Inheritance diagram for Sleipnir::CCoalesceMotifLibraryImpl:
Data Structures | |
| struct | SKnowns |
Protected Types | |
| enum | EType { ETypeKMer, ETypeRC, ETypePST } |
|
typedef std::map< std::pair < uint32_t, uint32_t > , uint32_t > | TMapPrIII |
Protected Member Functions | |
| CCoalesceMotifLibraryImpl (size_t iK) | |
| std::string | GetMotif (uint32_t) const |
| CPST * | CreatePST (uint32_t &) |
| uint32_t | MergeKMers (const std::string &, const std::string &, float, bool) |
| uint32_t | MergeKMerRC (uint32_t, uint32_t, float, bool) |
| uint32_t | MergeKMerPST (const std::string &, const CPST &, float, bool) |
| uint32_t | MergeRCs (uint32_t, uint32_t, float, bool) |
| uint32_t | MergeRCPST (uint32_t, const CPST &, float, bool) |
| uint32_t | MergePSTs (const CPST &, const CPST &, float, bool) |
| float | AlignKMers (const std::string &, const std::string &, float) const |
| float | AlignKMerRC (const std::string &, uint32_t, float) const |
| float | AlignKMerPST (const std::string &, const CPST &, float) const |
| float | AlignRCs (uint32_t, uint32_t, float) const |
| float | AlignRCPST (uint32_t, const CPST &, float) const |
| float | AlignPSTs (const CPST &, const CPST &, float) const |
| uint32_t | RemoveRCs (const CPST &, float, float) |
| bool | GetPWM (uint32_t, float, float, float, bool, CFullMatrix< uint16_t > &) const |
| EType | GetType (uint32_t iMotif) const |
| uint32_t | GetKMers () const |
| uint32_t | GetRCs () const |
| uint32_t | GetBaseRCs () const |
| uint32_t | GetBasePSTs () const |
| CPST * | GetPST (uint32_t iMotif) const |
| uint32_t | GetPSTs () const |
| float | Align (const std::string &strFixed, const std::string &strMobile, float dCutoff, int &iRet) const |
| std::string | GetRCOne (uint32_t iMotif) const |
Static Protected Member Functions | |
| static size_t | CountKMers (size_t iK) |
| static size_t | CountRCs (size_t iK) |
| static std::string | GetComplement (const std::string &strKMer) |
| static char | GetComplement (char cBase) |
| static uint32_t | KMer2ID (const std::string &strKMer, bool fRC=false) |
| static std::string | ID2KMer (uint32_t iID, size_t iK) |
| static bool | IsIgnorableKMer (const std::string &strKMer) |
| static bool | GetPWM (const std::string &strKMer, CFullMatrix< uint16_t > &MatPWM) |
| static std::string | GetReverseComplement (const std::string &strKMer) |
| static float | GetInformation (const CFullMatrix< uint16_t > &MatPWM) |
Protected Attributes | |
| float | m_dPenaltyGap |
| float | m_dPenaltyMismatch |
| size_t | m_iK |
| std::vector< uint32_t > | m_veciKMer2RC |
| std::vector< uint32_t > | m_veciRC2KMer |
| std::vector< CPST * > | m_vecpPSTs |
| TMapPrIII | m_mappriiiMerged |
| SKnowns | m_sKnowns |
Static Protected Attributes | |
| static const char | c_szBases [] = "ACGT" |
| static const char | c_szComplements [] = "TGCA" |
| static const size_t | c_iShift = 2 |
| static const char | c_cSeparator = '|' |
| static const char | c_cCluster = 'C' |
Detailed Description
Definition at line 37 of file coalescemotifsi.h.
The documentation for this class was generated from the following files:
- src/coalescemotifsi.h
- src/coalescemotifs.cpp
