NCBI C++ ToolKit
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COMSSASearch Class Reference

Search Toolkit Book for COMSSASearch

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

+ Inheritance diagram for COMSSASearch:
+ Collaboration diagram for COMSSASearch:

Public Member Functions

 COMSSASearch (void)
 
 ~COMSSASearch (void)
 
void CopyCMSSearch (CRef< COMSSASearch > OldSearch)
 copy a search onto this search More...
 
void CopySpectra (CRef< COMSSASearch > OldSearch)
 copy a spectra from old search into this search More...
 
void CopyHitsets (CRef< COMSSASearch > OldSearch)
 copy Hitsets from old search into new this search More...
 
void CopySettings (CRef< COMSSASearch > OldSearch)
 copy Settings from old search into new this search More...
 
const string FileEnding (const ESerialDataFormat FileType) const
 return a file ending based on encoding type More...
 
void FindMinMaxSearchSettingId (int &Min, int &Max) const
 find the maximum and minimum search setting id in this search More...
 
void FindMinMaxSpectrumNumber (int &Min, int &Max) const
 find the maximum and minimum spectrum number in this search More...
 
const bool CheckLibraryNameAndSize (const string Name, const int Size) const
 check for matching library name and size in all search settings More...
 
void RenumberSearchSettingId (const int Min)
 renumber search settings by adding a minimum value More...
 
void RenumberSpectrumNumber (const int Min)
 renumber spectrum numbers by adding a minimum value More...
 
const TOidGetOids (void) const
 get the oid list More...
 
TOidSetOids (void)
 set the oid list More...
 
void PopulateOidList (void)
 fill in the oid list from existing object More...
 
void AppendBioseq (const int oid, CConstRef< CBioseq > Bioseq)
 add a bioseq to the bioseq list More...
 
void AppendSearch (CRef< COMSSASearch > OldSearch)
 add a search to this object More...
 
- Public Member Functions inherited from CMSSearch
 CMSSearch (void)
 
 ~CMSSearch (void)
 
int SetUpSearchSettings (CRef< CMSSearchSettings > &SearchSettings, bool IsIterative)
 take a search settings object, give it an id, and put it in the right place More...
 
- Public Member Functions inherited from CMSSearch_Base
 CMSSearch_Base (void)
 
virtual ~CMSSearch_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetRequest (void) const
 Check if a value has been assigned to Request data member. More...
 
bool CanGetRequest (void) const
 Check if it is safe to call GetRequest method. More...
 
void ResetRequest (void)
 Reset Request data member. More...
 
const TRequestGetRequest (void) const
 Get the Request member data. More...
 
TRequestSetRequest (void)
 Assign a value to Request data member. More...
 
bool IsSetResponse (void) const
 Check if a value has been assigned to Response data member. More...
 
bool CanGetResponse (void) const
 Check if it is safe to call GetResponse method. More...
 
void ResetResponse (void)
 Reset Response data member. More...
 
const TResponseGetResponse (void) const
 Get the Response member data. More...
 
TResponseSetResponse (void)
 Assign a value to Response 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
 

Protected Member Functions

void FindMinMaxForOneSetting (const CMSSearchSettings &SearchSettings, int &Min, int &Max) const
 helper function for FindMinMaxSearchSettingId More...
 
void RenumberOneSearchSettingId (CMSSearchSettings &SearchSettings, const int Min)
 renumber one search setting More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Types

typedef CMSSearch Tparent
 

Private Member Functions

 COMSSASearch (const COMSSASearch &value)
 
COMSSASearchoperator= (const COMSSASearch &value)
 

Private Attributes

TOid Oids
 list of oids in used in search More...
 

Additional Inherited Members

- Public Types inherited from CMSSearch_Base
enum class  E_memberIndex { e__allMandatory = 0 , e_request , e_response }
 
typedef list< CRef< CMSRequest > > TRequest
 
typedef list< CRef< CMSResponse > > TResponse
 
typedef Tparent::CMemberIndex< E_memberIndex, 3 > 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...
 

Detailed Description

Definition at line 55 of file msmerge.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 57 of file msmerge.hpp.

Constructor & Destructor Documentation

◆ COMSSASearch() [1/2]

COMSSASearch::COMSSASearch ( void  )
inline

Definition at line 62 of file msmerge.hpp.

◆ ~COMSSASearch()

COMSSASearch::~COMSSASearch ( void  )
inline

Definition at line 64 of file msmerge.hpp.

◆ COMSSASearch() [2/2]

COMSSASearch::COMSSASearch ( const COMSSASearch value)
private

Member Function Documentation

◆ AppendBioseq()

void COMSSASearch::AppendBioseq ( const int  oid,
CConstRef< CBioseq Bioseq 
)

add a bioseq to the bioseq list

Definition at line 246 of file msmerge.cpp.

References CConstRef< C, Locker >::GetPointerOrNull(), and CMSSearch_Base::SetResponse().

Referenced by AppendSearch().

◆ AppendSearch()

void COMSSASearch::AppendSearch ( CRef< COMSSASearch OldSearch)

◆ CheckLibraryNameAndSize()

const bool COMSSASearch::CheckLibraryNameAndSize ( const string  Name,
const int  Size 
) const

check for matching library name and size in all search settings

Returns
true if all match

Definition at line 174 of file msmerge.cpp.

References Get(), CMSSearch_Base::GetRequest(), CMSSearch_Base::GetResponse(), ITERATE, NCBI_THROW, and ncbi::grid::netcache::search::fields::size.

Referenced by AppendSearch().

◆ CopyCMSSearch()

void COMSSASearch::CopyCMSSearch ( CRef< COMSSASearch OldSearch)

copy a search onto this search

Parameters
OldSearchthe search to be copied

Definition at line 63 of file msmerge.cpp.

References CObjectOStream::Flush().

◆ CopyHitsets()

void COMSSASearch::CopyHitsets ( CRef< COMSSASearch OldSearch)

copy Hitsets from old search into new this search

Parameters
OldSearchthe search to be copied

Definition at line 152 of file msmerge.cpp.

References NON_CONST_ITERATE, and CMSSearch_Base::SetResponse().

Referenced by AppendSearch().

◆ CopySettings()

void COMSSASearch::CopySettings ( CRef< COMSSASearch OldSearch)

copy Settings from old search into new this search

Parameters
OldSearchthe search to be copied

Definition at line 160 of file msmerge.cpp.

References NON_CONST_ITERATE, and CMSSearch_Base::SetRequest().

Referenced by AppendSearch().

◆ CopySpectra()

void COMSSASearch::CopySpectra ( CRef< COMSSASearch OldSearch)

copy a spectra from old search into this search

Parameters
OldSearchthe search to be copied

Definition at line 144 of file msmerge.cpp.

References NON_CONST_ITERATE, and CMSSearch_Base::SetRequest().

Referenced by AppendSearch().

◆ FileEnding()

const string COMSSASearch::FileEnding ( const ESerialDataFormat  FileType) const

return a file ending based on encoding type

Parameters
FileTypeencoding type
Returns
file extension without separator

Definition at line 79 of file msmerge.cpp.

References eSerial_AsnBinary, eSerial_AsnText, and eSerial_Xml.

◆ FindMinMaxForOneSetting()

void COMSSASearch::FindMinMaxForOneSetting ( const CMSSearchSettings SearchSettings,
int Min,
int Max 
) const
protected

helper function for FindMinMaxSearchSettingId

Definition at line 89 of file msmerge.cpp.

References CMSSearchSettings_Base::GetSettingid().

Referenced by FindMinMaxSearchSettingId().

◆ FindMinMaxSearchSettingId()

void COMSSASearch::FindMinMaxSearchSettingId ( int Min,
int Max 
) const

find the maximum and minimum search setting id in this search

Parameters
Minminimum
Maxmaximum

Definition at line 100 of file msmerge.cpp.

References FindMinMaxForOneSetting(), Get(), CMSSearch_Base::GetRequest(), ITERATE, max(), min(), and NCBI_THROW.

Referenced by AppendSearch().

◆ FindMinMaxSpectrumNumber()

void COMSSASearch::FindMinMaxSpectrumNumber ( int Min,
int Max 
) const

find the maximum and minimum spectrum number in this search

Parameters
Minminimum
Maxmaximum

Definition at line 121 of file msmerge.cpp.

References Get(), CMSSearch_Base::GetRequest(), ITERATE, max(), min(), and NCBI_THROW.

Referenced by AppendSearch().

◆ GetOids()

const TOid & COMSSASearch::GetOids ( void  ) const
inline

get the oid list

Definition at line 202 of file msmerge.hpp.

References Oids.

Referenced by AppendSearch().

◆ operator=()

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

◆ PopulateOidList()

void COMSSASearch::PopulateOidList ( void  )

fill in the oid list from existing object

Definition at line 237 of file msmerge.cpp.

References ITERATE, SetOids(), and CMSSearch_Base::SetResponse().

Referenced by AppendSearch().

◆ RenumberOneSearchSettingId()

void COMSSASearch::RenumberOneSearchSettingId ( CMSSearchSettings SearchSettings,
const int  Min 
)
protected

renumber one search setting

Definition at line 196 of file msmerge.cpp.

References CMSSearchSettings_Base::SetSettingid().

Referenced by RenumberSearchSettingId().

◆ RenumberSearchSettingId()

void COMSSASearch::RenumberSearchSettingId ( const int  Min)

renumber search settings by adding a minimum value

Parameters
Minminimum value to add

Definition at line 205 of file msmerge.cpp.

References CMSSearch_Base::GetRequest(), NON_CONST_ITERATE, RenumberOneSearchSettingId(), CMSSearch_Base::SetRequest(), and CMSSearch_Base::SetResponse().

◆ RenumberSpectrumNumber()

void COMSSASearch::RenumberSpectrumNumber ( const int  Min)

renumber spectrum numbers by adding a minimum value

Parameters
Minminimum value to add

Definition at line 222 of file msmerge.cpp.

References NON_CONST_ITERATE, CMSSearch_Base::SetRequest(), and CMSSearch_Base::SetResponse().

◆ SetOids()

TOid & COMSSASearch::SetOids ( void  )
inline

set the oid list

Definition at line 209 of file msmerge.hpp.

References Oids.

Referenced by PopulateOidList().

Member Data Documentation

◆ Oids

TOid COMSSASearch::Oids
private

list of oids in used in search

Definition at line 196 of file msmerge.hpp.

Referenced by GetOids(), and SetOids().


The documentation for this class was generated from the following files:
Modified on Tue Apr 16 20:15:25 2024 by modify_doxy.py rev. 669887