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CCleave Class Reference

Search Toolkit Book for CCleave

#include "msms.hpp"
(Private to src/algo/ms/omssa.)

+ Inheritance diagram for CCleave:
+ Collaboration diagram for CCleave:

Public Member Functions

 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...
 
boolSetNMethionine (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...
 
CObjectoperator= (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
 

Protected Attributes

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...
 

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< Uint8TCounter
 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...
 

Detailed Description

Definition at line 469 of file msms.hpp.

Constructor & Destructor Documentation

◆ CCleave()

CCleave::CCleave ( void  )

Definition at line 74 of file msms.cpp.

References kProton, kWater, MSSCALE2INT, ProtonMass, and TermMass.

Member Function Documentation

◆ CalcAndCut()

bool CCleave::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.

Note that output is 0 and the positions of the aa's to be cleaved. Should be interpreted as [0, pos1], (pos1, pos2], ..., (posn, end]. This weirdness is historical – the C++ string class uses an identifier for end-of-string and has no identifier for before start of string.

Parameters
SeqStartpointer to start of sequence
SeqEndpointer to end of sequence
PepStart** to the start of peptide
Massescumulative masses of peptides
NumModnumber of variable mods
MaxNumModupper bound on number of variable mods
EndMassthe end masses of the peptides
VariableModslist of variable mods
FixedModslist of fixed modifications
ModListmod site info
IntCalcMassinteger AA masses
PrecursorIntCalcMassinteger precursor masses
Modsetlist of possible mods
Maxproductionsmax number of product ions to calculate
Returns
are we at the end of the sequence?

Note that output is 0 and the positions of the aa's to be cleaved. Should be interpreted as [0, pos1], (pos1, pos2], ..., (posn, end]. This weirdness is historical – the C++ string class uses an identifier for end-of-string and has no identifier for before start of string.

Parameters
SeqStartpointer to start of sequence
SeqEndpointer to end of sequence
PepStart** to the start of peptide
Massescumulative masses of peptides
NumModnumber of variable mods
MaxNumModupper bound on number of variable mods
EndMassthe end masses of the peptides
VariableModslist of variable mods
FixedModslist of fixed modifications
ModListmod site info
IntCalcMassinteger AA masses
PrecursorIntCalcMassinteger precursor masses
Modsetlist of possible mods
Maxproductionsmax number of product ions to calculate
Returns
true if end of sequence

Definition at line 116 of file msms.cpp.

References CalcMass(), CheckAAMods(), CheckCleave(), CheckMods(), eMSModType_modaa, eMSModType_modc, eMSModType_modcaa, eMSModType_modcp, eMSModType_modcpaa, eMSModType_modn, eMSModType_modnaa, eMSModType_modnp, eMSModType_modnpaa, EndMass(), GetTopDown(), and NMethionine.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ CalcMass()

void CCleave::CalcMass ( char  SeqChar,
int Masses,
const int IntCalcMass 
)
inline

Definition at line 762 of file msms.hpp.

References CAA::GetMap(), and ReverseAA.

Referenced by CalcAndCut().

◆ CheckAAMods()

void CCleave::CheckAAMods ( EMSModType  ModType,
CMSMod VariableMods,
int NumMod,
char  SeqChar,
int  MaxNumMod,
CMod  ModList[],
const char *  iPepStart,
bool  setfixed,
CRef< CMSModSpecSet > &  Modset 
)
inline

◆ CheckCleave()

bool CCleave::CheckCleave ( const char *  iPepStart,
const char *  iSeqStart 
)
inline

Check to see if we are at a cleavage point Used by CalcAndCut.

Parameters
iPepStartpointer to location of sequence cursor
iSeqStartpoints to start of the sequence
iPepStartpointer to location of sequence cursor

Definition at line 736 of file msms.hpp.

References CheckCleaveChar(), CheckProline, GetStop(), NMethionine, NonSpecific, and TopDown.

Referenced by CalcAndCut().

◆ CheckCleaveChar()

bool CCleave::CheckCleaveChar ( const char *  iPepStart) const
inline

is the character given one of the cleavage chars?

Parameters
iPepStartposition in the sequence

Definition at line 720 of file msms.hpp.

References CleaveAt, CleaveOffset, and kCleave.

Referenced by CheckCleave(), and CSearch< LEGACY, NHITS >::Search().

◆ CheckMods()

void CCleave::CheckMods ( EMSModType  NonSpecificIn,
EMSModType  Specific,
CMSMod VariableMods,
CMSMod FixedMods,
int NumMod,
char  SeqChar,
int  MaxNumMod,
CMod  ModList[],
const char *  iPepStart,
CRef< CMSModSpecSet > &  Modset 
)
inline

checks all mods for a particular type

Definition at line 833 of file msms.hpp.

References CheckAAMods(), and CheckNonSpecificMods().

Referenced by CalcAndCut().

◆ CheckNonSpecificMods()

void CCleave::CheckNonSpecificMods ( EMSModType  ModType,
CMSMod VariableMods,
int NumMod,
int  MaxNumMod,
CMod  ModList[],
const char *  iPepStart,
bool  setfixed,
CRef< CMSModSpecSet > &  Modset 
)
inline

◆ EndMass()

void CCleave::EndMass ( int Masses)
inline

Definition at line 772 of file msms.hpp.

References TermMass.

Referenced by CalcAndCut().

◆ findfirst()

int CCleave::findfirst ( char *  Seq,
int  Pos,
int  SeqLen 
)

Definition at line 82 of file msms.cpp.

References CleaveAt, i, and kCleave.

◆ GetCheckProline()

bool CCleave::GetCheckProline ( void  ) const
inline

Should we check for proline?

Definition at line 696 of file msms.hpp.

References CheckProline.

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetCleaveAt()

const string CCleave::GetCleaveAt ( void  ) const
inline

What are the cleavage chars?

Definition at line 684 of file msms.hpp.

References CleaveAt, CSeqConvert::Convert(), CSeqUtil::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, kCleave, and out().

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetCleaveNum()

int CCleave::GetCleaveNum ( void  ) const
inline

Get the number of cleavage chars.

Definition at line 878 of file msms.hpp.

References kCleave.

Referenced by CPepXML::ConvertFromOMSSA(), and CSearch< LEGACY, NHITS >::Search().

◆ GetCleaveOffset()

const char * CCleave::GetCleaveOffset ( void  ) const
inline

Get the the cleave offset, 0 = cterm, 1 = nterm.

Definition at line 884 of file msms.hpp.

References CleaveOffset.

◆ GetCleaveSense()

const char * CCleave::GetCleaveSense ( void  ) const
inline

Should we check for proline?

Definition at line 706 of file msms.hpp.

References CleaveOffset.

Referenced by CPepXML::ConvertFromOMSSA().

◆ GetNMethionine()

bool CCleave::GetNMethionine ( void  ) const
inline

Is there n-term methionine cleavage?

Definition at line 890 of file msms.hpp.

References NMethionine.

◆ GetNonSpecific()

bool CCleave::GetNonSpecific ( void  ) const
inline

Is this a non-specific search?

Definition at line 860 of file msms.hpp.

References NonSpecific.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ GetStop()

const char * CCleave::GetStop ( void  ) const
inline

Get the enzyme stop value.

Definition at line 866 of file msms.hpp.

References Stop.

Referenced by CheckCleave(), and CSearch< LEGACY, NHITS >::Search().

◆ GetTopDown()

bool CCleave::GetTopDown ( void  ) const
inline

Is the enzyme really a top-down search?

Definition at line 854 of file msms.hpp.

References TopDown.

Referenced by CalcAndCut().

◆ SetNMethionine()

bool & CCleave::SetNMethionine ( void  )
inline

Set n-term methionine cleavage.

Definition at line 897 of file msms.hpp.

References NMethionine.

Referenced by CSearch< LEGACY, NHITS >::Search().

◆ SetStop()

const char *& CCleave::SetStop ( void  )
inline

Set the enzyme stop value.

Definition at line 872 of file msms.hpp.

References Stop.

Referenced by CSearch< LEGACY, NHITS >::Search().

Member Data Documentation

◆ CheckProline

bool CCleave::CheckProline
protected

◆ CleaveAt

const char* CCleave::CleaveAt
protected

◆ CleaveOffset

const char* CCleave::CleaveOffset
protected

◆ kCleave

int CCleave::kCleave
protected

◆ NMethionine

bool CCleave::NMethionine
protected

n-terminal methionine cleavage

Definition at line 673 of file msms.hpp.

Referenced by CalcAndCut(), CheckCleave(), GetNMethionine(), and SetNMethionine().

◆ NonSpecific

bool CCleave::NonSpecific
protected

◆ ProtonMass

int CCleave::ProtonMass
protected

Definition at line 628 of file msms.hpp.

Referenced by CCleave().

◆ ReverseAA

CAA CCleave::ReverseAA
protected

Definition at line 630 of file msms.hpp.

Referenced by CalcMass().

◆ Stop

const char* CCleave::Stop
protected

Stop Stop position for no-enzyme and semi-tryptic searches.

Definition at line 658 of file msms.hpp.

Referenced by GetStop(), and SetStop().

◆ TermMass

int CCleave::TermMass
protected

Definition at line 629 of file msms.hpp.

Referenced by CCleave(), and EndMass().

◆ TopDown

bool CCleave::TopDown
protected

The documentation for this class was generated from the following files:
Modified on Wed May 22 11:34:55 2024 by modify_doxy.py rev. 669887