- Generated on Fri Jul 19 2024 12:16:03 for bpp-seq3 by
1.9.1
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bpp-seq3
3.0.0
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This is the complete list of members for bpp::SequenceTools, including all inherited members.
| areSequencesIdentical(const SequenceInterface &seq1, const SequenceInterface &seq2) | bpp::SequenceTools | static |
| areSymbolListsIdentical(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2) | bpp::SymbolListTools | static |
| areSymbolListsIdentical(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2) | bpp::SymbolListTools | static |
| areSymbolListsIdentical(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2) | bpp::SymbolListTools | inlinestatic |
| bowkerTest(const SequenceInterface &seq1, const SequenceInterface &seq2) | bpp::SequenceTools | static |
| changeGapsToUnknownCharacters(IntSymbolListInterface &l) | bpp::SymbolListTools | static |
| changeGapsToUnknownCharacters(ProbabilisticSymbolListInterface &l) | bpp::SymbolListTools | static |
| changeGapsToUnknownCharacters(CruxSymbolListInterface &l) | bpp::SymbolListTools | inlinestatic |
| changeUnresolvedCharactersToGaps(IntSymbolListInterface &l) | bpp::SymbolListTools | static |
| changeUnresolvedCharactersToGaps(ProbabilisticSymbolListInterface &l) | bpp::SymbolListTools | static |
| changeUnresolvedCharactersToGaps(CruxSymbolListInterface &l) | bpp::SymbolListTools | inlinestatic |
| combineSequences(const SequenceInterface &s1, const SequenceInterface &s2) | bpp::SequenceTools | static |
| complement(SequenceInterface &seq) | bpp::SequenceTools | static |
| concatenate(const SequenceInterface &seq1, const SequenceInterface &seq2) | bpp::SequenceTools | inlinestatic |
| DNARep_ | bpp::SequenceTools | privatestatic |
| entropy(const CruxSymbolListInterface &list, bool resolveUnknowns) | bpp::SymbolListTools | inlinestatic |
| findFirstOf(const SequenceInterface &seq, const SequenceInterface &motif, bool strict=true) | bpp::SequenceTools | static |
| getCDS(SequenceInterface &sequence, const GeneticCode &gCode, bool checkInit, bool checkStop, bool includeInit=true, bool includeStop=true) | bpp::SequenceTools | static |
| getComplement(const SequenceInterface &sequence) | bpp::SequenceTools | static |
| getCounts(const IntSymbolListInterface &list, std::map< int, count_type > &counts) | bpp::SymbolListTools | inlinestatic |
| getCounts(const ProbabilisticSymbolListInterface &list, std::map< int, double_t > &counts) | bpp::SymbolListTools | inlinestatic |
| getCounts(const CruxSymbolListInterface &list, std::map< int, double > &counts, bool resolveUnknowns=false) | bpp::SymbolListTools | inlinestatic |
| getCounts(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, count_type >> &counts) | bpp::SymbolListTools | inlinestatic |
| getCounts(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts) | bpp::SymbolListTools | inlinestatic |
| getCounts(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts, bool resolveUnknowns) | bpp::SymbolListTools | inlinestatic |
| getCountsResolveUnknowns(const IntSymbolListInterface &list, std::map< int, double > &counts) | bpp::SymbolListTools | inlinestatic |
| getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list, std::map< int, double > &counts) | bpp::SymbolListTools | inlinestatic |
| getCountsResolveUnknowns(const IntSymbolListInterface &list1, const IntSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts) | bpp::SymbolListTools | static |
| getCountsResolveUnknowns(const ProbabilisticSymbolListInterface &list1, const ProbabilisticSymbolListInterface &list2, std::map< int, std::map< int, double >> &counts) | bpp::SymbolListTools | static |
| getFrequencies(const CruxSymbolListInterface &list, std::map< int, double > &frequencies, bool resolveUnknowns=false) | bpp::SymbolListTools | static |
| getFrequencies(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, std::map< int, std::map< int, double >> &frequencies, bool resolveUnknowns=false) | bpp::SymbolListTools | static |
| getGCContent(const IntSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true) | bpp::SymbolListTools | static |
| getGCContent(const ProbabilisticSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true) | bpp::SymbolListTools | static |
| getGCContent(const CruxSymbolListInterface &list, bool ignoreUnresolved=true, bool ignoreGap=true) | bpp::SymbolListTools | inlinestatic |
| getInvert(const SequenceInterface &sequence) | bpp::SequenceTools | static |
| getMajorAllele(const CruxSymbolListInterface &list) | bpp::SymbolListTools | static |
| getMajorAlleleFrequency(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| getMinorAllele(const CruxSymbolListInterface &list) | bpp::SymbolListTools | static |
| getMinorAlleleFrequency(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| getNumberOfCompleteSites(const SequenceInterface &seq) | bpp::SequenceTools | static |
| getNumberOfDistinctCharacters(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| getNumberOfDistinctPositions(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2) | bpp::SymbolListTools | static |
| getNumberOfDistinctPositions(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2) | bpp::SymbolListTools | static |
| getNumberOfDistinctPositions(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2) | bpp::SymbolListTools | inlinestatic |
| getNumberOfPositionsWithoutGap(const IntSymbolListInterface &l1, const IntSymbolListInterface &l2) | bpp::SymbolListTools | static |
| getNumberOfPositionsWithoutGap(const ProbabilisticSymbolListInterface &l1, const ProbabilisticSymbolListInterface &l2) | bpp::SymbolListTools | static |
| getNumberOfPositionsWithoutGap(const CruxSymbolListInterface &l1, const CruxSymbolListInterface &l2) | bpp::SymbolListTools | inlinestatic |
| getNumberOfSites(const SequenceInterface &seq) | bpp::SequenceTools | static |
| getNumberOfUnresolvedSites(const SequenceInterface &seq) | bpp::SequenceTools | static |
| getPercentIdentity(const SequenceInterface &seq1, const SequenceInterface &seq2, bool ignoreGaps=false) | bpp::SequenceTools | static |
| getPutativeHaplotypes(const SequenceInterface &seq, std::vector< std::unique_ptr< SequenceInterface >> &hap, unsigned int level=2) | bpp::SequenceTools | static |
| getRandomSequence(std::shared_ptr< const Alphabet > &alphabet, size_t length) | bpp::SequenceTools | static |
| getSequenceWithCompleteSites(const SequenceInterface &seq) | bpp::SequenceTools | static |
| getSequenceWithoutGaps(const SequenceInterface &seq) | bpp::SequenceTools | static |
| getSequenceWithoutStops(const SequenceInterface &seq, const GeneticCode &gCode) | bpp::SequenceTools | static |
| hasGap(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| hasGap(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| hasGap(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| hasSingleton(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| hasUnknown(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| hasUnknown(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| hasUnknown(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| hasUnresolved(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| heterozygosity(const CruxSymbolListInterface &list) | bpp::SymbolListTools | static |
| invert(SequenceInterface &seq) | bpp::SequenceTools | static |
| invertComplement(SequenceInterface &seq) | bpp::SequenceTools | static |
| isComplete(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| isComplete(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| isComplete(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| isConstant(const IntSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true) | bpp::SymbolListTools | static |
| isConstant(const ProbabilisticSymbolListInterface &site, bool unresolvedRaisesException=true) | bpp::SymbolListTools | static |
| isConstant(const CruxSymbolListInterface &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true) | bpp::SymbolListTools | inlinestatic |
| isDoubleton(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| isGapOnly(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| isGapOnly(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| isGapOnly(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| isGapOrUnresolvedOnly(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| isGapOrUnresolvedOnly(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| isGapOrUnresolvedOnly(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| isParsimonyInformativeSite(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| isTriplet(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| jointEntropy(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns) | bpp::SymbolListTools | static |
| mutualInformation(const CruxSymbolListInterface &list1, const CruxSymbolListInterface &list2, bool resolveUnknowns) | bpp::SymbolListTools | static |
| numberOfGaps(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| numberOfGaps(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| numberOfGaps(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| numberOfUnresolved(const IntSymbolListInterface &site) | bpp::SymbolListTools | static |
| numberOfUnresolved(const ProbabilisticSymbolListInterface &site) | bpp::SymbolListTools | static |
| numberOfUnresolved(const CruxSymbolListInterface &site) | bpp::SymbolListTools | inlinestatic |
| removeGaps(SequenceInterface &seq) | bpp::SequenceTools | static |
| removeStops(SequenceInterface &seq, const GeneticCode &gCode) | bpp::SequenceTools | static |
| replaceStopsWithGaps(SequenceInterface &seq, const GeneticCode &gCode) | bpp::SequenceTools | static |
| reverseTranscript(const Sequence &sequence) | bpp::SequenceTools | static |
| RNARep_ | bpp::SequenceTools | privatestatic |
| RNY_ | bpp::SequenceTools | privatestatic |
| RNYslice(const SequenceInterface &sequence, int ph) | bpp::SequenceTools | static |
| RNYslice(const SequenceInterface &sequence) | bpp::SequenceTools | static |
| SequenceTools() | bpp::SequenceTools | inline |
| subseq(const SequenceInterface &sequence, size_t begin, size_t end, SequenceInterface &output) | bpp::SequenceTools | inlinestatic |
| subseq(const SequenceInterface &sequence, size_t begin, size_t end) | bpp::SequenceTools | inlinestatic |
| subtractHaplotype(const SequenceInterface &s, const SequenceInterface &h, std::string name="", unsigned int level=1) | bpp::SequenceTools | static |
| SymbolListTools() | bpp::SymbolListTools | inline |
| transc_ | bpp::SequenceTools | privatestatic |
| transcript(const Sequence &sequence) | bpp::SequenceTools | static |
| variabilityFactorial(const IntSymbolListInterface &list) | bpp::SymbolListTools | static |
| variabilityShannon(const CruxSymbolListInterface &list, bool resolveUnknowns) | bpp::SymbolListTools | static |
| ~SequenceTools() | bpp::SequenceTools | inlinevirtual |
| ~SymbolListTools() | bpp::SymbolListTools | inlinevirtual |
1.9.1