NCBI C++ ToolKit
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Asp-N, Nterm of D. More...
#include "msms.hpp"
(Private to src/algo/ms/omssa
.)
Public Member Functions | |
CAspN (void) | |
CAspN. 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... | |
CAspN::CAspN | ( | void | ) |
Definition at line 376 of file msms.cpp.
References CCleave::CheckProline, CCleave::CleaveAt, CCleave::CleaveOffset, CCleave::kCleave, CCleave::NonSpecific, and CCleave::TopDown.