Package org.forester.surfacing
Class SurfacingUtil
- java.lang.Object
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- org.forester.surfacing.SurfacingUtil
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public final class SurfacingUtil extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.util.regex.Pattern
PATTERN_SP_STYLE_TAXONOMY
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<BinaryDomainCombination> binary_domain_combinations)
static void
addAllDomainIdsToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<java.lang.String> domain_ids)
static DescriptiveStatistics
calculateDescriptiveStatisticsForMeanValues(java.util.Set<DomainSimilarity> similarities)
static void
checkForOutputFileWriteability(java.io.File outfile)
static void
checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, java.lang.String[][] input_file_properties, java.lang.String automated_pairwise_comparison_suffix, java.io.File outdir)
static void
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
static java.util.Map<java.lang.String,java.util.List<GoId>>
createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings)
static java.util.Map<java.lang.String,java.util.Set<java.lang.String>>
createDomainIdToSecondaryFeaturesMap(java.io.File secondary_features_map_file)
static Phylogeny
createNjTreeBasedOnMatrixToFile(java.io.File nj_tree_outfile, DistanceMatrix distance)
static java.lang.StringBuilder
createParametersAsString(boolean ignore_dufs, double ie_value_max, double fs_e_value_max, int max_allowed_overlap, boolean no_engulfing_overlaps, java.io.File cutoff_scores_file, BinaryDomainCombination.DomainCombinationType dc_type)
static void
createSplitWriters(java.io.File out_dir, java.lang.String my_outfile, java.util.Map<java.lang.Character,java.io.Writer> split_writers)
static java.util.Map<java.lang.String,java.lang.Integer>
createTaxCodeToIdMap(Phylogeny phy)
static void
decoratePrintableDomainSimilarities(java.util.SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness)
static void
doit(java.util.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, java.util.Map<java.lang.String,java.util.List<java.lang.Integer>> average_protein_lengths_by_dc)
static void
domainsPerProteinsStatistics(java.lang.String genome, java.util.List<Protein> protein_list, DescriptiveStatistics all_genomes_domains_per_potein_stats, java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.util.SortedSet<java.lang.String> domains_which_are_always_single, java.util.SortedSet<java.lang.String> domains_which_are_sometimes_single_sometimes_not, java.util.SortedSet<java.lang.String> domains_which_never_single, java.io.Writer writer)
static void
executeDomainLengthAnalysis(java.lang.String[][] input_file_properties, int number_of_genomes, DomainLengthsTable domain_lengths_table, java.io.File outfile)
static void
executeFitchGainsAnalysis(java.io.File output_file, java.util.List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, java.util.SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis)
Warning: This side-effects 'all_bin_domain_combinations_encountered'!static void
executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, java.lang.String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, java.lang.String parameters_str, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> positive_filter, boolean output_binary_domain_combinations_for_graphs, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, java.util.List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, java.util.Map<java.lang.String,DescriptiveStatistics> protein_length_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_number_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_length_stats_by_domain, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
static void
executeParsimonyAnalysisForSecondaryFeatures(java.lang.String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, java.lang.String parameters_str, java.util.Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
static void
executePlusMinusAnalysis(java.io.File output_file, java.util.List<java.lang.String> plus_minus_analysis_high_copy_base, java.util.List<java.lang.String> plus_minus_analysis_high_copy_target, java.util.List<java.lang.String> plus_minus_analysis_low_copy, java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, java.util.List<java.lang.Object> plus_minus_analysis_numbers)
static void
extractProteinNames(java.util.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species)
static void
extractProteinNames(java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.lang.String domain_id, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, double domain_e_cutoff)
static java.util.SortedSet<java.lang.String>
getAllDomainIds(java.util.List<GenomeWideCombinableDomains> gwcd_list)
static java.util.SortedMap<java.lang.String,java.lang.Integer>
getDomainCounts(java.util.List<Protein> protein_domain_collections)
static int
getNumberOfNodesLackingName(Phylogeny p, java.lang.StringBuilder names)
static void
log(java.lang.String msg, java.io.Writer w)
static Phylogeny[]
obtainAndPreProcessIntrees(java.io.File[] intree_files, int number_of_genomes, java.lang.String[][] input_file_properties)
static Phylogeny
obtainFirstIntree(java.io.File intree_file)
static java.lang.String
obtainHexColorStringDependingOnTaxonomyGroup(java.lang.String tax_code, Phylogeny phy)
static java.lang.String
obtainTaxonomyGroup(java.lang.String tax_code, Phylogeny species_tree)
static void
performDomainArchitectureAnalysis(java.util.SortedMap<java.lang.String,java.util.Set<java.lang.String>> domain_architecutures, java.util.SortedMap<java.lang.String,java.lang.Integer> domain_architecuture_counts, int min_count, java.io.File da_counts_outfile, java.io.File unique_da_outfile)
static void
preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, java.lang.String date_time, java.lang.String method, java.lang.String name, java.lang.String parameters_str)
static void
preparePhylogenyForParsimonyAnalyses(Phylogeny intree, java.lang.String[][] input_file_properties)
static void
printOutPercentageOfMultidomainProteins(java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.io.Writer log_writer)
static void
processFilter(java.io.File filter_file, java.util.SortedSet<java.lang.String> filter)
static java.lang.String[][]
processInputGenomesFile(java.io.File input_genomes)
static void
processPlusMinusAnalysisOption(CommandLineArguments cla, java.util.List<java.lang.String> high_copy_base, java.util.List<java.lang.String> high_copy_target, java.util.List<java.lang.String> low_copy, java.util.List<java.lang.Object> numbers)
static void
processPlusMinusFile(java.io.File plus_minus_file, java.util.List<java.lang.String> high_copy_base, java.util.List<java.lang.String> high_copy_target, java.util.List<java.lang.String> low_copy, java.util.List<java.lang.Object> numbers)
static java.lang.StringBuffer
proteinToDomainCombinations(Protein protein, java.lang.String protein_id, java.lang.String separator)
static java.util.List<Domain>
sortDomainsWithAscendingConfidenceValues(Protein protein)
static int
storeDomainArchitectures(java.lang.String genome, java.util.SortedMap<java.lang.String,java.util.Set<java.lang.String>> domain_architecutures, java.util.List<Protein> protein_list, java.util.Map<java.lang.String,java.lang.Integer> distinct_domain_architecuture_counts)
static void
writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, java.lang.String outdir, java.lang.String suffix_for_filename)
static void
writeBinaryDomainCombinationsFileForGraphAnalysis(java.lang.String[][] input_file_properties, java.io.File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
static void
writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.util.Map<java.lang.String,java.lang.String> descriptions)
static void
writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, BinaryDomainCombination.OutputFormat bc_output_format)
static void
writeBinaryStatesMatrixToList(java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.lang.String title_for_html, java.lang.String prefix_for_html, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> all_pfams_encountered, java.util.SortedSet<java.lang.String> pfams_gained_or_lost, java.lang.String suffix_for_per_node_events_file, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map)
static void
writeDomainCombinationsCountsFile(java.lang.String[][] input_file_properties, java.io.File output_dir, java.io.Writer per_genome_domain_promiscuity_statistics_writer, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
static void
writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer simple_tab_writer, java.io.Writer single_writer, java.util.Map<java.lang.Character,java.io.Writer> split_writers, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy, java.util.Set<java.lang.String> pos_filter_doms)
static void
writeHtmlHead(java.io.Writer w, java.lang.String title)
static void
writeMatrixToFile(java.io.File matrix_outfile, java.util.List<DistanceMatrix> matrices)
static void
writeMatrixToFile(CharacterStateMatrix<?> matrix, java.lang.String filename, CharacterStateMatrix.Format format)
static void
writePhylogenyToFile(Phylogeny phylogeny, java.lang.String filename)
static void
writePresentToNexus(java.io.File output_file, java.io.File positive_filter_file, java.util.SortedSet<java.lang.String> filter, java.util.List<GenomeWideCombinableDomains> gwcd_list)
static void
writeProteinListsForAllSpecies(java.io.File output_dir, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, java.util.Set<java.lang.String> pos_filter_doms)
static void
writeTaxonomyLinks(java.io.Writer writer, java.lang.String species, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map)
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Method Detail
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addAllBinaryDomainCombinationToSet
public static void addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<BinaryDomainCombination> binary_domain_combinations)
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addAllDomainIdsToSet
public static void addAllDomainIdsToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<java.lang.String> domain_ids)
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calculateDescriptiveStatisticsForMeanValues
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(java.util.Set<DomainSimilarity> similarities)
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checkForOutputFileWriteability
public static void checkForOutputFileWriteability(java.io.File outfile)
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checkWriteabilityForPairwiseComparisons
public static void checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, java.lang.String[][] input_file_properties, java.lang.String automated_pairwise_comparison_suffix, java.io.File outdir)
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collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
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createDomainIdToGoIdMap
public static java.util.Map<java.lang.String,java.util.List<GoId>> createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings)
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createDomainIdToSecondaryFeaturesMap
public static java.util.Map<java.lang.String,java.util.Set<java.lang.String>> createDomainIdToSecondaryFeaturesMap(java.io.File secondary_features_map_file) throws java.io.IOException
- Throws:
java.io.IOException
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createNjTreeBasedOnMatrixToFile
public static Phylogeny createNjTreeBasedOnMatrixToFile(java.io.File nj_tree_outfile, DistanceMatrix distance)
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createParametersAsString
public static java.lang.StringBuilder createParametersAsString(boolean ignore_dufs, double ie_value_max, double fs_e_value_max, int max_allowed_overlap, boolean no_engulfing_overlaps, java.io.File cutoff_scores_file, BinaryDomainCombination.DomainCombinationType dc_type)
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createSplitWriters
public static void createSplitWriters(java.io.File out_dir, java.lang.String my_outfile, java.util.Map<java.lang.Character,java.io.Writer> split_writers) throws java.io.IOException
- Throws:
java.io.IOException
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createTaxCodeToIdMap
public static java.util.Map<java.lang.String,java.lang.Integer> createTaxCodeToIdMap(Phylogeny phy)
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decoratePrintableDomainSimilarities
public static void decoratePrintableDomainSimilarities(java.util.SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness)
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doit
public static void doit(java.util.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, java.util.Map<java.lang.String,java.util.List<java.lang.Integer>> average_protein_lengths_by_dc) throws java.io.IOException
- Throws:
java.io.IOException
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domainsPerProteinsStatistics
public static void domainsPerProteinsStatistics(java.lang.String genome, java.util.List<Protein> protein_list, DescriptiveStatistics all_genomes_domains_per_potein_stats, java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.util.SortedSet<java.lang.String> domains_which_are_always_single, java.util.SortedSet<java.lang.String> domains_which_are_sometimes_single_sometimes_not, java.util.SortedSet<java.lang.String> domains_which_never_single, java.io.Writer writer)
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executeDomainLengthAnalysis
public static void executeDomainLengthAnalysis(java.lang.String[][] input_file_properties, int number_of_genomes, DomainLengthsTable domain_lengths_table, java.io.File outfile) throws java.io.IOException
- Throws:
java.io.IOException
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executeFitchGainsAnalysis
public static void executeFitchGainsAnalysis(java.io.File output_file, java.util.List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, java.util.SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis) throws java.io.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:
java.io.IOException
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executeParsimonyAnalysis
public static void executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, java.lang.String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, java.lang.String parameters_str, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> positive_filter, boolean output_binary_domain_combinations_for_graphs, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, java.util.List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, java.util.Map<java.lang.String,DescriptiveStatistics> protein_length_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_number_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_length_stats_by_domain, java.util.Map<java.lang.String,java.lang.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.
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executeParsimonyAnalysisForSecondaryFeatures
public static void executeParsimonyAnalysisForSecondaryFeatures(java.lang.String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, java.lang.String parameters_str, java.util.Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
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executePlusMinusAnalysis
public static void executePlusMinusAnalysis(java.io.File output_file, java.util.List<java.lang.String> plus_minus_analysis_high_copy_base, java.util.List<java.lang.String> plus_minus_analysis_high_copy_target, java.util.List<java.lang.String> plus_minus_analysis_low_copy, java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, java.util.List<java.lang.Object> plus_minus_analysis_numbers)
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extractProteinNames
public static void extractProteinNames(java.util.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species) throws java.io.IOException
- Throws:
java.io.IOException
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extractProteinNames
public static void extractProteinNames(java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.lang.String domain_id, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, double domain_e_cutoff) throws java.io.IOException
- Throws:
java.io.IOException
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getAllDomainIds
public static java.util.SortedSet<java.lang.String> getAllDomainIds(java.util.List<GenomeWideCombinableDomains> gwcd_list)
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getDomainCounts
public static java.util.SortedMap<java.lang.String,java.lang.Integer> getDomainCounts(java.util.List<Protein> protein_domain_collections)
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getNumberOfNodesLackingName
public static int getNumberOfNodesLackingName(Phylogeny p, java.lang.StringBuilder names)
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log
public static void log(java.lang.String msg, java.io.Writer w)
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obtainAndPreProcessIntrees
public static Phylogeny[] obtainAndPreProcessIntrees(java.io.File[] intree_files, int number_of_genomes, java.lang.String[][] input_file_properties)
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obtainFirstIntree
public static Phylogeny obtainFirstIntree(java.io.File intree_file)
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obtainHexColorStringDependingOnTaxonomyGroup
public static java.lang.String obtainHexColorStringDependingOnTaxonomyGroup(java.lang.String tax_code, Phylogeny phy) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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obtainTaxonomyGroup
public static java.lang.String obtainTaxonomyGroup(java.lang.String tax_code, Phylogeny species_tree) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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performDomainArchitectureAnalysis
public static void performDomainArchitectureAnalysis(java.util.SortedMap<java.lang.String,java.util.Set<java.lang.String>> domain_architecutures, java.util.SortedMap<java.lang.String,java.lang.Integer> domain_architecuture_counts, int min_count, java.io.File da_counts_outfile, java.io.File unique_da_outfile)
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preparePhylogeny
public static void preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, java.lang.String date_time, java.lang.String method, java.lang.String name, java.lang.String parameters_str)
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preparePhylogenyForParsimonyAnalyses
public static void preparePhylogenyForParsimonyAnalyses(Phylogeny intree, java.lang.String[][] input_file_properties)
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printOutPercentageOfMultidomainProteins
public static void printOutPercentageOfMultidomainProteins(java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.io.Writer log_writer)
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processFilter
public static void processFilter(java.io.File filter_file, java.util.SortedSet<java.lang.String> filter)
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processInputGenomesFile
public static java.lang.String[][] processInputGenomesFile(java.io.File input_genomes)
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processPlusMinusAnalysisOption
public static void processPlusMinusAnalysisOption(CommandLineArguments cla, java.util.List<java.lang.String> high_copy_base, java.util.List<java.lang.String> high_copy_target, java.util.List<java.lang.String> low_copy, java.util.List<java.lang.Object> numbers)
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processPlusMinusFile
public static void processPlusMinusFile(java.io.File plus_minus_file, java.util.List<java.lang.String> high_copy_base, java.util.List<java.lang.String> high_copy_target, java.util.List<java.lang.String> low_copy, java.util.List<java.lang.Object> numbers)
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proteinToDomainCombinations
public static java.lang.StringBuffer proteinToDomainCombinations(Protein protein, java.lang.String protein_id, java.lang.String separator)
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sortDomainsWithAscendingConfidenceValues
public static java.util.List<Domain> sortDomainsWithAscendingConfidenceValues(Protein protein)
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storeDomainArchitectures
public static int storeDomainArchitectures(java.lang.String genome, java.util.SortedMap<java.lang.String,java.util.Set<java.lang.String>> domain_architecutures, java.util.List<Protein> protein_list, java.util.Map<java.lang.String,java.lang.Integer> distinct_domain_architecuture_counts)
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writeAllDomainsChangedOnAllSubtrees
public static void writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, java.lang.String outdir, java.lang.String suffix_for_filename) throws java.io.IOException
- Throws:
java.io.IOException
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writeBinaryDomainCombinationsFileForGraphAnalysis
public static void writeBinaryDomainCombinationsFileForGraphAnalysis(java.lang.String[][] input_file_properties, java.io.File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
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writeBinaryStatesMatrixAsListToFile
public static void writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.util.Map<java.lang.String,java.lang.String> descriptions)
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writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis
public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, BinaryDomainCombination.OutputFormat bc_output_format)
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writeBinaryStatesMatrixToList
public static void writeBinaryStatesMatrixToList(java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.lang.String title_for_html, java.lang.String prefix_for_html, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> all_pfams_encountered, java.util.SortedSet<java.lang.String> pfams_gained_or_lost, java.lang.String suffix_for_per_node_events_file, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map)
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writeDomainCombinationsCountsFile
public static void writeDomainCombinationsCountsFile(java.lang.String[][] input_file_properties, java.io.File output_dir, java.io.Writer per_genome_domain_promiscuity_statistics_writer, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
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writeDomainSimilaritiesToFile
public static void writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer simple_tab_writer, java.io.Writer single_writer, java.util.Map<java.lang.Character,java.io.Writer> split_writers, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy, java.util.Set<java.lang.String> pos_filter_doms) throws java.io.IOException
- Throws:
java.io.IOException
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writeHtmlHead
public static void writeHtmlHead(java.io.Writer w, java.lang.String title) throws java.io.IOException
- Throws:
java.io.IOException
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writeMatrixToFile
public static void writeMatrixToFile(CharacterStateMatrix<?> matrix, java.lang.String filename, CharacterStateMatrix.Format format)
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writeMatrixToFile
public static void writeMatrixToFile(java.io.File matrix_outfile, java.util.List<DistanceMatrix> matrices)
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writePhylogenyToFile
public static void writePhylogenyToFile(Phylogeny phylogeny, java.lang.String filename)
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writePresentToNexus
public static void writePresentToNexus(java.io.File output_file, java.io.File positive_filter_file, java.util.SortedSet<java.lang.String> filter, java.util.List<GenomeWideCombinableDomains> gwcd_list)
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writeProteinListsForAllSpecies
public static void writeProteinListsForAllSpecies(java.io.File output_dir, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, java.util.Set<java.lang.String> pos_filter_doms)
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writeTaxonomyLinks
public static void writeTaxonomyLinks(java.io.Writer writer, java.lang.String species, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map) throws java.io.IOException
- Throws:
java.io.IOException
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