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... | |
| TEvalue & | SetEvalue (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... | |
| TPvalue & | SetPvalue (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... | |
| TCharge & | SetCharge (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 TPephits & | GetPephits (void) const |
| Get the Pephits member data. More... | |
| TPephits & | SetPephits (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 TMzhits & | GetMzhits (void) const |
| Get the Mzhits member data. More... | |
| TMzhits & | SetMzhits (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 TPepstring & | GetPepstring (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) |
| TPepstring & | SetPepstring (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... | |
| TMass & | SetMass (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 TMods & | GetMods (void) const |
| Get the Mods member data. More... | |
| TMods & | SetMods (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 TPepstart & | GetPepstart (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) |
| TPepstart & | SetPepstart (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 TPepstop & | GetPepstop (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) |
| TPepstop & | SetPepstop (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... | |
| TProtlength & | SetProtlength (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... | |
| TTheomass & | SetTheomass (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... | |
| TOid & | SetOid (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 TScores & | GetScores (void) const |
| Get the Scores member data. More... | |
| TScores & | SetScores (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 TLibaccession & | GetLibaccession (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) |
| TLibaccession & | SetLibaccession (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 CTypeInfo * | GetThisTypeInfo (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 string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (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... | |
| 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... | |
| 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) | |
| CMSHits & | operator= (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< Uint8 > | TCounter |
| 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
|
private |
Definition at line 57 of file MSHits.hpp.
Constructor & Destructor Documentation
◆ CMSHits() [1/2]
|
inline |
Definition at line 85 of file MSHits.hpp.
◆ ~CMSHits()
| CMSHits::~CMSHits | ( | void | ) |
Definition at line 53 of file MSHits.cpp.
◆ CMSHits() [2/2]
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=()
The documentation for this class was generated from the following files:
- include/objects/omssa/MSHits.hpp
- src/objects/omssa/MSHits.cpp
