NCBI C++ ToolKit
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CMSHits Class Reference

Represents ASN.1 type MSHits defined in file omssa.asn

Search Toolkit Book for CMSHits

@MSHits.hpp User-defined methods of the data storage class. More...

#include <objects/omssa/MSHits.hpp>

+ Inheritance diagram for CMSHits:
+ Collaboration diagram for CMSHits:

Public Member Functions

 CMSHits (void)
 
 ~CMSHits (void)
 
void MakeModString (string &StringOut, CRef< CMSModSpecSet > Modset) const
 Makes a string of mods, positions for display purposes. More...
 
void MakePepString (string &StringOut) const
 Makes a peptide AA string, lower case for mods. More...
 
- Public Member Functions inherited from CMSHits_Base
 CMSHits_Base (void)
 
virtual ~CMSHits_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetEvalue (void) const
 E-value (expect value) Check if a value has been assigned to Evalue data member. More...
 
bool CanGetEvalue (void) const
 Check if it is safe to call GetEvalue method. More...
 
void ResetEvalue (void)
 Reset Evalue data member. More...
 
TEvalue GetEvalue (void) const
 Get the Evalue member data. More...
 
void SetEvalue (TEvalue value)
 Assign a value to Evalue data member. More...
 
TEvalueSetEvalue (void)
 Assign a value to Evalue data member. More...
 
bool IsSetPvalue (void) const
 P-value (probability value) Check if a value has been assigned to Pvalue data member. More...
 
bool CanGetPvalue (void) const
 Check if it is safe to call GetPvalue method. More...
 
void ResetPvalue (void)
 Reset Pvalue data member. More...
 
TPvalue GetPvalue (void) const
 Get the Pvalue member data. More...
 
void SetPvalue (TPvalue value)
 Assign a value to Pvalue data member. More...
 
TPvalueSetPvalue (void)
 Assign a value to Pvalue data member. More...
 
bool IsSetCharge (void) const
 the charge state used in search. More...
 
bool CanGetCharge (void) const
 Check if it is safe to call GetCharge method. More...
 
void ResetCharge (void)
 Reset Charge data member. More...
 
TCharge GetCharge (void) const
 Get the Charge member data. More...
 
void SetCharge (TCharge value)
 Assign a value to Charge data member. More...
 
TChargeSetCharge (void)
 Assign a value to Charge data member. More...
 
bool IsSetPephits (void) const
 peptides that match this hit Check if a value has been assigned to Pephits data member. More...
 
bool CanGetPephits (void) const
 Check if it is safe to call GetPephits method. More...
 
void ResetPephits (void)
 Reset Pephits data member. More...
 
const TPephitsGetPephits (void) const
 Get the Pephits member data. More...
 
TPephitsSetPephits (void)
 Assign a value to Pephits data member. More...
 
bool IsSetMzhits (void) const
 ions hit Check if a value has been assigned to Mzhits data member. More...
 
bool CanGetMzhits (void) const
 Check if it is safe to call GetMzhits method. More...
 
void ResetMzhits (void)
 Reset Mzhits data member. More...
 
const TMzhitsGetMzhits (void) const
 Get the Mzhits member data. More...
 
TMzhitsSetMzhits (void)
 Assign a value to Mzhits data member. More...
 
bool IsSetPepstring (void) const
 the peptide sequence Check if a value has been assigned to Pepstring data member. More...
 
bool CanGetPepstring (void) const
 Check if it is safe to call GetPepstring method. More...
 
void ResetPepstring (void)
 Reset Pepstring data member. More...
 
const TPepstringGetPepstring (void) const
 Get the Pepstring member data. More...
 
void SetPepstring (const TPepstring &value)
 Assign a value to Pepstring data member. More...
 
void SetPepstring (TPepstring &&value)
 
TPepstringSetPepstring (void)
 Assign a value to Pepstring data member. More...
 
bool IsSetMass (void) const
 scaled experimental mass of peptide in Da Check if a value has been assigned to Mass data member. More...
 
bool CanGetMass (void) const
 Check if it is safe to call GetMass method. More...
 
void ResetMass (void)
 Reset Mass data member. More...
 
TMass GetMass (void) const
 Get the Mass member data. More...
 
void SetMass (TMass value)
 Assign a value to Mass data member. More...
 
TMassSetMass (void)
 Assign a value to Mass data member. More...
 
bool IsSetMods (void) const
 modifications to sequence Check if a value has been assigned to Mods data member. More...
 
bool CanGetMods (void) const
 Check if it is safe to call GetMods method. More...
 
void ResetMods (void)
 Reset Mods data member. More...
 
const TModsGetMods (void) const
 Get the Mods member data. More...
 
TModsSetMods (void)
 Assign a value to Mods data member. More...
 
bool IsSetPepstart (void) const
 AA before the peptide (depricated) Check if a value has been assigned to Pepstart data member. More...
 
bool CanGetPepstart (void) const
 Check if it is safe to call GetPepstart method. More...
 
void ResetPepstart (void)
 Reset Pepstart data member. More...
 
const TPepstartGetPepstart (void) const
 Get the Pepstart member data. More...
 
void SetPepstart (const TPepstart &value)
 Assign a value to Pepstart data member. More...
 
void SetPepstart (TPepstart &&value)
 
TPepstartSetPepstart (void)
 Assign a value to Pepstart data member. More...
 
bool IsSetPepstop (void) const
 AA after the peptide (depricated) Check if a value has been assigned to Pepstop data member. More...
 
bool CanGetPepstop (void) const
 Check if it is safe to call GetPepstop method. More...
 
void ResetPepstop (void)
 Reset Pepstop data member. More...
 
const TPepstopGetPepstop (void) const
 Get the Pepstop member data. More...
 
void SetPepstop (const TPepstop &value)
 Assign a value to Pepstop data member. More...
 
void SetPepstop (TPepstop &&value)
 
TPepstopSetPepstop (void)
 Assign a value to Pepstop data member. More...
 
bool IsSetProtlength (void) const
 length of protein hit (depricated) Check if a value has been assigned to Protlength data member. More...
 
bool CanGetProtlength (void) const
 Check if it is safe to call GetProtlength method. More...
 
void ResetProtlength (void)
 Reset Protlength data member. More...
 
TProtlength GetProtlength (void) const
 Get the Protlength member data. More...
 
void SetProtlength (TProtlength value)
 Assign a value to Protlength data member. More...
 
TProtlengthSetProtlength (void)
 Assign a value to Protlength data member. More...
 
bool IsSetTheomass (void) const
 scaled theoretical mass of peptide hit Check if a value has been assigned to Theomass data member. More...
 
bool CanGetTheomass (void) const
 Check if it is safe to call GetTheomass method. More...
 
void ResetTheomass (void)
 Reset Theomass data member. More...
 
TTheomass GetTheomass (void) const
 Get the Theomass member data. More...
 
void SetTheomass (TTheomass value)
 Assign a value to Theomass data member. More...
 
TTheomassSetTheomass (void)
 Assign a value to Theomass data member. More...
 
bool IsSetOid (void) const
 blast library oid (depricated) Check if a value has been assigned to Oid data member. More...
 
bool CanGetOid (void) const
 Check if it is safe to call GetOid method. More...
 
void ResetOid (void)
 Reset Oid data member. More...
 
TOid GetOid (void) const
 Get the Oid member data. More...
 
void SetOid (TOid value)
 Assign a value to Oid data member. More...
 
TOidSetOid (void)
 Assign a value to Oid data member. More...
 
bool IsSetScores (void) const
 optional scores (for library search) Check if a value has been assigned to Scores data member. More...
 
bool CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void ResetScores (void)
 Reset Scores data member. More...
 
const TScoresGetScores (void) const
 Get the Scores member data. More...
 
TScoresSetScores (void)
 Assign a value to Scores data member. More...
 
bool IsSetLibaccession (void) const
 library search accesssion Check if a value has been assigned to Libaccession data member. More...
 
bool CanGetLibaccession (void) const
 Check if it is safe to call GetLibaccession method. More...
 
void ResetLibaccession (void)
 Reset Libaccession data member. More...
 
const TLibaccessionGetLibaccession (void) const
 Get the Libaccession member data. More...
 
void SetLibaccession (const TLibaccession &value)
 Assign a value to Libaccession data member. More...
 
void SetLibaccession (TLibaccession &&value)
 
TLibaccessionSetLibaccession (void)
 Assign a value to Libaccession data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (void) const =0
 
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
 Set object to copy of another one. More...
 
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
 Check if both objects contain the same values. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
void ThrowUnassigned (TMemberIndex index) const
 
void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
 
bool HasNamespaceName (void) const
 Check if object data type has namespace name. More...
 
const stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. 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...
 
- 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
 

Private Types

typedef CMSHits_Base Tparent
 

Private Member Functions

 CMSHits (const CMSHits &value)
 
CMSHitsoperator= (const CMSHits &value)
 

Additional Inherited Members

- Public Types inherited from CMSHits_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_evalue , e_pvalue , e_charge ,
  e_pephits , e_mzhits , e_pepstring , e_mass ,
  e_mods , e_pepstart , e_pepstop , e_protlength ,
  e_theomass , e_oid , e_scores , e_libaccession
}
 
typedef double TEvalue
 
typedef double TPvalue
 
typedef int TCharge
 
typedef list< CRef< CMSPepHit > > TPephits
 
typedef list< CRef< CMSMZHit > > TMzhits
 
typedef string TPepstring
 
typedef int TMass
 
typedef list< CRef< CMSModHit > > TMods
 
typedef string TPepstart
 
typedef string TPepstop
 
typedef int TProtlength
 
typedef int TTheomass
 
typedef int TOid
 
typedef list< CRef< CMSScoreSet > > TScores
 
typedef string TLibaccession
 
typedef Tparent::CMemberIndex< E_memberIndex, 16 > TmemberIndex
 
- 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 CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- 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 CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- 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

@MSHits.hpp User-defined methods of the data storage class.

This file was originally generated by application DATATOOL using the following specifications: 'omssa.asn'.

New methods or data members can be added to it if needed. See also: MSHits_.hpp

Definition at line 55 of file MSHits.hpp.

Member Typedef Documentation

◆ Tparent

typedef CMSHits_Base CMSHits::Tparent
private

Definition at line 57 of file MSHits.hpp.

Constructor & Destructor Documentation

◆ CMSHits() [1/2]

CMSHits::CMSHits ( void  )
inline

Definition at line 85 of file MSHits.hpp.

◆ ~CMSHits()

CMSHits::~CMSHits ( void  )

Definition at line 53 of file MSHits.cpp.

◆ CMSHits() [2/2]

CMSHits::CMSHits ( const CMSHits value)
private

Member Function Documentation

◆ MakeModString()

void CMSHits::MakeModString ( string StringOut,
CRef< CMSModSpecSet Modset 
) const

Makes a string of mods, positions for display purposes.

Definition at line 61 of file MSHits.cpp.

References CMSHits_Base::CanGetMods(), eMSMod_max, CMSModSpecSet::GetModName(), CMSHits_Base::GetMods(), i, NStr::IntToString(), and ITERATE.

◆ MakePepString()

void CMSHits::MakePepString ( string StringOut) const

Makes a peptide AA string, lower case for mods.

Definition at line 78 of file MSHits.cpp.

References CMSHits_Base::CanGetPepstring(), CMSHits_Base::GetMods(), CMSHits_Base::GetPepstring(), i, ITERATE, tolower(), and NStr::ToUpper().

◆ operator=()

CMSHits& CMSHits::operator= ( const CMSHits value)
private

The documentation for this class was generated from the following files:
Modified on Sun Mar 03 03:10:27 2024 by modify_doxy.py rev. 669887