public final class SurfacingUtil
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.util.regex.Pattern |
PATTERN_SP_STYLE_TAXONOMY |
Modifier and Type | Method and 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(CharacterStateMatrix<?> matrix,
java.lang.String filename,
CharacterStateMatrix.Format format) |
static void |
writeMatrixToFile(java.io.File matrix_outfile,
java.util.List<DistanceMatrix> matrices) |
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) |
public static final java.util.regex.Pattern PATTERN_SP_STYLE_TAXONOMY
public static void addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<BinaryDomainCombination> binary_domain_combinations)
public static void addAllDomainIdsToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<java.lang.String> domain_ids)
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(java.util.Set<DomainSimilarity> similarities)
public static void checkForOutputFileWriteability(java.io.File outfile)
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)
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
public static java.util.Map<java.lang.String,java.util.List<GoId>> createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings)
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
java.io.IOException
public static Phylogeny createNjTreeBasedOnMatrixToFile(java.io.File nj_tree_outfile, DistanceMatrix distance)
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)
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
java.io.IOException
public static java.util.Map<java.lang.String,java.lang.Integer> createTaxCodeToIdMap(Phylogeny phy)
public static void decoratePrintableDomainSimilarities(java.util.SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness)
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
java.io.IOException
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)
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
java.io.IOException
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
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
- java.io.IOException
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)
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.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)
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)
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
java.io.IOException
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
java.io.IOException
public static java.util.SortedSet<java.lang.String> getAllDomainIds(java.util.List<GenomeWideCombinableDomains> gwcd_list)
public static java.util.SortedMap<java.lang.String,java.lang.Integer> getDomainCounts(java.util.List<Protein> protein_domain_collections)
public static int getNumberOfNodesLackingName(Phylogeny p, java.lang.StringBuilder names)
public static void log(java.lang.String msg, java.io.Writer w)
public static Phylogeny[] obtainAndPreProcessIntrees(java.io.File[] intree_files, int number_of_genomes, java.lang.String[][] input_file_properties)
public static Phylogeny obtainFirstIntree(java.io.File intree_file)
public static java.lang.String obtainHexColorStringDependingOnTaxonomyGroup(java.lang.String tax_code, Phylogeny phy) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
public static java.lang.String obtainTaxonomyGroup(java.lang.String tax_code, Phylogeny species_tree) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
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)
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)
public static void preparePhylogenyForParsimonyAnalyses(Phylogeny intree, java.lang.String[][] input_file_properties)
public static void printOutPercentageOfMultidomainProteins(java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.io.Writer log_writer)
public static void processFilter(java.io.File filter_file, java.util.SortedSet<java.lang.String> filter)
public static java.lang.String[][] processInputGenomesFile(java.io.File input_genomes)
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)
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)
public static java.lang.StringBuffer proteinToDomainCombinations(Protein protein, java.lang.String protein_id, java.lang.String separator)
public static java.util.List<Domain> sortDomainsWithAscendingConfidenceValues(Protein protein)
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)
public static void writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, java.lang.String outdir, java.lang.String suffix_for_filename) throws java.io.IOException
java.io.IOException
public static void writeBinaryDomainCombinationsFileForGraphAnalysis(java.lang.String[][] input_file_properties, java.io.File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
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)
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)
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)
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)
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
java.io.IOException
public static void writeHtmlHead(java.io.Writer w, java.lang.String title) throws java.io.IOException
java.io.IOException
public static void writeMatrixToFile(CharacterStateMatrix<?> matrix, java.lang.String filename, CharacterStateMatrix.Format format)
public static void writeMatrixToFile(java.io.File matrix_outfile, java.util.List<DistanceMatrix> matrices)
public static void writePhylogenyToFile(Phylogeny phylogeny, java.lang.String filename)
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)
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)
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
java.io.IOException