org.forester.surfacing
Class SurfacingUtil
java.lang.Object
org.forester.surfacing.SurfacingUtil
public final class SurfacingUtil
- extends Object
Method Summary |
static void |
addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome,
SortedSet<BinaryDomainCombination> binary_domain_combinations)
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static void |
addAllDomainIdsToSet(GenomeWideCombinableDomains genome,
SortedSet<DomainId> domain_ids)
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static void |
addHtmlHead(Writer w,
String title)
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static DescriptiveStatistics |
calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities)
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static int |
calculateOverlap(Domain domain,
List<Boolean> covered_positions)
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static void |
checkForOutputFileWriteability(File outfile)
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static void |
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
BinaryDomainCombination.DomainCombinationType dc_type,
List<BinaryDomainCombination> all_binary_domains_combination_gained,
boolean get_gains)
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static Map<DomainId,List<GoId>> |
createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings)
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static Map<DomainId,Set<String>> |
createDomainIdToSecondaryFeaturesMap(File secondary_features_map_file)
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static Phylogeny |
createNjTreeBasedOnMatrixToFile(File nj_tree_outfile,
DistanceMatrix distance)
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static void |
decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity> domain_similarities,
DomainSimilarityCalculator.Detailedness detailedness,
DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output,
Map<GoId,GoTerm> go_id_to_term_map,
GoNameSpace go_namespace_limit)
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static void |
executeDomainLengthAnalysis(String[][] input_file_properties,
int number_of_genomes,
DomainLengthsTable domain_lengths_table,
File outfile)
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static void |
executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony,
boolean radomize_fitch_parsimony,
String outfile_name,
DomainParsimonyCalculator domain_parsimony,
Phylogeny phylogeny,
Map<DomainId,List<GoId>> domain_id_to_go_ids_map,
Map<GoId,GoTerm> go_id_to_term_map,
GoNameSpace go_namespace_limit,
String parameters_str,
Map<DomainId,Set<String>>[] domain_id_to_secondary_features_maps,
SortedSet<DomainId> 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)
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static void |
executeParsimonyAnalysisForSecondaryFeatures(String outfile_name,
DomainParsimonyCalculator secondary_features_parsimony,
Phylogeny phylogeny,
String parameters_str,
Map<Species,MappingResults> mapping_results_map)
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static void |
extractProteinNames(List<Protein> proteins,
List<DomainId> query_domain_ids_nc_order,
Writer out,
String separator)
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static void |
extractProteinNames(SortedMap<Species,List<Protein>> protein_lists_per_species,
DomainId domain_id,
Writer out,
String separator)
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static SortedSet<DomainId> |
getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list)
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static SortedMap<String,Integer> |
getDomainCounts(List<Protein> protein_domain_collections)
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static int |
getNumberOfNodesLackingName(Phylogeny p,
StringBuilder names)
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static boolean |
isEngulfed(Domain domain,
List<Boolean> covered_positions)
Returns true is Domain domain falls in an uninterrupted stretch of
covered positions. |
static void |
preparePhylogeny(Phylogeny p,
DomainParsimonyCalculator domain_parsimony,
String date_time,
String method,
String name,
String parameters_str)
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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,
String outdir,
String suffix_for_filename)
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static void |
writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties,
File output_dir,
GenomeWideCombinableDomains gwcd,
int i,
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
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static void |
writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
Map<String,String> descriptions)
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static void |
writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
BinaryDomainCombination.OutputFormat bc_output_format)
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static void |
writeBinaryStatesMatrixToList(Map<DomainId,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<DomainId,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)
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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)
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static DescriptiveStatistics |
writeDomainSimilaritiesToFile(StringBuilder html_desc,
StringBuilder html_title,
Writer w,
SortedSet<DomainSimilarity> similarities,
boolean treat_as_binary,
List<Species> species_order,
PrintableDomainSimilarity.PRINT_OPTION print_option,
DomainSimilarity.DomainSimilaritySortField sort_field,
DomainSimilarity.DomainSimilarityScoring scoring,
boolean verbose)
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static void |
writeMatrixToFile(CharacterStateMatrix<?> matrix,
String filename,
CharacterStateMatrix.Format format)
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static void |
writeMatrixToFile(File matrix_outfile,
List<DistanceMatrix> matrices)
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static void |
writePhylogenyToFile(Phylogeny phylogeny,
String filename)
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static void |
writeTaxonomyLinks(Writer writer,
String species)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PATTERN_SP_STYLE_TAXONOMY
public static final Pattern PATTERN_SP_STYLE_TAXONOMY
addAllBinaryDomainCombinationToSet
public static void addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome,
SortedSet<BinaryDomainCombination> binary_domain_combinations)
addAllDomainIdsToSet
public static void addAllDomainIdsToSet(GenomeWideCombinableDomains genome,
SortedSet<DomainId> domain_ids)
addHtmlHead
public static void addHtmlHead(Writer w,
String title)
throws IOException
- Throws:
IOException
calculateDescriptiveStatisticsForMeanValues
public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities)
calculateOverlap
public static int calculateOverlap(Domain domain,
List<Boolean> covered_positions)
checkForOutputFileWriteability
public static void checkForOutputFileWriteability(File outfile)
collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile
public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
BinaryDomainCombination.DomainCombinationType dc_type,
List<BinaryDomainCombination> all_binary_domains_combination_gained,
boolean get_gains)
createDomainIdToGoIdMap
public static Map<DomainId,List<GoId>> createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings)
createDomainIdToSecondaryFeaturesMap
public static Map<DomainId,Set<String>> createDomainIdToSecondaryFeaturesMap(File secondary_features_map_file)
throws IOException
- Throws:
IOException
createNjTreeBasedOnMatrixToFile
public static Phylogeny createNjTreeBasedOnMatrixToFile(File nj_tree_outfile,
DistanceMatrix distance)
decoratePrintableDomainSimilarities
public static void decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity> domain_similarities,
DomainSimilarityCalculator.Detailedness detailedness,
DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output,
Map<GoId,GoTerm> go_id_to_term_map,
GoNameSpace go_namespace_limit)
executeDomainLengthAnalysis
public static void executeDomainLengthAnalysis(String[][] input_file_properties,
int number_of_genomes,
DomainLengthsTable domain_lengths_table,
File outfile)
throws IOException
- Throws:
IOException
executeParsimonyAnalysis
public static void executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony,
boolean radomize_fitch_parsimony,
String outfile_name,
DomainParsimonyCalculator domain_parsimony,
Phylogeny phylogeny,
Map<DomainId,List<GoId>> domain_id_to_go_ids_map,
Map<GoId,GoTerm> go_id_to_term_map,
GoNameSpace go_namespace_limit,
String parameters_str,
Map<DomainId,Set<String>>[] domain_id_to_secondary_features_maps,
SortedSet<DomainId> 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)
- Parameters:
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.
executeParsimonyAnalysisForSecondaryFeatures
public static void executeParsimonyAnalysisForSecondaryFeatures(String outfile_name,
DomainParsimonyCalculator secondary_features_parsimony,
Phylogeny phylogeny,
String parameters_str,
Map<Species,MappingResults> mapping_results_map)
extractProteinNames
public static void extractProteinNames(List<Protein> proteins,
List<DomainId> query_domain_ids_nc_order,
Writer out,
String separator)
throws IOException
- Throws:
IOException
extractProteinNames
public static void extractProteinNames(SortedMap<Species,List<Protein>> protein_lists_per_species,
DomainId domain_id,
Writer out,
String separator)
throws IOException
- Throws:
IOException
getAllDomainIds
public static SortedSet<DomainId> getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list)
getDomainCounts
public static SortedMap<String,Integer> getDomainCounts(List<Protein> protein_domain_collections)
getNumberOfNodesLackingName
public static int getNumberOfNodesLackingName(Phylogeny p,
StringBuilder names)
isEngulfed
public static boolean isEngulfed(Domain domain,
List<Boolean> covered_positions)
- Returns true is Domain domain falls in an uninterrupted stretch of
covered positions.
- Parameters:
domain
- covered_positions
-
- Returns:
preparePhylogeny
public static void preparePhylogeny(Phylogeny p,
DomainParsimonyCalculator domain_parsimony,
String date_time,
String method,
String name,
String parameters_str)
removeOverlappingDomains
public 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
- Parameters:
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
-
- Returns:
writeAllDomainsChangedOnAllSubtrees
public static void writeAllDomainsChangedOnAllSubtrees(Phylogeny p,
boolean get_gains,
String outdir,
String suffix_for_filename)
throws IOException
- Throws:
IOException
writeBinaryDomainCombinationsFileForGraphAnalysis
public static void writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties,
File output_dir,
GenomeWideCombinableDomains gwcd,
int i,
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
writeBinaryStatesMatrixAsListToFile
public static void writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
Map<String,String> descriptions)
writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis
public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
CharacterStateMatrix.GainLossStates state,
String filename,
String indentifier_characters_separator,
String character_separator,
BinaryDomainCombination.OutputFormat bc_output_format)
writeBinaryStatesMatrixToList
public static void writeBinaryStatesMatrixToList(Map<DomainId,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<DomainId,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)
writeDomainCombinationsCountsFile
public static void writeDomainCombinationsCountsFile(String[][] input_file_properties,
File output_dir,
Writer per_genome_domain_promiscuity_statistics_writer,
GenomeWideCombinableDomains gwcd,
int i,
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
writeDomainSimilaritiesToFile
public static DescriptiveStatistics writeDomainSimilaritiesToFile(StringBuilder html_desc,
StringBuilder html_title,
Writer w,
SortedSet<DomainSimilarity> similarities,
boolean treat_as_binary,
List<Species> species_order,
PrintableDomainSimilarity.PRINT_OPTION print_option,
DomainSimilarity.DomainSimilaritySortField sort_field,
DomainSimilarity.DomainSimilarityScoring scoring,
boolean verbose)
throws IOException
- Throws:
IOException
writeMatrixToFile
public static void writeMatrixToFile(CharacterStateMatrix<?> matrix,
String filename,
CharacterStateMatrix.Format format)
writeMatrixToFile
public static void writeMatrixToFile(File matrix_outfile,
List<DistanceMatrix> matrices)
writePhylogenyToFile
public static void writePhylogenyToFile(Phylogeny phylogeny,
String filename)
writeTaxonomyLinks
public static void writeTaxonomyLinks(Writer writer,
String species)
throws IOException
- Throws:
IOException