NCBI C++ ToolKit
Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Static Protected Member Functions | Private Types | Private Member Functions | Private Attributes | Static Private Attributes | List of all members

Represents ASN.1 type Search defined in file blastxml2.asn

Search Toolkit Book for CSearch

CSearch –. More...

#include <objects/blastxml2/Search.hpp>

+ Inheritance diagram for CSearch< LEGACY, NHITS >:
+ Collaboration diagram for CSearch< LEGACY, NHITS >:

Public Member Functions

 CSearch (void)
 
 ~CSearch (void)
 
 CSearch (const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)
 Object constructor. More...
 
void SetSubjInfo ()
 Set the parameters of the current subject sequence. More...
 
TSeqPos DecodeOffset (TWord offset)
 Decode offset value into subject position. More...
 
 CSearch (int tNum)
 
 ~CSearch (void)
 
int InitBlast (const char *blastdb, bool use_mmap=false)
 init blast databases. More...
 
void Search (CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)
 Performs the ms/ms search. More...
 
void SetupSearch (CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)
 Setup the ms/ms search. More...
 
CMSMatchedPeakSetPepCharge (CMSHit &Hit, int SeriesCharge, int Ion, int MinIntensity, int Which, CMSPeak *Peaks, int Maxproductions)
 fill out MatchedPeakSet More...
 
boolSetRankScore (void)
 Sets the scoring to use rank statistics. More...
 
boolSetPoissonOnly (void)
 Sets the scoring to use rank statistics only with Poisson. More...
 
const bool GetPoissonOnly (void) const
 Gets the scoring to use rank statistics only with Poisson. More...
 
boolSetIterative (void)
 Sets iterate search. More...
 
const bool GetIterative (void) const
 Gets iterate search. More...
 
virtual void * Main (void)
 Derived (user-created) class must provide a real thread function. More...
 
virtual void OnExit (void)
 Override this to execute finalization code. More...
 
void CopySettings (CRef< CSearch > fromObj)
 
void TestPersist (void)
 
void SetResult (CRef< CMSPeakSet > PeakSet)
 
- Public Member Functions inherited from CSearch_Base< LEGACY, NHITS, derived_t >
 CSearch_Base (void)
 
virtual ~CSearch_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetQuery_id (void) const
 SeqId of query Check if a value has been assigned to Query_id data member. More...
 
bool CanGetQuery_id (void) const
 Check if it is safe to call GetQuery_id method. More...
 
void ResetQuery_id (void)
 Reset Query_id data member. More...
 
const TQuery_idGetQuery_id (void) const
 Get the Query_id member data. More...
 
void SetQuery_id (const TQuery_id &value)
 Assign a value to Query_id data member. More...
 
void SetQuery_id (TQuery_id &&value)
 
TQuery_idSetQuery_id (void)
 Assign a value to Query_id data member. More...
 
bool IsSetQuery_title (void) const
 Definition line of query Check if a value has been assigned to Query_title data member. More...
 
bool CanGetQuery_title (void) const
 Check if it is safe to call GetQuery_title method. More...
 
void ResetQuery_title (void)
 Reset Query_title data member. More...
 
const TQuery_titleGetQuery_title (void) const
 Get the Query_title member data. More...
 
void SetQuery_title (const TQuery_title &value)
 Assign a value to Query_title data member. More...
 
void SetQuery_title (TQuery_title &&value)
 
TQuery_titleSetQuery_title (void)
 Assign a value to Query_title data member. More...
 
bool IsSetQuery_len (void) const
 length of query sequence Check if a value has been assigned to Query_len data member. More...
 
bool CanGetQuery_len (void) const
 Check if it is safe to call GetQuery_len method. More...
 
void ResetQuery_len (void)
 Reset Query_len data member. More...
 
TQuery_len GetQuery_len (void) const
 Get the Query_len member data. More...
 
void SetQuery_len (TQuery_len value)
 Assign a value to Query_len data member. More...
 
TQuery_lenSetQuery_len (void)
 Assign a value to Query_len data member. More...
 
bool IsSetQuery_masking (void) const
 Masked offsets. More...
 
bool CanGetQuery_masking (void) const
 Check if it is safe to call GetQuery_masking method. More...
 
void ResetQuery_masking (void)
 Reset Query_masking data member. More...
 
const TQuery_maskingGetQuery_masking (void) const
 Get the Query_masking member data. More...
 
TQuery_maskingSetQuery_masking (void)
 Assign a value to Query_masking data member. More...
 
bool IsSetHits (void) const
 Hits one for every db sequence Check if a value has been assigned to Hits data member. More...
 
bool CanGetHits (void) const
 Check if it is safe to call GetHits method. More...
 
void ResetHits (void)
 Reset Hits data member. More...
 
const THitsGetHits (void) const
 Get the Hits member data. More...
 
THitsSetHits (void)
 Assign a value to Hits data member. More...
 
bool IsSetStat (void) const
 search statistics Check if a value has been assigned to Stat data member. More...
 
bool CanGetStat (void) const
 Check if it is safe to call GetStat method. More...
 
void ResetStat (void)
 Reset Stat data member. More...
 
const TStatGetStat (void) const
 Get the Stat member data. More...
 
void SetStat (TStat &value)
 Assign a value to Stat data member. More...
 
TStatSetStat (void)
 Assign a value to Stat data member. More...
 
bool IsSetMessage (void) const
 Some (error?) information Check if a value has been assigned to Message data member. More...
 
bool CanGetMessage (void) const
 Check if it is safe to call GetMessage method. More...
 
void ResetMessage (void)
 Reset Message data member. More...
 
const TMessageGetMessage (void) const
 Get the Message member data. More...
 
void SetMessage (const TMessage &value)
 Assign a value to Message data member. More...
 
void SetMessage (TMessage &&value)
 
TMessageSetMessage (void)
 Assign a value to Message data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
 CSearch_Base (const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)
 Object constructor. More...
 
CConstRef< CDbIndex::CSearchResultsoperator() ()
 Performs the search. 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
 
- Public Member Functions inherited from CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
 CSearch_Base (void)
 
 CSearch_Base (const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)
 Object constructor. More...
 
virtual ~CSearch_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetQuery_id (void) const
 SeqId of query Check if a value has been assigned to Query_id data member. More...
 
bool CanGetQuery_id (void) const
 Check if it is safe to call GetQuery_id method. More...
 
void ResetQuery_id (void)
 Reset Query_id data member. More...
 
const TQuery_idGetQuery_id (void) const
 Get the Query_id member data. More...
 
void SetQuery_id (const TQuery_id &value)
 Assign a value to Query_id data member. More...
 
void SetQuery_id (TQuery_id &&value)
 
TQuery_idSetQuery_id (void)
 Assign a value to Query_id data member. More...
 
bool IsSetQuery_title (void) const
 Definition line of query Check if a value has been assigned to Query_title data member. More...
 
bool CanGetQuery_title (void) const
 Check if it is safe to call GetQuery_title method. More...
 
void ResetQuery_title (void)
 Reset Query_title data member. More...
 
const TQuery_titleGetQuery_title (void) const
 Get the Query_title member data. More...
 
void SetQuery_title (const TQuery_title &value)
 Assign a value to Query_title data member. More...
 
void SetQuery_title (TQuery_title &&value)
 
TQuery_titleSetQuery_title (void)
 Assign a value to Query_title data member. More...
 
bool IsSetQuery_len (void) const
 length of query sequence Check if a value has been assigned to Query_len data member. More...
 
bool CanGetQuery_len (void) const
 Check if it is safe to call GetQuery_len method. More...
 
void ResetQuery_len (void)
 Reset Query_len data member. More...
 
TQuery_len GetQuery_len (void) const
 Get the Query_len member data. More...
 
void SetQuery_len (TQuery_len value)
 Assign a value to Query_len data member. More...
 
TQuery_lenSetQuery_len (void)
 Assign a value to Query_len data member. More...
 
bool IsSetQuery_masking (void) const
 Masked offsets. More...
 
bool CanGetQuery_masking (void) const
 Check if it is safe to call GetQuery_masking method. More...
 
void ResetQuery_masking (void)
 Reset Query_masking data member. More...
 
const TQuery_maskingGetQuery_masking (void) const
 Get the Query_masking member data. More...
 
TQuery_maskingSetQuery_masking (void)
 Assign a value to Query_masking data member. More...
 
bool IsSetHits (void) const
 Hits one for every db sequence Check if a value has been assigned to Hits data member. More...
 
bool CanGetHits (void) const
 Check if it is safe to call GetHits method. More...
 
void ResetHits (void)
 Reset Hits data member. More...
 
const THitsGetHits (void) const
 Get the Hits member data. More...
 
THitsSetHits (void)
 Assign a value to Hits data member. More...
 
bool IsSetStat (void) const
 search statistics Check if a value has been assigned to Stat data member. More...
 
bool CanGetStat (void) const
 Check if it is safe to call GetStat method. More...
 
void ResetStat (void)
 Reset Stat data member. More...
 
const TStatGetStat (void) const
 Get the Stat member data. More...
 
void SetStat (TStat &value)
 Assign a value to Stat data member. More...
 
TStatSetStat (void)
 Assign a value to Stat data member. More...
 
bool IsSetMessage (void) const
 Some (error?) information Check if a value has been assigned to Message data member. More...
 
bool CanGetMessage (void) const
 Check if it is safe to call GetMessage method. More...
 
void ResetMessage (void)
 Reset Message data member. More...
 
const TMessageGetMessage (void) const
 Get the Message member data. More...
 
void SetMessage (const TMessage &value)
 Assign a value to Message data member. More...
 
void SetMessage (TMessage &&value)
 
TMessageSetMessage (void)
 Assign a value to Message data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
CConstRef< CDbIndex::CSearchResultsoperator() ()
 Performs the search. More...
 
- Public Member Functions inherited from CThread
 CThread (void)
 Constructor. More...
 
bool Run (TRunMode flags=fRunDefault)
 Run the thread. More...
 
void Detach (void)
 Inform the thread that user does not need to wait for its termination. More...
 
void Join (void **exit_data=0)
 Wait for the thread termination. More...
 
bool Discard (void)
 If the thread has not been Run() yet, then schedule the thread object for destruction, and return TRUE. More...
 
bool IsTerminated (void) const
 Check if the thread has been terminated. More...
 

Static Public Member Functions

static void ResetGlobals (void)
 Reset global parameters used in threaded search. 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 Member Functions inherited from CThread
static void Exit (void *exit_data)
 Cancel current thread. More...
 
static TID GetSelf (void)
 
static bool IsMain (void)
 
static CThreadGetCurrentThread (void)
 Get current CThread object (or NULL, if main thread) More...
 
static void GetSystemID (TThreadSystemID *id)
 Get system ID of the current thread - for internal use only. More...
 
static unsigned int GetThreadsCount ()
 Get total amount of threads This amount does not contain main thread. More...
 
static void SetCurrentThreadName (const CTempString &)
 Set name for the current thread. More...
 
static void InitializeMainThreadId (void)
 Initialize main thread's TID. More...
 
static bool IsAppExiting (void)
 Check if the application is exiting (entered the destructor). More...
 
static void SetWaitForAllThreadsTimeout (const CTimeout &timeout)
 Set timeout for stopping all threads on application exit. More...
 

Static Public Attributes

static CRef< CMSPeakSetSharedPeakSet = null
 
- 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

void DoubleCompare (list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward, list< CMSMatchedPeakSet * > &Double, bool DoubleForward)
 
void MatchAndSort (CMSPeak *Peaks, CMSHit &Hit, EMSPeakListTypes Which, int minintensity, const TSeriesChargePairList::const_iterator &iPairList, list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward)
 Creates match ion match lists. More...
 
void Spectrum2Peak (CRef< CMSPeakSet > PeakSet)
 
void CountModSites (int &NumModSites, int NumMod, CMod ModList[])
 count the number of unique sites modified More...
 
void SetIons (list< EMSIonSeries > &Ions)
 set up the ions to use More...
 
int CreateLadders (const char *Sequence, int iSearch, int position, int endposition, int *Masses, int iMissed, CAA &AA, int iMod, CMod ModList[], int NumMod)
 create the ladders from sequence More...
 
int CompareLadders (int iMod, CMSPeak *Peaks, bool OrLadders, const TMassPeak *MassPeak)
 compare ladders to experiment More...
 
bool CompareLaddersTop (int iMod, CMSPeak *Peaks, const TMassPeak *MassPeak)
 
bool CheckFixed (int i, int NumFixed, CMod ModList[], int *ModIndex)
 Checks to see that given modindex points to a site shared by a fixed mod. More...
 
void InitModIndex (int *ModIndex, int &iMod, int NumMod, int NumModSites, CMod ModList[])
 
unsigned MakeBoolMask (int *ModIndex, int iMod)
 
void MakeBoolMap (bool *ModMask, int *ModIndex, int &iMod, int &NumMod)
 
bool CalcModIndex (int *ModIndex, int &iMod, int &NumMod, int NumFixed, int NumModSites, CMod CModList[])
 
unsigned MakeIntFromBoolMap (bool *ModMask, int &NumMod)
 
const int Getnumseq (void) const
 
void AddModsToHit (CMSHits *Hit, CMSHit *MSHit)
 Adds modification information to hitset. More...
 
void AddIonsToHit (CMSHits *Hit, CMSHit *MSHit)
 Adds ion information to hitset. More...
 
void CreateSequence (int Start, int Stop, string &seqstring, CSeqDBSequence &Sequence)
 Generate a peptide sequence. More...
 
void WriteBioseqs (void)
 write oidset to result More...
 
void CalcNSort (TScoreList &ScoreList, double Threshold, CMSPeak *Peaks)
 calculate the evalues of the top hits and sort More...
 
void DeleteVariableOverlap (int &NumMod, CMod ModList[])
 delete variable mods that overlap with fixed mods More...
 
void UpdateWithNewPep (int Missed, const char *PepStart[], const char *PepEnd[], int NumMod[], CMod ModList[][32], int Masses[], int EndMasses[], int NumModSites[], CRef< CMSModSpecSet > &Modset)
 update sites and masses for new peptide More...
 
void CreateModCombinations (int Missed, const char *PepStart[], int Masses[], int EndMasses[], int NumMod[], int NumMassAndMask[], int NumModSites[], CMod ModList[][32])
 
void InitLadders (std::list< EMSIonSeries > &Ions)
 initialize mass ladders More...
 
void MakeOidSet (void)
 makes map of oid from previous search used in iterative searching More...
 
const bool ReSearch (const int Number) const
 examines a hitset to see if any good hits More...
 
CMSResponse::TOidSetSetOidSet (void)
 get the oidset More...
 
const CMSResponse::TOidSetGetOidSet (void) const
 get the oidset More...
 
boolSetRestrictedSearch (void)
 is this search restricted to the oid set? More...
 
const bool GetRestrictedSearch (void) const
 is this search restricted to the oid set? More...
 
Int1 GetLadderCalc (int i) const
 Get the bit that indicates whether a ladder was calculated. More...
 
Int1SetLadderCalc (int i)
 Set the bit that indicates whether a ladder was calculated. More...
 
void ClearLadderCalc (int Max)
 Clear the ladder calc array up to max index. More...
 
TMassMaskSetMassAndMask (int i, int j)
 Set the mask and mass of mod bit array. More...
 
CRef< CMSSearchSettings > & SetSettings (void)
 Set search settings. More...
 
CConstRef< CMSSearchSettingsGetSettings (void) const
 Get search settings. More...
 
CRef< CMSRequest > & SetRequest (void)
 Set search request. More...
 
CConstRef< CMSRequestGetRequest (void) const
 Get search request. More...
 
CRef< CMSResponse > & SetResponse (void)
 Set search response. More...
 
CConstRef< CMSResponseGetResponse (void) const
 Get search response. More...
 
CRef< CCleave > & SetEnzyme (void)
 Set search enzyme. More...
 
CConstRef< CCleaveGetEnzyme (void) const
 Get search enzyme. More...
 
CLadderContainerSetLadderContainer (void)
 set the ladder container More...
 
const CLadderContainerGetLadderContainer (void) const
 get the ladder container More...
 
- Protected Member Functions inherited from CSearch_Base< LEGACY, NHITS, derived_t >
void SearchInt ()
 Helper method to search a particular segment of the query. More...
 
void ProcessBoundaryOffset (TWord offset, TWord bounds)
 Process a seed candidate that is close to the masked out or ambigous region of the subject. More...
 
void ProcessOffset (TWord offset)
 Process a regular seed candidate. More...
 
void ExtendLeft (TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) const
 Extend a seed candidate to the left. More...
 
void ExtendRight (TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) const
 Extend a seed candidate to the right. More...
 
void ComputeSeeds ()
 Compute the seeds after all roots are collected. More...
 
unsigned long ProcessRoot (TTrackedSeeds &seeds, const SSeedRoot *root)
 Process a single root. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Member Functions inherited from CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
void SearchInt ()
 Helper method to search a particular segment of the query. More...
 
void ProcessBoundaryOffset (TWord offset, TWord bounds)
 Process a seed candidate that is close to the masked out or ambigous region of the subject. More...
 
void ProcessOffset (TWord offset)
 Process a regular seed candidate. More...
 
void ExtendLeft (TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) const
 Extend a seed candidate to the left. More...
 
void ExtendRight (TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) const
 Extend a seed candidate to the right. More...
 
void ComputeSeeds ()
 Compute the seeds after all roots are collected. More...
 
unsigned long ProcessRoot (TTrackedSeeds &seeds, const SSeedRoot *root)
 Process a single root. More...
 
- Protected Member Functions inherited from CThread
virtual ~CThread (void)
 To be called only internally! NOTE: destructor of the derived (user-provided) class should be declared "protected", too! More...
 
TThreadHandle GetThreadHandle ()
 

Static Protected Member Functions

static void MakeModString (string &seqstring, string &modseqstring, CMSHit *MSHit)
 Makes a string hashed out of the sequence plus mods. More...
 

Private Types

typedef CSearch_Base Tparent
 
Convenience declarations.
typedef CSearch_Base< LEGACY, NHITS, CSearchTBase
 
typedef TBase::TIndex_Impl TIndex_Impl
 
typedef TBase::TSearchOptions TSearchOptions
 

Private Member Functions

 CSearch (const CSearch &value)
 
CSearchoperator= (const CSearch &value)
 

Private Attributes

CRef< CSeqDBrdfp
 blast library More...
 
CMassArray MassArray
 
CMassArray PrecursorMassArray
 
CMSMod VariableMods
 
CMSMod FixedMods
 
int numseq
 
CRef< CCleaveEnzyme
 the enzyme in use More...
 
CRef< CMSRequestMyRequest
 Search request. More...
 
CRef< CMSResponseMyResponse
 Search response. More...
 
CRef< CMSSearchSettingsMySettings
 Search params. More...
 
CLadderContainer LadderContainer
 ion series mass ladders More...
 
AutoPtr< Int1, ArrayDeleter< Int1 > > LadderCalc
 bool array that indicates if the ladders been calculated More...
 
AutoPtr< TMassMask, ArrayDeleter< TMassMask > > MassAndMask
 contains bit mask of modifications and resulting mass More...
 
int MaxModPerPep
 maximum number of mod combinations per peptide More...
 
bool UseRankScore
 boolean to turn on rank scoring More...
 
bool PoissonOnly
 boolean to only use Poisson score when using Rank scoring More...
 
bool Iterative
 boolean to turn on iterative search More...
 
CMSResponse::TOidSet OidSet
 set of oids to be searched More...
 
bool RestrictedSearch
 is this a oid restricted search More...
 
int ThreadNum
 The threadid number. More...
 
CRef< CMSRequestinitRequestIn
 These are so CSearch::Main() can call CSearch::Search() in a threaded run, this requires CSearch::SetupSearch() to be called before CSearch::Run() More...
 
CRef< CMSResponseinitResponseIn
 
CRef< CMSModSpecSetinitModset
 
CRef< CMSSearchSettingsinitSettingsIn
 
TOMSSACallback initCallback
 
void * initCallbackData
 

Static Private Attributes

static int MaxMZ = 0
 maximum m/z value of all spectra precursors used to bound non-specific cleavage searches More...
 
static int iSearchGlobal = -1
 Tracks the iSearch number for all search threads. More...
 

Additional Inherited Members

- Public Types inherited from CSearch_Base< LEGACY, NHITS, derived_t >
enum class  E_memberIndex {
  e__allMandatory = 0 , e_query_id , e_query_title , e_query_len ,
  e_query_masking , e_hits , e_stat , e_message
}
 
typedef string TQuery_id
 
typedef string TQuery_title
 
typedef int TQuery_len
 
typedef list< CRef< CRange > > TQuery_masking
 
typedef list< CRef< CHit > > THits
 
typedef CStatistics TStat
 
typedef string TMessage
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex
 
typedef CDbIndex_Impl< LEGACY > TIndex_Impl
 
typedef TIndex_Impl::TSubjectMap TSubjectMap
 
typedef CTrackedSeeds< NHITS > TTrackedSeeds
 
typedef derived_t TDerived
 
- 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...
 
- Public Types inherited from CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
enum class  E_memberIndex
 
typedef string TQuery_id
 
typedef string TQuery_title
 
typedef int TQuery_len
 
typedef list< CRef< CRange > > TQuery_masking
 
typedef list< CRef< CHit > > THits
 
typedef CStatistics TStat
 
typedef string TMessage
 
typedef Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex
 
typedef CDbIndex_Impl< LEGACY > TIndex_Impl
 
typedef TIndex_Impl::TSubjectMap TSubjectMap
 
typedef CTrackedSeeds< NHITS > TTrackedSeeds
 
typedef CSearch< LEGACY, NHITS > TDerived
 
- Public Types inherited from CThread
enum  ERunMode {
  fRunDefault = 0x00 , fRunDetached = 0x01 , fRunBound = 0x10 , fRunUnbound = 0x20 ,
  fRunNice = 0x40 , fRunAllowST = 0x100 , fRunCloneRequestContext = 0x200
}
 Which mode should the thread run in. More...
 
typedef int TRunMode
 Bitwise OR'd flags for thread creation passed to Run(). More...
 
typedef unsigned int TID
 Get ID of current thread. More...
 
- Protected Types inherited from CSearch_Base< LEGACY, NHITS, derived_t >
typedef CDbIndex::SSearchOptions TSearchOptions
 Alias for convenience. More...
 
typedef STrackedSeed< NHITS > TTrackedSeed
 Alias for convenience. More...
 
typedef std::vector< TTrackedSeedsTTrackedSeedsSet
 Representation of the set of currently tracked seeds for all subject sequences. More...
 
- Protected Types inherited from CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
typedef CDbIndex::SSearchOptions TSearchOptions
 Alias for convenience. More...
 
typedef STrackedSeed< NHITS > TTrackedSeed
 Alias for convenience. More...
 
typedef std::vector< TTrackedSeedsTTrackedSeedsSet
 Representation of the set of currently tracked seeds for all subject sequences. More...
 
- Protected Attributes inherited from CSearch_Base< LEGACY, NHITS, derived_t >
const TIndex_Implindex_impl_
 The index implementation object. More...
 
const BLAST_SequenceBlkquery_
 The query sequence encoded in BLASTNA. More...
 
const BlastSeqLoclocs_
 Set of query locations to search. More...
 
TSearchOptions options_
 Search options. More...
 
TTrackedSeedsSet seeds_
 The set of currently tracked seeds. More...
 
TSeqNum subject_
 Logical id of the subject sequence containing the offset value currently being considered. More...
 
TWord subj_start_off_
 Start offset of subject_. More...
 
TWord subj_end_off_
 End offset of subject_. More...
 
TWord subj_start_
 Start position of subject_. More...
 
TWord subj_end_
 One past the end position of subject_. More...
 
TSeqPos qoff_
 Current query offset. More...
 
TSeqPos soff_
 Current subject offset. More...
 
TSeqPos qstart_
 Start of the current query segment. More...
 
TSeqPos qstop_
 One past the end of the current query segment. More...
 
CSeedRoots roots_
 Collection of initial soff/qoff pairs. More...
 
unsigned long code_bits_
 Number of bits to represent special offset prefix. More...
 
unsigned long min_offset_
 Minumum offset used by the index. More...
 
- Protected Attributes inherited from CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
const TIndex_Implindex_impl_
 The index implementation object. More...
 
const BLAST_SequenceBlkquery_
 The query sequence encoded in BLASTNA. More...
 
const BlastSeqLoclocs_
 Set of query locations to search. More...
 
TSearchOptions options_
 Search options. More...
 
TTrackedSeedsSet seeds_
 The set of currently tracked seeds. More...
 
TSeqNum subject_
 Logical id of the subject sequence containing the offset value currently being considered. More...
 
TWord subj_start_off_
 Start offset of subject_. More...
 
TWord subj_end_off_
 End offset of subject_. More...
 
TWord subj_start_
 Start position of subject_. More...
 
TWord subj_end_
 One past the end position of subject_. More...
 
TSeqPos qoff_
 Current query offset. More...
 
TSeqPos soff_
 Current subject offset. More...
 
TSeqPos qstart_
 Start of the current query segment. More...
 
TSeqPos qstop_
 One past the end of the current query segment. More...
 
CSeedRoots roots_
 Collection of initial soff/qoff pairs. More...
 
unsigned long code_bits_
 Number of bits to represent special offset prefix. More...
 
unsigned long min_offset_
 Minumum offset used by the index. More...
 

Detailed Description

template<bool LEGACY, unsigned long NHITS>
class CSearch< LEGACY, NHITS >

CSearch –.

CSearch CRTP (to be removed).

Definition at line 67 of file Search.hpp.

Member Typedef Documentation

◆ TBase

template<bool LEGACY, unsigned long NHITS>
typedef CSearch_Base< LEGACY, NHITS, CSearch > CSearch< LEGACY, NHITS >::TBase
private

Definition at line 1359 of file dbindex_search.cpp.

◆ TIndex_Impl

template<bool LEGACY, unsigned long NHITS>
typedef TBase::TIndex_Impl CSearch< LEGACY, NHITS >::TIndex_Impl
private

Definition at line 1360 of file dbindex_search.cpp.

◆ TSearchOptions

template<bool LEGACY, unsigned long NHITS>
typedef TBase::TSearchOptions CSearch< LEGACY, NHITS >::TSearchOptions
private

Definition at line 1361 of file dbindex_search.cpp.

Constructor & Destructor Documentation

◆ CSearch() [1/2]

template<bool LEGACY, unsigned long NHITS>
CSearch< LEGACY, NHITS >::CSearch ( const TIndex_Impl index_impl,
const BLAST_SequenceBlk query,
const BlastSeqLoc locs,
const TSearchOptions options 
)
inline

Object constructor.

Parameters
index_impl[I] the index implementation object
query[I] query data encoded in BLASTNA
locs[I] set of query locations to search
options[I] search options

Definition at line 1372 of file dbindex_search.cpp.

◆ CSearch() [2/2]

template<bool LEGACY, unsigned long NHITS>
CSearch< LEGACY, NHITS >::CSearch ( int  tNum)

Definition at line 412 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::ThreadNum.

◆ ~CSearch()

template<bool LEGACY, unsigned long NHITS>
CSearch< LEGACY, NHITS >::~CSearch ( void  )

Member Function Documentation

◆ AddIonsToHit()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::AddIonsToHit ( CMSHits Hit,
CMSHit MSHit 
)
protected

◆ AddModsToHit()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::AddModsToHit ( CMSHits Hit,
CMSHit MSHit 
)
protected

◆ CalcModIndex()

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::CalcModIndex ( int ModIndex,
int iMod,
int NumMod,
int  NumFixed,
int  NumModSites,
CMod  CModList[] 
)
inlineprotected

Definition at line 715 of file omssa.hpp.

References CMod::GetSite(), and i.

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

◆ CalcNSort()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::CalcNSort ( TScoreList ScoreList,
double  Threshold,
CMSPeak Peaks 
)
protected

◆ CheckFixed()

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::CheckFixed ( int  i,
int  NumFixed,
CMod  ModList[],
int ModIndex 
)
protected

Checks to see that given modindex points to a site shared by a fixed mod.

Parameters
iindex into ModIndex
NumFixednumber of fixed mods in ModIndex
ModListmodification information
ModIndexarray of iterators pointing to mod ordinals
Returns
true if shared

◆ ClearLadderCalc()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::ClearLadderCalc ( int  Max)
inlineprotected

Clear the ladder calc array up to max index.

Parameters
Maxthe number of indices to clear

Definition at line 778 of file omssa.hpp.

References AutoPtr< X, Del >::get(), and CSearch< LEGACY, NHITS >::LadderCalc.

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

◆ CompareLadders()

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::CompareLadders ( int  iMod,
CMSPeak Peaks,
bool  OrLadders,
const TMassPeak MassPeak 
)
protected

◆ CompareLaddersTop()

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::CompareLaddersTop ( int  iMod,
CMSPeak Peaks,
const TMassPeak MassPeak 
)
protected

◆ CopySettings()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::CopySettings ( CRef< CSearch< LEGACY, NHITS > >  fromObj)

◆ CountModSites()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::CountModSites ( int NumModSites,
int  NumMod,
CMod  ModList[] 
)
protected

count the number of unique sites modified

Parameters
NumModSitesthe number of unique mod sites
NumModthe number of mods
ModListmodification information

Definition at line 755 of file omssa.cpp.

References CMod::GetSite(), and i.

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

◆ CreateLadders()

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::CreateLadders ( const char *  Sequence,
int  iSearch,
int  position,
int  endposition,
int Masses,
int  iMissed,
CAA AA,
int  iMod,
CMod  ModList[],
int  NumMod 
)
protected

◆ CreateModCombinations()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::CreateModCombinations ( int  Missed,
const char *  PepStart[],
int  Masses[],
int  EndMasses[],
int  NumMod[],
int  NumMassAndMask[],
int  NumModSites[],
CMod  ModList[][32] 
)
protected

◆ CreateSequence()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::CreateSequence ( int  Start,
int  Stop,
string seqstring,
CSeqDBSequence Sequence 
)
protected

Generate a peptide sequence.

Parameters
Startstart of sequence
Stopstop of sequence
seqstringsequence string
Sequencesequence object

Definition at line 1494 of file omssa.cpp.

References UniqueAA.

Referenced by CSearch< LEGACY, NHITS >::PepCharge(), and CSearch< LEGACY, NHITS >::SetResult().

◆ DecodeOffset()

template<bool LEGACY, unsigned long NHITS>
TSeqPos CSearch< LEGACY, NHITS >::DecodeOffset ( TWord  offset)
inline

Decode offset value into subject position.

Parameters
offsetOffset value.
Returns
Corresponding position in the subject.

Definition at line 1397 of file dbindex_search.cpp.

References CSubjectMap::DecodeOffset(), CDbIndex_Impl< LEGACY >::GetSubjectMap(), CSearch_Base< LEGACY, NHITS, derived_t >::index_impl_, offset, CSearch< LEGACY, NHITS >::SetSubjInfo(), and CSearch_Base< LEGACY, NHITS, derived_t >::subject_.

◆ DeleteVariableOverlap()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::DeleteVariableOverlap ( int NumMod,
CMod  ModList[] 
)
protected

delete variable mods that overlap with fixed mods

Parameters
NumModthe number of modifications
ModListmodification information

Definition at line 627 of file omssa.cpp.

References i, and CMod::SetFixed().

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

◆ DoubleCompare()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::DoubleCompare ( list< CMSMatchedPeakSet * > &  SingleForward,
list< CMSMatchedPeakSet * > &  SingleBackward,
list< CMSMatchedPeakSet * > &  Double,
bool  DoubleForward 
)
protected
Parameters
SingleForwardsingly charged NC ions
SingleBackwardsingly charged CN ions
Doubledouble charged product ions
DoubleForwardis the double series a forward series?

Definition at line 1869 of file omssa.cpp.

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

◆ GetEnzyme()

template<bool LEGACY, unsigned long NHITS>
CConstRef< CCleave > CSearch< LEGACY, NHITS >::GetEnzyme ( void  ) const
inlineprotected

◆ GetIterative()

template<bool LEGACY, unsigned long NHITS>
const bool CSearch< LEGACY, NHITS >::GetIterative ( void  ) const
inline

◆ GetLadderCalc()

template<bool LEGACY, unsigned long NHITS>
Int1 CSearch< LEGACY, NHITS >::GetLadderCalc ( int  i) const
inlineprotected

Get the bit that indicates whether a ladder was calculated.

Parameters
ithe index of the ladder

Definition at line 766 of file omssa.hpp.

References AutoPtr< X, Del >::get(), i, and CSearch< LEGACY, NHITS >::LadderCalc.

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

◆ GetLadderContainer()

template<bool LEGACY, unsigned long NHITS>
const CLadderContainer & CSearch< LEGACY, NHITS >::GetLadderContainer ( void  ) const
inlineprotected

get the ladder container

Definition at line 906 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::LadderContainer.

◆ Getnumseq()

template<bool LEGACY, unsigned long NHITS>
const int CSearch< LEGACY, NHITS >::Getnumseq ( void  ) const
inlineprotected

◆ GetOidSet()

template<bool LEGACY, unsigned long NHITS>
const CMSResponse::TOidSet & CSearch< LEGACY, NHITS >::GetOidSet ( void  ) const
inlineprotected

get the oidset

Definition at line 862 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::OidSet.

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

◆ GetPoissonOnly()

template<bool LEGACY, unsigned long NHITS>
const bool CSearch< LEGACY, NHITS >::GetPoissonOnly ( void  ) const
inline

Gets the scoring to use rank statistics only with Poisson.

Definition at line 802 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::PoissonOnly.

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

◆ GetRequest()

template<bool LEGACY, unsigned long NHITS>
CConstRef< CMSRequest > CSearch< LEGACY, NHITS >::GetRequest ( void  ) const
inlineprotected

Get search request.

Definition at line 838 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MyRequest.

Referenced by CSearch< LEGACY, NHITS >::Spectrum2Peak().

◆ GetResponse()

template<bool LEGACY, unsigned long NHITS>
CConstRef< CMSResponse > CSearch< LEGACY, NHITS >::GetResponse ( void  ) const
inlineprotected

◆ GetRestrictedSearch()

template<bool LEGACY, unsigned long NHITS>
const bool CSearch< LEGACY, NHITS >::GetRestrictedSearch ( void  ) const
inlineprotected

is this search restricted to the oid set?

Definition at line 880 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::RestrictedSearch.

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

◆ GetSettings()

template<bool LEGACY, unsigned long NHITS>
CConstRef< CMSSearchSettings > CSearch< LEGACY, NHITS >::GetSettings ( void  ) const
inlineprotected

◆ InitBlast()

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::InitBlast ( const char *  blastdb,
bool  use_mmap = false 
)

init blast databases.

stream thru db if InitDB true

Parameters
blastdbname of blast database

Definition at line 429 of file omssa.cpp.

References CSeqDB::eProtein, CSeqDB::GetNumOIDs(), CSearch< LEGACY, NHITS >::numseq, CSearch< LEGACY, NHITS >::rdfp, and CRef< C, Locker >::Reset().

Referenced by COMSSA::Run().

◆ InitLadders()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::InitLadders ( std::list< EMSIonSeries > &  Ions)
protected

◆ InitModIndex()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::InitModIndex ( int ModIndex,
int iMod,
int  NumMod,
int  NumModSites,
CMod  ModList[] 
)
inlineprotected

Definition at line 654 of file omssa.hpp.

References CMod::GetSite(), and i.

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

◆ Main()

template<bool LEGACY, unsigned long NHITS>
void * CSearch< LEGACY, NHITS >::Main ( void  )
virtual

◆ MakeBoolMap()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::MakeBoolMap ( bool ModMask,
int ModIndex,
int iMod,
int NumMod 
)
inlineprotected

Definition at line 682 of file omssa.hpp.

◆ MakeBoolMask()

template<bool LEGACY, unsigned long NHITS>
unsigned CSearch< LEGACY, NHITS >::MakeBoolMask ( int ModIndex,
int  iMod 
)
inlineprotected

Definition at line 694 of file omssa.hpp.

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

◆ MakeIntFromBoolMap()

template<bool LEGACY, unsigned long NHITS>
unsigned CSearch< LEGACY, NHITS >::MakeIntFromBoolMap ( bool ModMask,
int NumMod 
)
inlineprotected

Definition at line 705 of file omssa.hpp.

◆ MakeModString()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::MakeModString ( string seqstring,
string modseqstring,
CMSHit MSHit 
)
staticprotected

Makes a string hashed out of the sequence plus mods.

Definition at line 1483 of file omssa.cpp.

References CMSModInfo::GetModEnum(), CMSHit::GetModInfo(), CMSHit::GetNumModInfo(), CMSModInfo::GetSite(), i, and NStr::IntToString().

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

◆ MakeOidSet()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::MakeOidSet ( void  )
protected

◆ MatchAndSort()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::MatchAndSort ( CMSPeak Peaks,
CMSHit Hit,
EMSPeakListTypes  Which,
int  minintensity,
const TSeriesChargePairList::const_iterator &  iPairList,
list< CMSMatchedPeakSet * > &  SingleForward,
list< CMSMatchedPeakSet * > &  SingleBackward 
)
protected

Creates match ion match lists.

Parameters
Peakspeak list
Hitthe hit
Whichwhich peak list to use
minintensityminimum intensity
iPairList
ForwardNC ions
BackwardCN ions

Definition at line 1844 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::GetSettings(), kIonDirection, and CSearch< LEGACY, NHITS >::PepCharge().

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

◆ OnExit()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::OnExit ( void  )
virtual

Override this to execute finalization code.

Unlike destructor, this code will be executed before thread termination and as a part of the thread.

Reimplemented from CThread.

Definition at line 966 of file omssa.cpp.

◆ PepCharge()

template<bool LEGACY, unsigned long NHITS>
CMSMatchedPeakSet * CSearch< LEGACY, NHITS >::PepCharge ( CMSHit Hit,
int  SeriesCharge,
int  Ion,
int  MinIntensity,
int  Which,
CMSPeak Peaks,
int  Maxproductions 
)

fill out MatchedPeakSet

Parameters
Hitthe match being evaluated
SeriesChargecharge of ion series
Ionwhich ion series
MinIntensitythe minimum intensity to consider
Whichwhich version of experimental peaks to use
Peaksexperimental peaks
Maxproductionsthe number of ions in each series actually searched
Returns
MatchedPeakSet that was filled out

Definition at line 1750 of file omssa.cpp.

References CMSPeak::CountMZRange(), CSearch< LEGACY, NHITS >::CreateSequence(), eMSBothTerminalBias, eMSCTerminalBias, eMSNoTerminalBias, eMSNTerminalBias, CMSSpectrumMatch::FillMatchedPeaks(), CSearch< LEGACY, NHITS >::GetEnzyme(), CMSSpectrumMatch::GetExpMass(), CRef< C, Locker >::GetPointer(), CMSHit::GetSeqIndex(), CSearch< LEGACY, NHITS >::GetSettings(), CMSHit::GetStart(), CMSHit::GetStop(), CMSPeak::GetTol(), kMSLadderMax, next(), prev(), CSearch< LEGACY, NHITS >::rdfp, CMSSpectrumMatch::SetIonSeriesMatchMap(), CMSMatchedPeakSet::SetMatchedPeakSet(), and CMSMatchedPeakSetMap::SetSeries().

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

◆ ReSearch()

template<bool LEGACY, unsigned long NHITS>
const bool CSearch< LEGACY, NHITS >::ReSearch ( const int  Number) const
protected

examines a hitset to see if any good hits

Parameters
Numberthe spectrum number of the hitset
Returns
true if no good hits

Definition at line 541 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::GetResponse(), CSearch< LEGACY, NHITS >::GetSettings(), and CRef< C, Locker >::IsNull().

Referenced by CSearch< LEGACY, NHITS >::Spectrum2Peak().

◆ ResetGlobals()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::ResetGlobals ( void  )
static

Reset global parameters used in threaded search.

Call whenever rerunning a search.

Definition at line 421 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::iSearchGlobal, CSearch< LEGACY, NHITS >::MaxMZ, CRef< C, Locker >::Reset(), and CSearch< LEGACY, NHITS >::SharedPeakSet.

◆ Search()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::Search ( CRef< CMSRequest MyRequestIn,
CRef< CMSResponse MyResponseIn,
CRef< CMSModSpecSet Modset,
CRef< CMSSearchSettings SettingsIn,
TOMSSACallback  Callback = 0,
void *  CallbackData = 0 
)

Performs the ms/ms search.

Parameters
MyRequestInthe user search params and spectra
MyResponseInthe results of the search
Modsetlist of modifications
SettingsInthe search settings
Callbackcallback function for progress meter
CallbackDatadata passed back to callback fcn

Definition at line 985 of file omssa.cpp.

References CMSPeak::AddHit(), CIntervalTree::AllIntervals(), CLadderContainer::Begin(), CCleave::CalcAndCut(), _MassPeak::Charge, CCleave::CheckCleaveChar(), CSeqDB::CheckOrFindOID(), CSearch< LEGACY, NHITS >::ClearLadderCalc(), CCleaveFactory::CleaveFactory(), CSearch< LEGACY, NHITS >::CompareLadders(), CSearch< LEGACY, NHITS >::CompareLaddersTop(), CSearch< LEGACY, NHITS >::CountModSites(), CSearch< LEGACY, NHITS >::CreateLadders(), CSearch< LEGACY, NHITS >::CreateModCombinations(), CSearch< LEGACY, NHITS >::DeleteVariableOverlap(), eMSModType_modcp, eMSModType_modcpaa, ERR_POST, Fatal(), CSearch< LEGACY, NHITS >::FixedMods, CCleave::GetCleaveNum(), CMod::GetEnum(), CSearch< LEGACY, NHITS >::GetEnzyme(), CMod::GetFixed(), CMassArray::GetIntMass(), CSearch< LEGACY, NHITS >::GetIterative(), CSearch< LEGACY, NHITS >::GetLadderCalc(), CAA::GetMap(), CMSSearchSettings_Base::GetMinnoenzyme(), CMSModSpecSet::GetModType(), CMSSearchSettings_Base::GetNmethionine(), CCleave::GetNonSpecific(), CSearch< LEGACY, NHITS >::Getnumseq(), CRef< C, Locker >::GetPointer(), CSearch< LEGACY, NHITS >::GetResponse(), CSearch< LEGACY, NHITS >::GetRestrictedSearch(), CSearch< LEGACY, NHITS >::GetSettings(), CMod::GetSite(), GetStop(), CCleave::GetStop(), CSeqDB::GetTaxIDs(), CIntervalTreeIterator< Traits >::GetValue(), Info(), CMassArray::Init(), CMSMod::Init(), CSearch< LEGACY, NHITS >::InitLadders(), CIntervalTree::IntervalsContaining(), CSearch< LEGACY, NHITS >::iSearchGlobal, CSearch< LEGACY, NHITS >::LadderCalc, CSearch< LEGACY, NHITS >::MakeOidSet(), _MassPeak::Mass, _MassMask::Mass, CSearch< LEGACY, NHITS >::MassAndMask, CSearch< LEGACY, NHITS >::MassArray, MAXMISSEDCLEAVE, MAXMOD, MAXMOD2, CSearch< LEGACY, NHITS >::MaxModPerPep, CSearch< LEGACY, NHITS >::MaxMZ, MSSCALE, CLadderContainer::Next(), _MassPeak::Peak, CSearch< LEGACY, NHITS >::PrecursorMassArray, CSearch< LEGACY, NHITS >::rdfp, AutoPtr< X, Del >::reset(), CRef< C, Locker >::Reset(), CMod::Reset(), CMSSpectrumMatch::SetCharge(), CMSSearchSettings_Base::SetDoublenum(), CSearch< LEGACY, NHITS >::SetEnzyme(), CMSSpectrumMatch::SetExpMass(), CMSSpectrumMatch::SetHits(), CMSPeakSet::SetIntervalTree(), CSearch< LEGACY, NHITS >::SetIons(), CSearch< LEGACY, NHITS >::SetLadderCalc(), CSearch< LEGACY, NHITS >::SetLadderContainer(), CSearch< LEGACY, NHITS >::SetMassAndMask(), CCleave::SetNMethionine(), CSearch< LEGACY, NHITS >::SetOidSet(), CMSPeak::SetPeptidesExamined(), CSearch< LEGACY, NHITS >::SetRequest(), CSearch< LEGACY, NHITS >::SetResponse(), CMSResponse_Base::SetScale(), CMSSearchSettings_Base::SetScale(), CMSHit::SetSeqIndex(), CSearch< LEGACY, NHITS >::SetSettings(), CMSSearchSettings_Base::SetSinglenum(), CMSHit::SetStart(), CCleave::SetStop(), CMSHit::SetStop(), CSearch< LEGACY, NHITS >::SharedPeakSet, CSearch< LEGACY, NHITS >::Spectrum2Peak(), CSearch< LEGACY, NHITS >::UpdateWithNewPep(), CSearch< LEGACY, NHITS >::UseRankScore, CSearch< LEGACY, NHITS >::VariableMods, and Warning().

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

◆ SetEnzyme()

template<bool LEGACY, unsigned long NHITS>
CRef< CCleave > & CSearch< LEGACY, NHITS >::SetEnzyme ( void  )
inlineprotected

Set search enzyme.

Definition at line 886 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::Enzyme.

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

◆ SetIons()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::SetIons ( list< EMSIonSeries > &  Ions)
protected

set up the ions to use

Parameters
Ionslist of ions to be set up

Definition at line 888 of file omssa.cpp.

References ERR_POST, Fatal(), CSearch< LEGACY, NHITS >::GetSettings(), i, and ncbi::grid::netcache::search::fields::size.

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

◆ SetIterative()

template<bool LEGACY, unsigned long NHITS>
bool & CSearch< LEGACY, NHITS >::SetIterative ( void  )
inline

Sets iterate search.

Definition at line 808 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::Iterative.

Referenced by COMSSA::Run().

◆ SetLadderCalc()

template<bool LEGACY, unsigned long NHITS>
Int1 & CSearch< LEGACY, NHITS >::SetLadderCalc ( int  i)
inlineprotected

Set the bit that indicates whether a ladder was calculated.

Parameters
ithe index of the ladder

Definition at line 772 of file omssa.hpp.

References AutoPtr< X, Del >::get(), i, and CSearch< LEGACY, NHITS >::LadderCalc.

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

◆ SetLadderContainer()

template<bool LEGACY, unsigned long NHITS>
CLadderContainer & CSearch< LEGACY, NHITS >::SetLadderContainer ( void  )
inlineprotected

◆ SetMassAndMask()

template<bool LEGACY, unsigned long NHITS>
TMassMask & CSearch< LEGACY, NHITS >::SetMassAndMask ( int  i,
int  j 
)
inlineprotected

Set the mask and mass of mod bit array.

Parameters
ithe index for missed cleavages
jthe index for modification combinations

Definition at line 784 of file omssa.hpp.

References i, CSearch< LEGACY, NHITS >::MassAndMask, and CSearch< LEGACY, NHITS >::MaxModPerPep.

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

◆ SetOidSet()

template<bool LEGACY, unsigned long NHITS>
CMSResponse::TOidSet & CSearch< LEGACY, NHITS >::SetOidSet ( void  )
inlineprotected

◆ SetPoissonOnly()

template<bool LEGACY, unsigned long NHITS>
bool & CSearch< LEGACY, NHITS >::SetPoissonOnly ( void  )
inline

Sets the scoring to use rank statistics only with Poisson.

Definition at line 796 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::PoissonOnly.

Referenced by COMSSA::Run().

◆ SetRankScore()

template<bool LEGACY, unsigned long NHITS>
bool & CSearch< LEGACY, NHITS >::SetRankScore ( void  )
inline

Sets the scoring to use rank statistics.

Definition at line 790 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::UseRankScore.

Referenced by COMSSA::Run().

◆ SetRequest()

template<bool LEGACY, unsigned long NHITS>
CRef< CMSRequest > & CSearch< LEGACY, NHITS >::SetRequest ( void  )
inlineprotected

Set search request.

Definition at line 832 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MyRequest.

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

◆ SetResponse()

template<bool LEGACY, unsigned long NHITS>
CRef< CMSResponse > & CSearch< LEGACY, NHITS >::SetResponse ( void  )
inlineprotected

◆ SetRestrictedSearch()

template<bool LEGACY, unsigned long NHITS>
bool & CSearch< LEGACY, NHITS >::SetRestrictedSearch ( void  )
inlineprotected

is this search restricted to the oid set?

Definition at line 874 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::RestrictedSearch.

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

◆ SetResult()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::SetResult ( CRef< CMSPeakSet PeakSet)

Definition at line 1508 of file omssa.cpp.

References _TRACE, CSearch< LEGACY, NHITS >::AddIonsToHit(), CSearch< LEGACY, NHITS >::AddModsToHit(), multimap_checker< Container >::begin(), CSearch< LEGACY, NHITS >::CalcNSort(), multimap_checker< Container >::clear(), set< Key, Compare >::clear(), CSearch< LEGACY, NHITS >::CreateSequence(), multimap_checker< Container >::empty(), eMSHitError_notenuffpeaks, map_checker< Container >::end(), multimap_checker< Container >::end(), ERR_POST, Error(), map_checker< Container >::find(), FindBestChoice(), CMSResponse::FindHitSet(), finite, CBlast_def_line_set_Base::Get(), GetCharge(), CMSSpectrumMatch::GetCharge(), CMSPeak::GetError(), CMSSpectrumMatch::GetExpMass(), CSeqDB::GetHdr(), CSearch< LEGACY, NHITS >::GetIterative(), CMSPeak::GetName(), CMSPeak::GetNumber(), CSearch< LEGACY, NHITS >::Getnumseq(), CMSPeakSet::GetPeaks(), CRef< C, Locker >::GetPointer(), GetSeqIdString(), CMSHit::GetSeqIndex(), CSearch< LEGACY, NHITS >::GetSettings(), CMSHit::GetStart(), CMSHit::GetStop(), CMSSpectrumMatch::GetTheoreticalMass(), Info(), set< Key, Compare >::insert(), isnan, CRef< C, Locker >::IsNull(), ITERATE, kHighEval, CSearch< LEGACY, NHITS >::MakeModString(), CSearch< LEGACY, NHITS >::rdfp, CSeq_id::Score(), CMSPepHit_Base::SetAccession(), CMSHits_Base::SetCharge(), CMSResponse_Base::SetDbversion(), CMSPepHit_Base::SetDefline(), CMSHits_Base::SetEvalue(), CMSPepHit_Base::SetGi(), CMSResponse_Base::SetHitsets(), CMSHits_Base::SetMass(), CMSPepHit_Base::SetOid(), CSearch< LEGACY, NHITS >::SetOidSet(), CMSHits_Base::SetPephits(), CMSHits_Base::SetPepstart(), CMSHits_Base::SetPepstop(), CMSHits_Base::SetPepstring(), CMSPepHit_Base::SetProtlength(), CMSHits_Base::SetPvalue(), CSearch< LEGACY, NHITS >::SetResponse(), CMSPepHit_Base::SetStart(), CMSPepHit_Base::SetStop(), CMSHits_Base::SetTheomass(), UniqueAA, CSearch< LEGACY, NHITS >::UseRankScore, Warning(), and CSearch< LEGACY, NHITS >::WriteBioseqs().

◆ SetSettings()

template<bool LEGACY, unsigned long NHITS>
CRef< CMSSearchSettings > & CSearch< LEGACY, NHITS >::SetSettings ( void  )
inlineprotected

◆ SetSubjInfo()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::SetSubjInfo ( )
inline

◆ SetupSearch()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::SetupSearch ( CRef< CMSRequest MyRequestIn,
CRef< CMSResponse MyResponseIn,
CRef< CMSModSpecSet Modset,
CRef< CMSSearchSettings SettingsIn,
TOMSSACallback  Callback = 0,
void *  CallbackData = 0 
)

Setup the ms/ms search.

Parameters
MyRequestInthe user search params and spectra
MyResponseInthe results of the search
Modsetlist of modifications
SettingsInthe search settings
Callbackcallback function for progress meter
CallbackDatadata passed back to callback fcn

Definition at line 940 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::initCallback, CSearch< LEGACY, NHITS >::initCallbackData, CSearch< LEGACY, NHITS >::initModset, CSearch< LEGACY, NHITS >::initRequestIn, CSearch< LEGACY, NHITS >::initResponseIn, and CSearch< LEGACY, NHITS >::initSettingsIn.

Referenced by COMSSA::Run().

◆ Spectrum2Peak()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::Spectrum2Peak ( CRef< CMSPeakSet PeakSet)
protected

◆ TestPersist()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::TestPersist ( void  )
inline

Definition at line 219 of file omssa.hpp.

◆ UpdateWithNewPep()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::UpdateWithNewPep ( int  Missed,
const char *  PepStart[],
const char *  PepEnd[],
int  NumMod[],
CMod  ModList[][32],
int  Masses[],
int  EndMasses[],
int  NumModSites[],
CRef< CMSModSpecSet > &  Modset 
)
protected

update sites and masses for new peptide

Parameters
Missedhow many missed cleavages
PepStartarray of peptide starts
PepEndarray of peptide ends
NumModarray of the number of mods
ModListmodification info
Massespeptide masses
EndMassespeptide end masses
NumModSitesarray of number of unfixed mod sites
Modsetmodification specifications

Definition at line 663 of file omssa.cpp.

References eMSModType_modn, eMSModType_modnaa, eMSModType_modnp, eMSModType_modnpaa, CMSModSpecSet::GetModType(), and MAXMOD.

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

◆ WriteBioseqs()

template<bool LEGACY, unsigned long NHITS>
void CSearch< LEGACY, NHITS >::WriteBioseqs ( void  )
protected

Member Data Documentation

◆ Enzyme

template<bool LEGACY, unsigned long NHITS>
CRef<CCleave> CSearch< LEGACY, NHITS >::Enzyme
private

the enzyme in use

Definition at line 558 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetEnzyme(), and CSearch< LEGACY, NHITS >::SetEnzyme().

◆ FixedMods

template<bool LEGACY, unsigned long NHITS>
CMSMod CSearch< LEGACY, NHITS >::FixedMods
private

Definition at line 552 of file omssa.hpp.

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

◆ initCallback

template<bool LEGACY, unsigned long NHITS>
TOMSSACallback CSearch< LEGACY, NHITS >::initCallback
private

◆ initCallbackData

template<bool LEGACY, unsigned long NHITS>
void* CSearch< LEGACY, NHITS >::initCallbackData
private

◆ initModset

template<bool LEGACY, unsigned long NHITS>
CRef<CMSModSpecSet> CSearch< LEGACY, NHITS >::initModset
private

◆ initRequestIn

template<bool LEGACY, unsigned long NHITS>
CRef<CMSRequest> CSearch< LEGACY, NHITS >::initRequestIn
private

These are so CSearch::Main() can call CSearch::Search() in a threaded run, this requires CSearch::SetupSearch() to be called before CSearch::Run()

Definition at line 640 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::CopySettings(), CSearch< LEGACY, NHITS >::Main(), and CSearch< LEGACY, NHITS >::SetupSearch().

◆ initResponseIn

template<bool LEGACY, unsigned long NHITS>
CRef<CMSResponse> CSearch< LEGACY, NHITS >::initResponseIn
private

◆ initSettingsIn

template<bool LEGACY, unsigned long NHITS>
CRef<CMSSearchSettings> CSearch< LEGACY, NHITS >::initSettingsIn
private

◆ iSearchGlobal

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::iSearchGlobal = -1
staticprivate

Tracks the iSearch number for all search threads.

Definition at line 629 of file omssa.hpp.

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

◆ Iterative

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::Iterative
private

boolean to turn on iterative search

Definition at line 614 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::CopySettings(), CSearch< LEGACY, NHITS >::GetIterative(), and CSearch< LEGACY, NHITS >::SetIterative().

◆ LadderCalc

template<bool LEGACY, unsigned long NHITS>
AutoPtr<Int1, ArrayDeleter<Int1> > CSearch< LEGACY, NHITS >::LadderCalc
private

bool array that indicates if the ladders been calculated

Definition at line 583 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::ClearLadderCalc(), CSearch< LEGACY, NHITS >::GetLadderCalc(), CSearch< LEGACY, NHITS >::Search(), and CSearch< LEGACY, NHITS >::SetLadderCalc().

◆ LadderContainer

template<bool LEGACY, unsigned long NHITS>
CLadderContainer CSearch< LEGACY, NHITS >::LadderContainer
private

ion series mass ladders

Definition at line 578 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetLadderContainer(), and CSearch< LEGACY, NHITS >::SetLadderContainer().

◆ MassAndMask

template<bool LEGACY, unsigned long NHITS>
AutoPtr<TMassMask, ArrayDeleter<TMassMask> > CSearch< LEGACY, NHITS >::MassAndMask
private

contains bit mask of modifications and resulting mass

Definition at line 588 of file omssa.hpp.

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

◆ MassArray

template<bool LEGACY, unsigned long NHITS>
CMassArray CSearch< LEGACY, NHITS >::MassArray
private

◆ MaxModPerPep

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::MaxModPerPep
private

◆ MaxMZ

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::MaxMZ = 0
staticprivate

maximum m/z value of all spectra precursors used to bound non-specific cleavage searches

Definition at line 599 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::ResetGlobals(), CSearch< LEGACY, NHITS >::Search(), and CSearch< LEGACY, NHITS >::Spectrum2Peak().

◆ MyRequest

template<bool LEGACY, unsigned long NHITS>
CRef<CMSRequest> CSearch< LEGACY, NHITS >::MyRequest
private

Search request.

Definition at line 563 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetRequest(), and CSearch< LEGACY, NHITS >::SetRequest().

◆ MyResponse

template<bool LEGACY, unsigned long NHITS>
CRef<CMSResponse> CSearch< LEGACY, NHITS >::MyResponse
private

Search response.

Definition at line 568 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetResponse(), and CSearch< LEGACY, NHITS >::SetResponse().

◆ MySettings

template<bool LEGACY, unsigned long NHITS>
CRef<CMSSearchSettings> CSearch< LEGACY, NHITS >::MySettings
private

Search params.

Definition at line 573 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetSettings(), and CSearch< LEGACY, NHITS >::SetSettings().

◆ numseq

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::numseq
private

◆ OidSet

template<bool LEGACY, unsigned long NHITS>
CMSResponse::TOidSet CSearch< LEGACY, NHITS >::OidSet
private

set of oids to be searched

Definition at line 619 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetOidSet(), and CSearch< LEGACY, NHITS >::SetOidSet().

◆ PoissonOnly

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::PoissonOnly
private

boolean to only use Poisson score when using Rank scoring

Definition at line 609 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetPoissonOnly(), and CSearch< LEGACY, NHITS >::SetPoissonOnly().

◆ PrecursorMassArray

template<bool LEGACY, unsigned long NHITS>
CMassArray CSearch< LEGACY, NHITS >::PrecursorMassArray
private

Definition at line 550 of file omssa.hpp.

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

◆ rdfp

template<bool LEGACY, unsigned long NHITS>
CRef<CSeqDB> CSearch< LEGACY, NHITS >::rdfp
private

◆ RestrictedSearch

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::RestrictedSearch
private

is this a oid restricted search

Definition at line 624 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::GetRestrictedSearch(), and CSearch< LEGACY, NHITS >::SetRestrictedSearch().

◆ SharedPeakSet

template<bool LEGACY, unsigned long NHITS>
CRef< CMSPeakSet > CSearch< LEGACY, NHITS >::SharedPeakSet = null
static

◆ ThreadNum

template<bool LEGACY, unsigned long NHITS>
int CSearch< LEGACY, NHITS >::ThreadNum
private

The threadid number.

Definition at line 634 of file omssa.hpp.

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

◆ UseRankScore

template<bool LEGACY, unsigned long NHITS>
bool CSearch< LEGACY, NHITS >::UseRankScore
private

◆ VariableMods

template<bool LEGACY, unsigned long NHITS>
CMSMod CSearch< LEGACY, NHITS >::VariableMods
private

Definition at line 551 of file omssa.hpp.

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


The documentation for this class was generated from the following files:
Modified on Mon Jul 15 05:34:34 2024 by modify_doxy.py rev. 669887