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<DomainId> domain_ids) |
static void |
addHtmlHead(java.io.Writer w,
java.lang.String title) |
static DescriptiveStatistics |
calculateDescriptiveStatisticsForMeanValues(java.util.Set<DomainSimilarity> similarities) |
static int |
calculateOverlap(Domain domain,
java.util.List<java.lang.Boolean> covered_positions) |
static void |
checkForOutputFileWriteability(java.io.File outfile) |
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<DomainId,java.util.List<GoId>> |
createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings) |
static java.util.Map<DomainId,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 void |
decoratePrintableDomainSimilarities(java.util.SortedSet<DomainSimilarity> domain_similarities,
DomainSimilarityCalculator.Detailedness detailedness,
DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output,
java.util.Map<GoId,GoTerm> go_id_to_term_map,
GoNameSpace go_namespace_limit) |
static void |
executeDomainLengthAnalysis(java.lang.String[][] input_file_properties,
int number_of_genomes,
DomainLengthsTable domain_lengths_table,
java.io.File outfile) |
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<DomainId,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<DomainId,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps,
java.util.SortedSet<DomainId> 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) |
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) |
static void |
extractProteinNames(java.util.List<Protein> proteins,
java.util.List<DomainId> query_domain_ids_nc_order,
java.io.Writer out,
java.lang.String separator) |
static void |
extractProteinNames(java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species,
DomainId domain_id,
java.io.Writer out,
java.lang.String separator) |
static java.util.SortedSet<DomainId> |
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 boolean |
isEngulfed(Domain domain,
java.util.List<java.lang.Boolean> covered_positions)
Returns true is Domain domain falls in an uninterrupted stretch of
covered positions.
|
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 Protein |
removeOverlappingDomains(int max_allowed_overlap,
boolean remove_engulfed_domains,
Protein protein)
Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
domain with 0.3 is ignored
-----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
ignored
|
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<DomainId,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<DomainId,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) |
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 DescriptiveStatistics |
writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc,
java.lang.StringBuilder html_title,
java.io.Writer w,
java.util.SortedSet<DomainSimilarity> similarities,
boolean treat_as_binary,
java.util.List<Species> species_order,
PrintableDomainSimilarity.PRINT_OPTION print_option,
DomainSimilarity.DomainSimilaritySortField sort_field,
DomainSimilarity.DomainSimilarityScoring scoring,
boolean verbose) |
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 |
writeTaxonomyLinks(java.io.Writer writer,
java.lang.String species) |
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<DomainId> domain_ids)
public static void addHtmlHead(java.io.Writer w, java.lang.String title) throws java.io.IOException
java.io.IOException
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(java.util.Set<DomainSimilarity> similarities)
public static int calculateOverlap(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
public static void checkForOutputFileWriteability(java.io.File outfile)
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<DomainId,java.util.List<GoId>> createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings)
public static java.util.Map<DomainId,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 void decoratePrintableDomainSimilarities(java.util.SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness, DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit)
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 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<DomainId,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<DomainId,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<DomainId> 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)
all_binary_domains_combination_lost_fitch
- 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)
public static void extractProteinNames(java.util.List<Protein> proteins, java.util.List<DomainId> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator) throws java.io.IOException
java.io.IOException
public static void extractProteinNames(java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, DomainId domain_id, java.io.Writer out, java.lang.String separator) throws java.io.IOException
java.io.IOException
public static java.util.SortedSet<DomainId> 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 boolean isEngulfed(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
domain
- covered_positions
- 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 Protein removeOverlappingDomains(int max_allowed_overlap, boolean remove_engulfed_domains, Protein protein)
max_allowed_overlap
- maximal allowed overlap (inclusive) to be still considered not
overlapping (zero or negative value to allow any overlap)remove_engulfed_domains
- to remove domains which are completely engulfed by coverage of
domains with better supportprotein
- 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<DomainId,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<DomainId,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)
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 DescriptiveStatistics writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer w, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, PrintableDomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilaritySortField sort_field, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose) 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 writeTaxonomyLinks(java.io.Writer writer, java.lang.String species) throws java.io.IOException
java.io.IOException