     // ' ', false ) );
2305     // sb.append( domain_combination.toStringBuffer() );
2306     // sb.append( ForesterUtil.getLineSeparator() );
2307     // }
2308     // return sb;
2309     // }
2310     private static void printHelp() {
2311         System.out.println();
2312         System.out.println( "Usage:" );
2313         System.out.println();
2314         System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications."
2315                 + surfacing_hmmpfam.PRG_NAME
2316                 + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
2317         System.out.println();
2318         System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
2319         System.out
2320                 .println( "       hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
2321         System.out.println();
2322         System.out.println( " Options: " );
2323         System.out.println( surfacing_hmmpfam.DETAILEDNESS_OPTION
2324                 + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" );
2325         System.out.println( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION
2326                 + ": to ignore combinations with self (default: not to ignore)" );
2327         System.out
2328                 .println( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
2329                         + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2330         System.out
2331                 .println( surfacing_hmmpfam.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
2332                         + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
2333         System.out.println( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION
2334                 + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
2335         System.out
2336                 .println( surfacing_hmmpfam.IGNORE_VIRAL_IDS
2337                         + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
2338         System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
2339                 + DOMAIN_SORT_FILD_DEFAULT + ")" );
2340         System.out.println( surfacing_hmmpfam.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
2341         System.out.println( surfacing_hmmpfam.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
2342         System.out.println( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
2343         System.out.println( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION
2344                 + ": to ignore engulfed lower confidence domains" );
2345         System.out.println( surfacing_hmmpfam.SPECIES_MATRIX_OPTION + ": species matrix" );
2346         System.out.println( surfacing_hmmpfam.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
2347         System.out.println( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
2348                 + DOMAINS_SORT_ORDER_DEFAULT + ")" );
2349         System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION
2350                 + ": domain similarity print option (default:" + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
2351         System.out.println( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
2352         System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
2353                 + ": sort by species count first" );
2354         System.out.println( surfacing_hmmpfam.OUTPUT_DIR_OPTION + ": output directory" );
2355         System.out.println( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
2356         System.out.println( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
2357         System.out.println( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
2358         System.out.println( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
2359                 + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
2360         System.out.println( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
2361                 + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
2362         System.out.println( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION
2363                 + ": to display multiple histograms (using fluorite)" );
2364         System.out
2365                 .println( JACKNIFE_OPTION
2366                         + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
2367                         + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
2368         System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
2369                 + JACKNIFE_RATIO_DEFAULT + "]" );
2370         System.out.println( JACKNIFE_RANDOM_SEED_OPTION
2371                 + ": seed for random number generator for jacknife resampling [default: "
2372                 + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
2373         //        System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
2374         //                + ": to infer NJ species trees based on shared domains/binary domain combinations" );
2375         System.out
2376                 .println( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
2377                         + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
2378         System.out.println( surfacing_hmmpfam.FILTER_POSITIVE_OPTION
2379                 + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
2380         System.out.println( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION
2381                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
2382         System.out.println( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION
2383                 + "=<file>: to filter out (ignore) domains listed in <file>" );
2384         System.out
2385                 .println( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
2386         System.out
2387                 .println( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
2388                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
2389         System.out.println( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
2390                 + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
2391         System.out.println( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
2392                 + ": to consider directedness and adjacency in binary combinations" );
2393         System.out
2394                 .println( surfacing_hmmpfam.SEQ_EXTRACT_OPTION
2395                         + "=<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')" );
2396         System.out.println( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
2397                 + "=<file>: to perfom parsimony analysis on secondary features" );
2398         System.out.println( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION
2399                 + "=<file>: to presence/absence genome analysis" );
2400         System.out.println( surfacing_hmmpfam.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
2401                 + ": to output binary domain combinations for (downstream) graph analysis" );
2402         System.out.println( surfacing_hmmpfam.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS
2403                 + ": to output all proteins per domain" );
2404         System.out.println();
2405         System.out.println();
2406         System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
2407                 + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
2408                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
2409                 + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
2410                 + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
2411                 + "=50 human mouse brafl strpu" );
2412         System.out.println();
2413     }
2414
2415     private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
2416         SortedSet<String> filter_str = null;
2417         try {
2418             filter_str = ForesterUtil.file2set( filter_file );
2419         }
2420         catch ( final IOException e ) {
2421             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
2422         }
2423         if ( filter_str != null ) {
2424             for( final String string : filter_str ) {
2425                 filter.add( new DomainId( string ) );
2426             }
2427         }
2428         if ( VERBOSE ) {
2429             System.out.println( "Filter:" );
2430             for( final DomainId domainId : filter ) {
2431                 System.out.println( domainId.getId() );
2432             }
2433         }
2434     }
2435
2436     private static String[][] processInputFileNames( final String[] names ) {
2437         final String[][] input_file_properties = new String[ names.length ][];
2438         for( int i = 0; i < names.length; ++i ) {
2439             if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
2440                 input_file_properties[ i ] = new String[ 3 ];
2441                 input_file_properties[ i ][ 0 ] = names[ i ];
2442                 input_file_properties[ i ][ 1 ] = names[ i ];
2443                 input_file_properties[ i ][ 2 ] = DEFAULT_SEARCH_PARAMETER;
2444             }
2445             else {
2446                 input_file_properties[ i ] = names[ i ].split( surfacing_hmmpfam.SEPARATOR_FOR_INPUT_VALUES + "" );
2447                 if ( input_file_properties[ i ].length != 3 ) {
2448                     ForesterUtil
2449                             .fatalError( surfacing_hmmpfam.PRG_NAME,
2450                                          "properties for the input files (hmmpfam output) are expected "
2451                                                  + "to be in the following format \"<hmmpfam output file>#<species>#<search"
2452                                                  + " parameter>\" (or just one word, which is both the filename and the species id), instead received \""
2453                                                  + names[ i ] + "\"" );
2454                 }
2455             }
2456             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
2457             if ( !ForesterUtil.isEmpty( error ) ) {
2458                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, error );
2459             }
2460         }
2461         return input_file_properties;
2462     }
2463
2464     private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
2465                                                         final List<String> high_copy_base,
2466                                                         final List<String> high_copy_target,
2467                                                         final List<String> low_copy,
2468                                                         final List<Object> numbers ) {
2469         if ( cla.isOptionSet( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2470             if ( !cla.isOptionValueSet( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) ) {
2471                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for 'plus-minus' file: -"
2472                         + surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
2473             }
2474             final File plus_minus_file = new File( cla.getOptionValue( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) );
2475             final String msg = ForesterUtil.isReadableFile( plus_minus_file );
2476             if ( !ForesterUtil.isEmpty( msg ) ) {
2477                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + plus_minus_file + "\": "
2478                         + msg );
2479             }
2480             processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
2481         }
2482     }
2483
2484     // First numbers is minimal difference, second is factor.
2485     private static void processPlusMinusFile( final File plus_minus_file,
2486                                               final List<String> high_copy_base,
2487                                               final List<String> high_copy_target,
2488                                               final List<String> low_copy,
2489                                               final List<Object> numbers ) {
2490         Set<String> species_set = null;
2491         int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
2492         double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
2493         try {
2494             species_set = ForesterUtil.file2set( plus_minus_file );
2495         }
2496         catch ( final IOException e ) {
2497             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
2498         }
2499         if ( species_set != null ) {
2500             for( final String species : species_set ) {
2501                 final String species_trimmed = species.substring( 1 );
2502                 if ( species.startsWith( "+" ) ) {
2503                     if ( low_copy.contains( species_trimmed ) ) {
2504                         ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
2505                                                  "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
2506                                                          + species_trimmed + "\"" );
2507                     }
2508                     high_copy_base.add( species_trimmed );
2509                 }
2510                 else if ( species.startsWith( "*" ) ) {
2511                     if ( low_copy.contains( species_trimmed ) ) {
2512                         ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
2513                                                  "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
2514                                                          + species_trimmed + "\"" );
2515                     }
2516                     high_copy_target.add( species_trimmed );
2517                 }
2518                 else if ( species.startsWith( "-" ) ) {
2519                     if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
2520                         ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
2521                                                  "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
2522                                                          + species_trimmed + "\"" );
2523                     }
2524                     low_copy.add( species_trimmed );
2525                 }
2526                 else if ( species.startsWith( "$D" ) ) {
2527                     try {
2528                         min_diff = Integer.parseInt( species.substring( 3 ) );
2529                     }
2530                     catch ( final NumberFormatException e ) {
2531                         ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
2532                                                  "could not parse integer value for minimal difference from: \""
2533                                                          + species.substring( 3 ) + "\"" );
2534                     }
2535                 }
2536                 else if ( species.startsWith( "$F" ) ) {
2537                     try {
2538                         factor = Double.parseDouble( species.substring( 3 ) );
2539                     }
2540                     catch ( final NumberFormatException e ) {
2541                         ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
2542                                                  "could not parse double value for factor from: \""
2543                                                          + species.substring( 3 ) + "\"" );
2544                     }
2545                 }
2546                 else if ( species.startsWith( "#" ) ) {
2547                     // Comment, ignore.
2548                 }
2549                 else {
2550                     ForesterUtil
2551                             .fatalError( surfacing_hmmpfam.PRG_NAME,
2552                                          "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
2553                                                  + species + "\"" );
2554                 }
2555                 numbers.add( new Integer( min_diff + "" ) );
2556                 numbers.add( new Double( factor + "" ) );
2557             }
2558         }
2559         else {
2560             ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "'plus minus' file [" + plus_minus_file
2561                     + "] appears empty" );
2562         }
2563     }
2564
2565     private static void writeProteinListsForAllSpecies( final File output_dir,
2566                                                         final SortedMap<Species, List<Protein>> protein_lists_per_species,
2567                                                         final List<GenomeWideCombinableDomains> gwcd_list ) {
2568         final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
2569         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2570             all_domains.addAll( gwcd.getAllDomainIds() );
2571         }
2572         for( final DomainId domain : all_domains ) {
2573             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
2574             SurfacingUtil.checkForOutputFileWriteability( out );
2575             try {
2576                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2577                 SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
2578                 proteins_file_writer.close();
2579             }
2580             catch ( final IOException e ) {
2581                 ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getLocalizedMessage() );
2582             }
2583             ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2584         }
2585     }
2586 }