Search Toolkit Book for CSemiTryptic
eMSEnzymes_semi_tryptic semi tryptic search (one end of peptide has to be tryptic) More...
#include "msms.hpp"
(Private to src/algo/ms/omssa.)
Inheritance diagram for CSemiTryptic:
Collaboration diagram for CSemiTryptic:
Public Member Functions | |
| CSemiTryptic (void) | |
| SemiTryptic. More... | |
| Public Member Functions inherited from CCleave | |
| CCleave (void) | |
| bool | CalcAndCut (const char *SeqStart, const char *SeqEnd, const char **PepStart, int *Masses, int &NumMod, int MaxNumMod, int *EndMasses, CMSMod &VariableMods, CMSMod &FixedMods, CMod ModList[], const int *IntCalcMass, const int *PrecursorIntCalcMass, CRef< CMSModSpecSet > &Modset, int Maxproductions) |
| cleaves the sequence. More... | |
| bool | CheckCleave (const char *iPepStart, const char *iSeqStart) |
| Check to see if we are at a cleavage point Used by CalcAndCut. More... | |
| bool | CheckCleaveChar (const char *iPepStart) const |
| is the character given one of the cleavage chars? More... | |
| void | CalcMass (char SeqChar, int *Masses, const int *IntCalcMass) |
| void | EndMass (int *Masses) |
| int | findfirst (char *Seq, int Pos, int SeqLen) |
| void | CheckNonSpecificMods (EMSModType ModType, CMSMod &VariableMods, int &NumMod, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset) |
| looks for non-specific ptms More... | |
| void | CheckAAMods (EMSModType ModType, CMSMod &VariableMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, bool setfixed, CRef< CMSModSpecSet > &Modset) |
| looks for amino acid specific ptms More... | |
| void | CheckMods (EMSModType NonSpecificIn, EMSModType Specific, CMSMod &VariableMods, CMSMod &FixedMods, int &NumMod, char SeqChar, int MaxNumMod, CMod ModList[], const char *iPepStart, CRef< CMSModSpecSet > &Modset) |
| checks all mods for a particular type More... | |
| bool | GetTopDown (void) const |
| Is the enzyme really a top-down search? More... | |
| const char * | GetStop (void) const |
| Get the enzyme stop value. More... | |
| const char *& | SetStop (void) |
| Set the enzyme stop value. More... | |
| bool | GetNonSpecific (void) const |
| Is this a non-specific search? More... | |
| int | GetCleaveNum (void) const |
| Get the number of cleavage chars. More... | |
| const char * | GetCleaveOffset (void) const |
| Get the the cleave offset, 0 = cterm, 1 = nterm. More... | |
| bool | GetNMethionine (void) const |
| Is there n-term methionine cleavage? More... | |
| bool & | SetNMethionine (void) |
| Set n-term methionine cleavage. More... | |
| const string | GetCleaveAt (void) const |
| What are the cleavage chars? More... | |
| bool | GetCheckProline (void) const |
| Should we check for proline? More... | |
| const char * | GetCleaveSense (void) const |
| Should we check for proline? More... | |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Additional Inherited Members | |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Protected Attributes inherited from CCleave | |
| int | ProtonMass |
| int | TermMass |
| CAA | ReverseAA |
| const char * | CleaveAt |
| where to cleave. More... | |
| const char * | CleaveOffset |
| what is the cleavage offset More... | |
| int | kCleave |
| How many cleavage characters. More... | |
| bool | TopDown |
| TopDown does this signify a top-down search. More... | |
| const char * | Stop |
| Stop Stop position for no-enzyme and semi-tryptic searches. More... | |
| bool | NonSpecific |
| Is this a non-specific search? More... | |
| bool | CheckProline |
| Should we apply the proline rule (no cleavage before proline) More... | |
| bool | NMethionine |
| n-terminal methionine cleavage More... | |
Detailed Description
eMSEnzymes_semi_tryptic semi tryptic search (one end of peptide has to be tryptic)
Constructor & Destructor Documentation
◆ CSemiTryptic()
| CSemiTryptic::CSemiTryptic | ( | void | ) |
SemiTryptic.
Definition at line 432 of file msms.cpp.
References CCleave::CheckProline, CCleave::CleaveAt, CCleave::CleaveOffset, CCleave::kCleave, CCleave::NonSpecific, and CCleave::TopDown.
The documentation for this class was generated from the following files:
