public final class SurfacingUtil extends Object
| Modifier and Type | Field and Description |
|---|---|
static Pattern |
PATTERN_SP_STYLE_TAXONOMY |
| Modifier and Type | Method and Description |
|---|---|
static void |
addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome,
SortedSet<BinaryDomainCombination> binary_domain_combinations) |
static void |
addAllDomainIdsToSet(GenomeWideCombinableDomains genome,
SortedSet<String> domain_ids) |
static DescriptiveStatistics |
calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities) |
static void |
checkForOutputFileWriteability(File outfile) |
static void |
checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
String[][] input_file_properties,
String automated_pairwise_comparison_suffix,
File outdir) |
static void |
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
BinaryDomainCombination.DomainCombinationType dc_type,
List<BinaryDomainCombination> all_binary_domains_combination_gained,
boolean get_gains) |
static Map<String,List<GoId>> |
createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings) |
static Map<String,Set<String>> |
createDomainIdToSecondaryFeaturesMap(File secondary_features_map_file) |
static Phylogeny |
createNjTreeBasedOnMatrixToFile(File nj_tree_outfile,
DistanceMatrix distance) |
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) |
static void |
createSplitWriters(File out_dir,
String my_outfile,
Map<Character,Writer> split_writers) |
static Map<String,Integer> |
createTaxCodeToIdMap(Phylogeny phy) |
static void |
decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity> domain_similarities,
DomainSimilarityCalculator.Detailedness detailedness) |
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) |
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) |
static void |
executeDomainLengthAnalysis(String[][] input_file_properties,
int number_of_genomes,
DomainLengthsTable domain_lengths_table,
File outfile) |
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)
Warning: This side-effects 'all_bin_domain_combinations_encountered'!
|
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) |
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) |
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) |
static void |
extractProteinNames(List<Protein> proteins,
List<String> query_domain_ids_nc_order,
Writer out,
String separator,
String limit_to_species) |
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) |
static SortedSet<String> |
getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list) |
static SortedMap<String,Integer> |
getDomainCounts(List<Protein> protein_domain_collections) |
static int |
getNumberOfNodesLackingName(Phylogeny p,
StringBuilder names) |
static void |
log(String msg,
Writer w) |
static Phylogeny[] |
obtainAndPreProcessIntrees(File[] intree_files,
int number_of_genomes,
String[][] input_file_properties) |
static Phylogeny |
obtainFirstIntree(File intree_file) |
static String |
obtainHexColorStringDependingOnTaxonomyGroup(String tax_code,
Phylogeny phy) |
static String |
obtainTaxonomyGroup(String tax_code,
Phylogeny species_tree) |
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) |
static void |
preparePhylogeny(Phylogeny p,
DomainParsimonyCalculator domain_parsimony,
String date_time,
String method,
String name,
String parameters_str) |
static void |
preparePhylogenyForParsimonyAnalyses(Phylogeny intree,
String[][] input_file_properties) |
static void |
printOutPercentageOfMultidomainProteins(SortedMap<Integer,Integer> all_genomes_domains_per_potein_histo,
Writer log_writer) |
static void |
processFilter(File filter_file,
SortedSet<String> filter) |
static String[][] |
processInputGenomesFile(File input_genomes) |
static void |
processPlusMinusAnalysisOption(CommandLineArguments cla,
List<String> high_copy_base,
List<String> high_copy_target,
List<String> low_copy,
List<Object> numbers) |
static void |
processPlusMinusFile(File plus_minus_file,
List<String> high_copy_base,
List<String> high_copy_target,
List<String> low_copy,
List<Object> numbers) |
static StringBuffer |
proteinToDomainCombinations(Protein protein,
String protein_id,
String separator) |
static List<Domain> |
sortDomainsWithAscendingConfidenceValues(Protein protein) |
static int |
storeDomainArchitectures(String genome,
SortedMap<String,Set<String>> domain_architecutures,
List<Protein> protein_list,
Map<String,Integer> distinct_domain_architecuture_counts) |
static void |
writeAllDomainsChangedOnAllSubtrees(Phylogeny p,
boolean get_gains,
String outdir,
String suffix_for_filename) |
static void |
writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties,
File output_dir,
GenomeWideCombinableDomains gwcd,
int i,
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order) |
static void |
writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
Map<String,String> descriptions) |
static void |
writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
BinaryDomainCombination.OutputFormat bc_output_format) |
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) |
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) |
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) |
static void |
writeHtmlHead(Writer w,
String title) |
static void |
writeMatrixToFile(CharacterStateMatrix<?> matrix,
String filename,
CharacterStateMatrix.Format format) |
static void |
writeMatrixToFile(File matrix_outfile,
List<DistanceMatrix> matrices) |
static void |
writePhylogenyToFile(Phylogeny phylogeny,
String filename) |
static void |
writePresentToNexus(File output_file,
File positive_filter_file,
SortedSet<String> filter,
List<GenomeWideCombinableDomains> gwcd_list) |
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) |
static void |
writeTaxonomyLinks(Writer writer,
String species,
Map<String,Integer> tax_code_to_id_map) |
public static final Pattern PATTERN_SP_STYLE_TAXONOMY
public static void addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations)
public static void addAllDomainIdsToSet(GenomeWideCombinableDomains genome, SortedSet<String> domain_ids)
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities)
public static void checkForOutputFileWriteability(File outfile)
public static void checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION domain_similarity_print_option, String[][] input_file_properties, String automated_pairwise_comparison_suffix, File outdir)
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
public static Map<String,List<GoId>> createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings)
public static Map<String,Set<String>> createDomainIdToSecondaryFeaturesMap(File secondary_features_map_file) throws IOException
IOExceptionpublic static Phylogeny createNjTreeBasedOnMatrixToFile(File nj_tree_outfile, DistanceMatrix distance)
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)
public static void createSplitWriters(File out_dir, String my_outfile, Map<Character,Writer> split_writers) throws IOException
IOExceptionpublic static void decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness)
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
IOExceptionpublic 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)
public static void executeDomainLengthAnalysis(String[][] input_file_properties, int number_of_genomes, DomainLengthsTable domain_lengths_table, File outfile) throws IOException
IOExceptionpublic 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
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 - IOExceptionpublic 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)
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(String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, String parameters_str, Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
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)
public static void extractProteinNames(List<Protein> proteins, List<String> query_domain_ids_nc_order, Writer out, String separator, String limit_to_species) throws IOException
IOExceptionpublic 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
IOExceptionpublic static SortedSet<String> getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list)
public static SortedMap<String,Integer> getDomainCounts(List<Protein> protein_domain_collections)
public static int getNumberOfNodesLackingName(Phylogeny p, StringBuilder names)
public static Phylogeny[] obtainAndPreProcessIntrees(File[] intree_files, int number_of_genomes, String[][] input_file_properties)
public static String obtainHexColorStringDependingOnTaxonomyGroup(String tax_code, Phylogeny phy) throws IllegalArgumentException
IllegalArgumentExceptionpublic static String obtainTaxonomyGroup(String tax_code, Phylogeny species_tree) throws IllegalArgumentException
IllegalArgumentExceptionpublic 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)
public static void preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, String date_time, String method, String name, String parameters_str)
public static void preparePhylogenyForParsimonyAnalyses(Phylogeny intree, String[][] input_file_properties)
public static void printOutPercentageOfMultidomainProteins(SortedMap<Integer,Integer> all_genomes_domains_per_potein_histo, Writer log_writer)
public static void processPlusMinusAnalysisOption(CommandLineArguments cla, List<String> high_copy_base, List<String> high_copy_target, List<String> low_copy, List<Object> numbers)
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)
public static StringBuffer proteinToDomainCombinations(Protein protein, String protein_id, String separator)
public static List<Domain> sortDomainsWithAscendingConfidenceValues(Protein protein)
public static int storeDomainArchitectures(String genome, SortedMap<String,Set<String>> domain_architecutures, List<Protein> protein_list, Map<String,Integer> distinct_domain_architecuture_counts)
public static void writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, String outdir, String suffix_for_filename) throws IOException
IOExceptionpublic static void writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties, File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
public static void writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, Map<String,String> descriptions)
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)
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)
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)
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
IOExceptionpublic static void writeHtmlHead(Writer w, String title) throws IOException
IOExceptionpublic static void writeMatrixToFile(CharacterStateMatrix<?> matrix, String filename, CharacterStateMatrix.Format format)
public static void writeMatrixToFile(File matrix_outfile, List<DistanceMatrix> matrices)
public static void writePresentToNexus(File output_file, File positive_filter_file, SortedSet<String> filter, List<GenomeWideCombinableDomains> gwcd_list)
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)
public static void writeTaxonomyLinks(Writer writer, String species, Map<String,Integer> tax_code_to_id_map) throws IOException
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