CSearch< LEGACY, NHITS > Class Template Reference

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...
CMSMatchedPeakSet *	PepCharge (CMSHit &Hit, int SeriesCharge, int Ion, int MinIntensity, int Which, CMSPeak *Peaks, int Maxproductions)
	fill out MatchedPeakSet More...
bool &	SetRankScore (void)
	Sets the scoring to use rank statistics. More...
bool &	SetPoissonOnly (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...
bool &	SetIterative (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_id &	GetQuery_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_id &	SetQuery_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_title &	GetQuery_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_title &	SetQuery_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_len &	SetQuery_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_masking &	GetQuery_masking (void) const
	Get the Query_masking member data. More...
TQuery_masking &	SetQuery_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 THits &	GetHits (void) const
	Get the Hits member data. More...
THits &	SetHits (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 TStat &	GetStat (void) const
	Get the Stat member data. More...
void	SetStat (TStat &value)
	Assign a value to Stat data member. More...
TStat &	SetStat (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 TMessage &	GetMessage (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)
TMessage &	SetMessage (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::CSearchResults >	operator() ()
	Performs the search. 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
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_id &	GetQuery_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_id &	SetQuery_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_title &	GetQuery_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_title &	SetQuery_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_len &	SetQuery_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_masking &	GetQuery_masking (void) const
	Get the Query_masking member data. More...
TQuery_masking &	SetQuery_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 THits &	GetHits (void) const
	Get the Hits member data. More...
THits &	SetHits (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 TStat &	GetStat (void) const
	Get the Stat member data. More...
void	SetStat (TStat &value)
	Assign a value to Stat data member. More...
TStat &	SetStat (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 TMessage &	GetMessage (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)
TMessage &	SetMessage (void)
	Assign a value to Message data member. More...
virtual void	Reset (void)
	Reset the whole object. More...
CConstRef< CDbIndex::CSearchResults >	operator() ()
	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 CThread *	GetCurrentThread (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< CMSPeakSet >	SharedPeakSet = 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::TOidSet &	SetOidSet (void)
	get the oidset More...
const CMSResponse::TOidSet &	GetOidSet (void) const
	get the oidset More...
bool &	SetRestrictedSearch (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...
Int1 &	SetLadderCalc (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...
TMassMask &	SetMassAndMask (int i, int j)
	Set the mask and mass of mod bit array. More...
CRef< CMSSearchSettings > &	SetSettings (void)
	Set search settings. More...
CConstRef< CMSSearchSettings >	GetSettings (void) const
	Get search settings. More...
CRef< CMSRequest > &	SetRequest (void)
	Set search request. More...
CConstRef< CMSRequest >	GetRequest (void) const
	Get search request. More...
CRef< CMSResponse > &	SetResponse (void)
	Set search response. More...
CConstRef< CMSResponse >	GetResponse (void) const
	Get search response. More...
CRef< CCleave > &	SetEnzyme (void)
	Set search enzyme. More...
CConstRef< CCleave >	GetEnzyme (void) const
	Get search enzyme. More...
CLadderContainer &	SetLadderContainer (void)
	set the ladder container More...
const CLadderContainer &	GetLadderContainer (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, CSearch >	TBase
typedef TBase::TIndex_Impl	TIndex_Impl
typedef TBase::TSearchOptions	TSearchOptions

Private Member Functions
	CSearch (const CSearch &value)
CSearch &	operator= (const CSearch &value)

Private Attributes
CRef< CSeqDB >	rdfp
	blast library More...
CMassArray	MassArray
CMassArray	PrecursorMassArray
CMSMod	VariableMods
CMSMod	FixedMods
int	numseq
CRef< CCleave >	Enzyme
	the enzyme in use More...
CRef< CMSRequest >	MyRequest
	Search request. More...
CRef< CMSResponse >	MyResponse
	Search response. More...
CRef< CMSSearchSettings >	MySettings
	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< CMSRequest >	initRequestIn
	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< CMSResponse >	initResponseIn
CRef< CMSModSpecSet >	initModset
CRef< CMSSearchSettings >	initSettingsIn
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< Uint8 >	TCounter
	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< TTrackedSeeds >	TTrackedSeedsSet
	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< TTrackedSeeds >	TTrackedSeedsSet
	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_Impl &	index_impl_
	The index implementation object. More...
const BLAST_SequenceBlk *	query_
	The query sequence encoded in BLASTNA. More...
const BlastSeqLoc *	locs_
	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_Impl &	index_impl_
	The index implementation object. More...
const BLAST_SequenceBlk *	query_
	The query sequence encoded in BLASTNA. More...
const BlastSeqLoc *	locs_
	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

Adds ion information to hitset.

Definition at line 1465 of file omssa.cpp.

References CMSBasicMatchedPeak::GetCharge(), CMSSpectrumMatch::GetHitInfo(), CMSSpectrumMatch::GetHits(), CMSBasicMatchedPeak::GetIonSeries(), CMSBasicPeak::GetMZ(), CMSBasicMatchedPeak::GetNumber(), i, and CMSHits_Base::SetMzhits().

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

AddModsToHit()

template<bool LEGACY, unsigned long NHITS>

void CSearch< LEGACY, NHITS >::AddModsToHit ( CMSHits *  Hit, CMSHit *  MSHit  )

protected

Adds modification information to hitset.

Definition at line 1447 of file omssa.cpp.

References CMSModInfo::GetIsFixed(), CMSModInfo::GetModEnum(), CMSHit::GetModInfo(), CMSHit::GetNumModInfo(), CMSModInfo::GetSite(), i, and CMSHits_Base::SetMods().

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

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

calculate the evalues of the top hits and sort

Parameters

Threshold	the noise threshold to apply to the peaks
Peaks	the spectrum to be scored

Definition at line 1889 of file omssa.cpp.

References _TRACE, a, CMSSpectrumMatch::CalcNormalTopHit(), CMSSpectrumMatch::CalcPoissonMean(), CMSSpectrumMatch::CalcPvalue(), CMSSpectrumMatch::CalcPvalueTopHit(), CMSSpectrumMatch::CalcRankProb(), CMSHit::CountHits(), CSearch< LEGACY, NHITS >::DoubleCompare(), ERR_POST, finite, CMSSpectrumMatch::GetCharge(), CMSPeak::GetConsiderMult(), CSearch< LEGACY, NHITS >::GetEnzyme(), CMSSpectrumMatch::GetExpMass(), CMSPeak::GetHitList(), CMSPeak::GetHitListIndex(), CSearch_Base< LEGACY, NHITS, derived_t >::GetHits(), CMSSpectrumMatch::GetMaxDelta(), CMSPeak::GetMaxI(), CMSPeak::GetNumCharges(), CMSPeak::GetPeptidesExamined(), CSearch< LEGACY, NHITS >::GetPoissonOnly(), CLadderContainer::GetSeriesChargePairList(), CSearch< LEGACY, NHITS >::GetSettings(), CMSPeak::GetWhich(), CMSPeak::HighLow(), Info(), multimap_checker< Container >::insert(), isnan, CSearch< LEGACY, NHITS >::MatchAndSort(), MSSCALE2INT, N, CSearch< LEGACY, NHITS >::SetLadderContainer(), and CSearch< LEGACY, NHITS >::UseRankScore.

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

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

i	index into ModIndex
NumFixed	number of fixed mods in ModIndex
ModList	modification information
ModIndex	array 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

Max	the 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

compare ladders to experiment

Definition at line 483 of file omssa.cpp.

References CLadderContainer::Begin(), _MassPeak::Charge, CMSPeak::CompareSortedRank(), CMSPeak::GetConsiderMult(), CMSPeak::GetWhich(), CLadderContainer::Next(), CSearch< LEGACY, NHITS >::SetLadderContainer(), and CMSPeak::SetPeakLists().

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

CompareLaddersTop()

template<bool LEGACY, unsigned long NHITS>

bool CSearch< LEGACY, NHITS >::CompareLaddersTop ( int  iMod, CMSPeak *  Peaks, const TMassPeak *  MassPeak  )

protected

Definition at line 514 of file omssa.cpp.

References CLadderContainer::Begin(), _MassPeak::Charge, CMSPeak::CompareTop(), CMSPeak::GetConsiderMult(), CLadderContainer::Next(), and CSearch< LEGACY, NHITS >::SetLadderContainer().

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

CopySettings()

template<bool LEGACY, unsigned long NHITS>

void CSearch< LEGACY, NHITS >::CopySettings

(

CRef< CSearch< LEGACY, NHITS > >

fromObj

)

Definition at line 970 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, CSearch< LEGACY, NHITS >::initSettingsIn, CSearch< LEGACY, NHITS >::Iterative, CSearch< LEGACY, NHITS >::numseq, CSearch< LEGACY, NHITS >::rdfp, and CSearch< LEGACY, NHITS >::UseRankScore.

Referenced by COMSSABase::RunSearch().

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

NumModSites	the number of unique mod sites
NumMod	the number of mods
ModList	modification 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

create the ladders from sequence

Definition at line 441 of file omssa.cpp.

References CLadderContainer::Begin(), CSearch< LEGACY, NHITS >::GetSettings(), CMSMatchedPeakSetMap::Key2Charge(), CMSMatchedPeakSetMap::Key2Series(), CSearch< LEGACY, NHITS >::MassArray, CLadderContainer::Next(), CSearch< LEGACY, NHITS >::SetLadderContainer(), CSearch< LEGACY, NHITS >::SetMassAndMask(), and CSearch< LEGACY, NHITS >::SetSettings().

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

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

Definition at line 774 of file omssa.cpp.

References CSearch< LEGACY, NHITS >::CalcModIndex(), eMSSearchType_exact, CSearch< LEGACY, NHITS >::GetSettings(), CSearch< LEGACY, NHITS >::InitModIndex(), kNeutron, CSearch< LEGACY, NHITS >::MakeBoolMask(), _MassMask::Mask, _MassMask::Mass, CSearch< LEGACY, NHITS >::MassAndMask, MAXMOD, CSearch< LEGACY, NHITS >::MaxModPerPep, MSSCALE2INT, CSearch< LEGACY, NHITS >::SetMassAndMask(), CSearch< LEGACY, NHITS >::SetSettings(), and ct::sort().

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

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

Start	start of sequence
Stop	stop of sequence
seqstring	sequence string
Sequence	sequence 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

offset

Offset 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

NumMod	the number of modifications
ModList	modification 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

SingleForward	singly charged NC ions
SingleBackward	singly charged CN ions
Double	double charged product ions
DoubleForward	is 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

Get search enzyme.

Definition at line 892 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::Enzyme.

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

GetIterative()

template<bool LEGACY, unsigned long NHITS>

const bool CSearch< LEGACY, NHITS >::GetIterative ( void  ) const

inline

Gets iterate search.

Definition at line 814 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::Iterative.

Referenced by COMSSA::Run(), CSearch< LEGACY, NHITS >::Search(), CSearch< LEGACY, NHITS >::SetResult(), and CSearch< LEGACY, NHITS >::Spectrum2Peak().

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

i	the 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

Definition at line 868 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::numseq.

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

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

Get search response.

Definition at line 850 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MyResponse.

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

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

Get search settings.

Definition at line 826 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MySettings.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort(), CSearch< LEGACY, NHITS >::CreateLadders(), CSearch< LEGACY, NHITS >::CreateModCombinations(), CSearch< LEGACY, NHITS >::InitLadders(), CSearch< LEGACY, NHITS >::MakeOidSet(), CSearch< LEGACY, NHITS >::MatchAndSort(), CSearch< LEGACY, NHITS >::PepCharge(), CSearch< LEGACY, NHITS >::ReSearch(), CSearch< LEGACY, NHITS >::Search(), CSearch< LEGACY, NHITS >::SetIons(), CSearch< LEGACY, NHITS >::SetResult(), and CSearch< LEGACY, NHITS >::Spectrum2Peak().

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

blastdb

name 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

initialize mass ladders

Parameters

Ions	list of ion types

Definition at line 901 of file omssa.cpp.

References CLadderContainer::CreateLadderArrays(), CSearch< LEGACY, NHITS >::GetSettings(), i, kMSLadderMax, CSearch< LEGACY, NHITS >::MaxModPerPep, CSearch< LEGACY, NHITS >::SetLadderContainer(), and CLadderContainer::SetSeriesChargePairList().

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

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

Derived (user-created) class must provide a real thread function.

Implements CThread.

Definition at line 955 of file omssa.cpp.

References bool, CSearch< LEGACY, NHITS >::initCallback, CSearch< LEGACY, NHITS >::initModset, CSearch< LEGACY, NHITS >::initRequestIn, CSearch< LEGACY, NHITS >::initResponseIn, CSearch< LEGACY, NHITS >::initSettingsIn, and CSearch< LEGACY, NHITS >::Search().

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

makes map of oid from previous search used in iterative searching

Definition at line 921 of file omssa.cpp.

References set< Key, Compare >::clear(), CSearch< LEGACY, NHITS >::GetResponse(), CSearch< LEGACY, NHITS >::GetSettings(), CSearch< LEGACY, NHITS >::SetOidSet(), and CSearch< LEGACY, NHITS >::SetRestrictedSearch().

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

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

Peaks	peak list
Hit	the hit
Which	which peak list to use
minintensity	minimum intensity
iPairList
Forward	NC ions
Backward	CN 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

Hit	the match being evaluated
SeriesCharge	charge of ion series
Ion	which ion series
MinIntensity	the minimum intensity to consider
Which	which version of experimental peaks to use
Peaks	experimental peaks
Maxproductions	the 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

Number

the 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

MyRequestIn	the user search params and spectra
MyResponseIn	the results of the search
Modset	list of modifications
SettingsIn	the search settings
Callback	callback function for progress meter
CallbackData	data 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

Ions	list 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

i	the 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

set the ladder container

this container holds theoretical mass ladders sorted by charge and series type

Definition at line 899 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::LadderContainer.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort(), CSearch< LEGACY, NHITS >::CompareLadders(), CSearch< LEGACY, NHITS >::CompareLaddersTop(), CSearch< LEGACY, NHITS >::CreateLadders(), CSearch< LEGACY, NHITS >::InitLadders(), and CSearch< LEGACY, NHITS >::Search().

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

i	the index for missed cleavages
j	the 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

get the oidset

Definition at line 856 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::OidSet.

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

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

Set search response.

Definition at line 844 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MyResponse.

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

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

Set search settings.

Definition at line 820 of file omssa.hpp.

References CSearch< LEGACY, NHITS >::MySettings.

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

SetSubjInfo()

template<bool LEGACY, unsigned long NHITS>

void CSearch< LEGACY, NHITS >::SetSubjInfo ( )

inline

Set the parameters of the current subject sequence.

Definition at line 1382 of file dbindex_search.cpp.

References CDbIndex_Impl< LEGACY >::GetSubjectMap(), CSearch_Base< LEGACY, NHITS, derived_t >::index_impl_, CSubjectMap::SetSubjInfo(), CSearch_Base< LEGACY, NHITS, derived_t >::subj_end_, CSearch_Base< LEGACY, NHITS, derived_t >::subj_start_, and CSearch_Base< LEGACY, NHITS, derived_t >::subject_.

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

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

MyRequestIn	the user search params and spectra
MyResponseIn	the results of the search
Modset	list of modifications
SettingsIn	the search settings
Callback	callback function for progress meter
CallbackData	data 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

Definition at line 564 of file omssa.cpp.

References CMSPeakSet::AddPeak(), eMSPeakListCharge1, eMSSpectrumFileType_dta, ERR_POST, Error(), CSearch< LEGACY, NHITS >::GetIterative(), CSearch< LEGACY, NHITS >::GetRequest(), CSearch< LEGACY, NHITS >::GetSettings(), CSearch< LEGACY, NHITS >::MaxMZ, MSSCALE2INT, PositiveSign(), CMSPeak::ReadAndProcess(), CSearch< LEGACY, NHITS >::ReSearch(), CMSPeakSet::SortPeaks(), transform(), and CMSPeak::Write().

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

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

Missed	how many missed cleavages
PepStart	array of peptide starts
PepEnd	array of peptide ends
NumMod	array of the number of mods
ModList	modification info
Masses	peptide masses
EndMasses	peptide end masses
NumModSites	array of number of unfixed mod sites
Modset	modification 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

write oidset to result

Definition at line 1736 of file omssa.cpp.

References CSeqDB::GetBioseq(), CSearch< LEGACY, NHITS >::GetOidSet(), CConstRef< C, Locker >::IsNull(), ITERATE, CSearch< LEGACY, NHITS >::rdfp, CMSResponse_Base::SetBioseqs(), and CSearch< LEGACY, NHITS >::SetResponse().

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

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

Definition at line 644 of file omssa.hpp.

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

initCallbackData

template<bool LEGACY, unsigned long NHITS>

void* CSearch< LEGACY, NHITS >::initCallbackData

private

Definition at line 645 of file omssa.hpp.

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

initModset

template<bool LEGACY, unsigned long NHITS>

CRef<CMSModSpecSet> CSearch< LEGACY, NHITS >::initModset

private

Definition at line 642 of file omssa.hpp.

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

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

Definition at line 641 of file omssa.hpp.

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

initSettingsIn

template<bool LEGACY, unsigned long NHITS>

CRef<CMSSearchSettings> CSearch< LEGACY, NHITS >::initSettingsIn

private

Definition at line 643 of file omssa.hpp.

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

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

Definition at line 549 of file omssa.hpp.

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

MaxModPerPep

template<bool LEGACY, unsigned long NHITS>

int CSearch< LEGACY, NHITS >::MaxModPerPep

private

maximum number of mod combinations per peptide

Definition at line 593 of file omssa.hpp.

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

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

Definition at line 553 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::CopySettings(), CSearch< LEGACY, NHITS >::Getnumseq(), and CSearch< LEGACY, NHITS >::InitBlast().

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

blast library

Definition at line 546 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::CopySettings(), CSearch< LEGACY, NHITS >::InitBlast(), CSearch< LEGACY, NHITS >::PepCharge(), CSearch< LEGACY, NHITS >::Search(), CSearch< LEGACY, NHITS >::SetResult(), and CSearch< LEGACY, NHITS >::WriteBioseqs().

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

Definition at line 225 of file omssa.hpp.

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

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

boolean to turn on rank scoring

Definition at line 604 of file omssa.hpp.

Referenced by CSearch< LEGACY, NHITS >::CalcNSort(), CSearch< LEGACY, NHITS >::CopySettings(), CSearch< LEGACY, NHITS >::Search(), CSearch< LEGACY, NHITS >::SetRankScore(), and CSearch< LEGACY, NHITS >::SetResult().

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().

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The documentation for this class was generated from the following files:

• include/objects/blastxml2/Search.hpp
• src/algo/blast/dbindex/dbindex_search.cpp
• src/algo/ms/omssa/omssa.hpp
• src/algo/ms/omssa/omssa.cpp
• src/objects/blastxml2/Search.cpp