Class SurfacingUtil

Method Details

• addAllBinaryDomainCombinationToSet

  public static void addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations)

• addAllDomainIdsToSet

  public static void addAllDomainIdsToSet(GenomeWideCombinableDomains genome, SortedSet<String> domain_ids)

• calculateDescriptiveStatisticsForMeanValues

  public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities)

• checkForOutputFileWriteability

  public static void checkForOutputFileWriteability(File outfile)

• checkWriteabilityForPairwiseComparisons

  public static void checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, String[][] input_file_properties, String automated_pairwise_comparison_suffix, File outdir)

• collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile

  public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)

• createDomainIdToGoIdMap

  public static Map<String,List<GoId>> createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings)

• createDomainIdToSecondaryFeaturesMap

  public static Map<String,Set<String>> createDomainIdToSecondaryFeaturesMap(File secondary_features_map_file) throws IOException

  Throws:

  IOException

• createNjTreeBasedOnMatrixToFile

  public static Phylogeny createNjTreeBasedOnMatrixToFile(File nj_tree_outfile, DistanceMatrix distance)

• createParametersAsString

  public static StringBuilder createParametersAsString(boolean ignore_dufs, double ie_value_max, double fs_e_value_max, int max_allowed_overlap, boolean no_engulfing_overlaps, File cutoff_scores_file, BinaryDomainCombination.DomainCombinationType dc_type)

• createSplitWriters

  public static void createSplitWriters(File out_dir, String my_outfile, Map<Character,Writer> split_writers) throws IOException

  Throws:

  IOException

• createTaxCodeToIdMap

  public static Map<String,Integer> createTaxCodeToIdMap(Phylogeny phy)

• decoratePrintableDomainSimilarities

  public static void decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness)

• doit

  public static void doit(List<Protein> proteins, List<String> query_domain_ids_nc_order, Writer out, String separator, String limit_to_species, Map<String,List<Integer>> average_protein_lengths_by_dc) throws IOException

  Throws:

  IOException

• domainsPerProteinsStatistics

  public static void domainsPerProteinsStatistics(String genome, List<Protein> protein_list, DescriptiveStatistics all_genomes_domains_per_potein_stats, SortedMap<Integer,Integer> all_genomes_domains_per_potein_histo, SortedSet<String> domains_which_are_always_single, SortedSet<String> domains_which_are_sometimes_single_sometimes_not, SortedSet<String> domains_which_never_single, Writer writer)

• executeDomainLengthAnalysis

  public static void executeDomainLengthAnalysis(String[][] input_file_properties, int number_of_genomes, DomainLengthsTable domain_lengths_table, File outfile) throws IOException

  Throws:

  IOException

• executeFitchGainsAnalysis

  public static void executeFitchGainsAnalysis(File output_file, List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis) throws IOException

  Warning: This side-effects 'all_bin_domain_combinations_encountered'!

  Parameters:

  output_file -

  all_bin_domain_combinations_changed -

  sum_of_all_domains_encountered -

  all_bin_domain_combinations_encountered -

  is_gains_analysis -

  protein_length_stats_by_dc -

  Throws:

  IOException

• executeParsimonyAnalysis

  public static void executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc, Map<String,DescriptiveStatistics> domain_length_stats_by_domain, Map<String,Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)

  Parameters:

  all_binary_domains_combination_lost_fitch -

  use_last_in_fitch_parsimony -

  perform_dc_fich -

  consider_directedness_and_adjacency_for_bin_combinations -

  all_binary_domains_combination_gained - if null ignored, otherwise this is to list all binary domain combinations which were gained under unweighted (Fitch) parsimony.

• executeParsimonyAnalysisForSecondaryFeatures

  public static void executeParsimonyAnalysisForSecondaryFeatures(String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, String parameters_str, Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)

• executePlusMinusAnalysis

  public static void executePlusMinusAnalysis(File output_file, List<String> plus_minus_analysis_high_copy_base, List<String> plus_minus_analysis_high_copy_target, List<String> plus_minus_analysis_low_copy, List<GenomeWideCombinableDomains> gwcd_list, SortedMap<Species,List<Protein>> protein_lists_per_species, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, List<Object> plus_minus_analysis_numbers)

• extractProteinNames

  public static void extractProteinNames(List<Protein> proteins, List<String> query_domain_ids_nc_order, Writer out, String separator, String limit_to_species) throws IOException

  Throws:

  IOException

• extractProteinNames

  public static void extractProteinNames(SortedMap<Species,List<Protein>> protein_lists_per_species, String domain_id, Writer out, String separator, String limit_to_species, double domain_e_cutoff) throws IOException

  Throws:

  IOException

• getAllDomainIds

  public static SortedSet<String> getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list)

• getDomainCounts

  public static SortedMap<String,Integer> getDomainCounts(List<Protein> protein_domain_collections)

• getNumberOfNodesLackingName

  public static int getNumberOfNodesLackingName(Phylogeny p, StringBuilder names)

• log

  public static void log(String msg, Writer w)

• obtainAndPreProcessIntrees

  public static Phylogeny[] obtainAndPreProcessIntrees(File[] intree_files, int number_of_genomes, String[][] input_file_properties)

• obtainFirstIntree

  public static Phylogeny obtainFirstIntree(File intree_file)

• obtainHexColorStringDependingOnTaxonomyGroup

  public static String obtainHexColorStringDependingOnTaxonomyGroup(String tax_code, Phylogeny phy) throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• obtainTaxonomyGroup

  public static String obtainTaxonomyGroup(String tax_code, Phylogeny species_tree) throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• performDomainArchitectureAnalysis

  public static void performDomainArchitectureAnalysis(SortedMap<String,Set<String>> domain_architecutures, SortedMap<String,Integer> domain_architecuture_counts, int min_count, File da_counts_outfile, File unique_da_outfile)

• preparePhylogeny

  public static void preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, String date_time, String method, String name, String parameters_str)

• preparePhylogenyForParsimonyAnalyses

  public static void preparePhylogenyForParsimonyAnalyses(Phylogeny intree, String[][] input_file_properties)

• printOutPercentageOfMultidomainProteins

  public static void printOutPercentageOfMultidomainProteins(SortedMap<Integer,Integer> all_genomes_domains_per_potein_histo, Writer log_writer)

• processFilter

  public static void processFilter(File filter_file, SortedSet<String> filter)

• processInputGenomesFile

  public static String[][] processInputGenomesFile(File input_genomes)

• processPlusMinusAnalysisOption

  public static void processPlusMinusAnalysisOption(CommandLineArguments cla, List<String> high_copy_base, List<String> high_copy_target, List<String> low_copy, List<Object> numbers)

• processPlusMinusFile

  public static void processPlusMinusFile(File plus_minus_file, List<String> high_copy_base, List<String> high_copy_target, List<String> low_copy, List<Object> numbers)

• proteinToDomainCombinations

  public static StringBuffer proteinToDomainCombinations(Protein protein, String protein_id, String separator)

• sortDomainsWithAscendingConfidenceValues

  public static List<Domain> sortDomainsWithAscendingConfidenceValues(Protein protein)

• storeDomainArchitectures

  public static int storeDomainArchitectures(String genome, SortedMap<String,Set<String>> domain_architecutures, List<Protein> protein_list, Map<String,Integer> distinct_domain_architecuture_counts)

• writeAllDomainsChangedOnAllSubtrees

  public static void writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, String outdir, String suffix_for_filename) throws IOException

  Throws:

  IOException

• writeBinaryDomainCombinationsFileForGraphAnalysis

  public static void writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties, File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)

• writeBinaryStatesMatrixAsListToFile

  public static void writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, Map<String,String> descriptions)

• writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis

  public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, BinaryDomainCombination.OutputFormat bc_output_format)

• writeBinaryStatesMatrixToList

  public static void writeBinaryStatesMatrixToList(Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, String title_for_html, String prefix_for_html, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> all_pfams_encountered, SortedSet<String> pfams_gained_or_lost, String suffix_for_per_node_events_file, Map<String,Integer> tax_code_to_id_map)

• writeDomainCombinationsCountsFile

  public static void writeDomainCombinationsCountsFile(String[][] input_file_properties, File output_dir, Writer per_genome_domain_promiscuity_statistics_writer, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)

• writeDomainSimilaritiesToFile

  public static void writeDomainSimilaritiesToFile(StringBuilder html_desc, StringBuilder html_title, Writer simple_tab_writer, Writer single_writer, Map<Character,Writer> split_writers, SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, Map<String,Integer> tax_code_to_id_map, Phylogeny phy, Set<String> pos_filter_doms) throws IOException

  Throws:

  IOException

• writeHtmlHead

  public static void writeHtmlHead(Writer w, String title) throws IOException

  Throws:

  IOException

• writeMatrixToFile

  public static void writeMatrixToFile(CharacterStateMatrix<?> matrix, String filename, CharacterStateMatrix.Format format)

• writeMatrixToFile

  public static void writeMatrixToFile(File matrix_outfile, List<DistanceMatrix> matrices)

• writePhylogenyToFile

  public static void writePhylogenyToFile(Phylogeny phylogeny, String filename)

• writePresentToNexus

  public static void writePresentToNexus(File output_file, File positive_filter_file, SortedSet<String> filter, List<GenomeWideCombinableDomains> gwcd_list)

• writeProteinListsForAllSpecies

  public static void writeProteinListsForAllSpecies(File output_dir, SortedMap<Species,List<Protein>> protein_lists_per_species, List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, Set<String> pos_filter_doms)

• writeTaxonomyLinks

  public static void writeTaxonomyLinks(Writer writer, String species, Map<String,Integer> tax_code_to_id_map) throws IOException

  Throws:

  IOException