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NCBI C++ ToolKit: include/algo/align/splign/compart_matching.hpp Source File

vector<CSeq_id_Handle>&

(

)

= 0;

(

= 0;

<GetNumSeqs(); ++

) {

GetSeq(

**

) {

GetSeq(m_idx,

); }

GetSeq(

idx,

**

) {

m_seq.resize(seq.size());

(seq.begin(), seq.end(), m_seq.begin());

(

) vec.

();

vector<CSeq_id_Handle>&

(

)

{

s_ids.Get(); }

(

) {

m_seqdb->GetNumSeqs(); }

m_seqdb->CheckOrFindOID(m_idx);

(

idx) {

m_seqdb->GetSeqLength(idx); }

m_FilePath(

::DeleteTrailingPathSeparator(FilePath)), m_qsrc(qsrc), m_sdb(sdb), m_XDropOff(s_GetDefaultDropOff())

(

& penalty) { m_Penalty = penalty; }

(

& min_idty) { m_MinCompartmentIdty = min_idty; }

(

)

{

m_MinCompartmentIdty; }

m_Start < rhs.

;

ostr << rhs.

<<

(dim_bits, init_value);

(dim_bits, src);

(dim_bits % 64 > 0) {

);

m_pBuffer->assign(dim_bits / 64, X);

(dim_bits % 64 > 0) {

);

dimw (dim_bits / 64);

m_pBuffer =

(dimw);

(src, src + dimw, &(m_pBuffer->front()));

1 & ((*m_pBuffer)[idx >> 6] >> (idx & 0x3F));

(*m_pBuffer)[idx >> 6] |= (

(1) << (idx & 0x3F));

(*m_pBuffer)[idx >> 6] &= ~(

(1) << (idx & 0x3F));

& (m_pBuffer->front());

(

(0);

< 64; ++

) {

m_MinCompartmentIdty,

, m_MinSingletonIdty;

x_InitBasic(

);

x_Cleanup(

);

x_InitFilteringVector (

& sdb,

strand);

x_InitParticipationVector(

strand);

x_CreateIndex (

& db,

index_more,

strand);

x_WriteIndexFile(

volume,

vector<Uint8>& MersAndCoords);

x_CleanVolumes (

& lbn,

& vol_extensions);

x_Search(

strand);

x_CompartVolume (vector<Uint8>* phits);

x_CompartPair (vector<Uint8>* pvol,

TSeqInfos::const_iterator ii_cdna,

TSeqInfos::const_iterator ii_genomic,

* pidx_compacted);

x_ExtendHit(

& left_limit,

& right_limit,

s_IsLowComplexity(

);

virtual const vector< CSeq_id_Handle > & GetIds(void) const

virtual Uint8 GetTotalLength(void)

virtual bool GetNext(void)

virtual int GetSeq(int idx, const char **buffer)

virtual int GetNumSeqs(void)

virtual ~CBlastSequenceSource(void)

virtual CBioseq_Handle GetSequence(const CSeq_id_Handle &)

virtual CConstRef< CSeq_id > GetSeqID(int idx)

CBlastSequenceSource(const string &db)

virtual void RetSequence(const char **buffer)

static CSafeStatic< vector< CSeq_id_Handle > > s_ids

virtual int GetSeqLength(int idx)

virtual void SetMemoryBound(Uint8)

Uint8 GetSetCount(void) const

void reset_at(const Uint8 idx)

void set_at(const Uint8 idx)

bool get_at(const Uint8 idx) const

void Init(Uint8 dim_bits, bool init_value)

CBoolVector(Uint8 dim_bits, bool init_value)

CBoolVector(Uint8 dim_bits, const Uint8 *src)

void Init(Uint8 dim_bits, const Uint8 *src)

const Uint8 * GetBuffer(void) const

const char * m_CurSeq_cDNA

double GetPenalty(void) const

int GetDropOff(void) const

double GetMinSingletonIdty(void) const

vector< SSeqInfo > TSeqInfos

CElementaryMatching(void)

void SetOutputMethod(bool om)

Compartmentization parameters - see CCompartmentFinder for details.

TSeqPos GetMaxIntron(void) const

void SetDropOff(int dropoff)

Controls the drop-off parameter used to extend hits over possible defects.

void SetHitsOnly(bool hits_only)

Set or clear the "hits only" mode.

void SetMinQueryLength(size_t min_qlen)

Sets the length cut-off for cDNA (query) sequences.

vector< THitRef > THitRefs

CRef< objects::CSeq_align_set > TResults

void SetPenalty(const double &penalty)

void SetMinIdty(const double &min_idty)

vector< string > TStrings

CElementaryMatching(ISequenceSource *qsrc, const string &sdb, const string &FilePath=".")

TId x_GetId(EIndexMode mode, Uint4 coord) const

TSeqInfos m_SeqInfos_Genomic

void SetMinHitLength(size_t min_hit_len)

In "hits only" mode, sets the min length of hits to report.

virtual ~CElementaryMatching()

TSeqInfos::const_iterator m_ii_cdna

TResults GetResults(void)

returns compartments.

void SetMaxIntron(const TSeqPos max_intron)

void SetMinSingletonIdty(const double &idty)

void SetMaxVolSize(size_t max_vol_size)

Controls the max size of an index volume.

TSeqInfos m_SeqInfos_cdna

vector< SHitIndexEntry > THitIndex

const char * m_CurSeq_Genomic

CRef< CBlastTabular > THitRef

static int s_GetDefaultDropOff(void)

double GetMinIdty(void) const

TSeqInfos::const_iterator m_ii_genomic

virtual const vector< CSeq_id_Handle > & GetIds(void) const =0

virtual Uint8 GetTotalLength(void)

virtual int GetSeqLength(void)

virtual bool GetNext(void)

virtual int GetNumSeqs(void)

virtual void ResetIndex(void)

virtual ~ISequenceSource(void)

virtual int GetSeq(const char **buffer)

virtual int GetCurrentIndex()

virtual CBioseq_Handle GetSequence(const CSeq_id_Handle &)=0

virtual void RetSequence(const char **)

virtual CConstRef< CSeq_id > GetSeqID()

bool GetSeqID(const CRef< CSeq_align > &seqAlign, CRef< CSeq_id > &SeqID, bool getSlave=true)

int GetSeqLength(const CBioseq &bioseq)

bool operator<(const CEquivRange &A, const CEquivRange &B)

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void SetCoding(TCoding coding)

void SetRandomizeAmbiguities(void)

Randomization of ambiguities and gaps in ncbi2na coding.

void GetPackedSeqData(string &buffer, TSeqPos start=0, TSeqPos stop=kInvalidSeqPos)

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void Run(void)

Enter the main loop.

#define NCBI_XALGOALIGN_EXPORT

@ e_Ncbi2na

2 bit nucleic acid code

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::KEY key

Static variables safety - create on demand, destroy on application termination.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Defines BLAST database access classes.

CRef< objects::CObjectManager > om

SSeqInfo(Uint4 start, Uint4 len, int id)

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