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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/splign_8hpp_source.html below:

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

SetAlignerScores(

);

PreserveScope(

preserve =

);

SetEndGapDetection(

on);

GetEndGapDetection(

)

;

SetPolyaDetection(

on);

GetPolyaDetection(

)

;

SetStrand(

strand);

SetMaxGenomicExtent(

mge);

s_GetDefaultMaxGenomicExtent(

);

GetMaxGenomicExtent(

)

;

SetMaxIntron(

max_intron);

GetMaxIntron(

)

;

SetCompartmentPenalty(

penalty);

s_GetDefaultCompartmentPenalty(

);

GetCompartmentPenalty(

)

;

SetMinCompartmentIdentity(

idty);

s_GetDefaultMinCompartmentIdty(

);

GetMinCompartmentIdentity(

)

;

SetMinSingletonIdentity(

idty);

GetMinSingletonIdentity(

)

;

SetMinSingletonIdentityBps(

idty);

GetMinSingletonIdentityBps(

)

;

SetMinExonIdentity(

idty);

s_GetDefaultMinExonIdty(

);

GetMinExonIdentity(

)

;

SetPolyaExtIdentity(

idty);

s_GetDefaultPolyaExtIdty(

);

GetPolyaExtIdentity(

)

;

SetMinPolyaLen(

);

s_GetDefaultMinPolyaLen(

);

GetMinPolyaLen(

)

;

SetMinHoleLen(

);

s_GetDefaultMinHoleLen(

);

GetMinHoleLen(

)

;

SetTrimToCodons(

);

s_GetDefaultTrimToCodons(

);

GetTrimToCodons(

)

;

SetMaxPartExonIdentDrop(

ident);

s_GetDefaultMaxPartExonIdentDrop(

);

GetMaxPartExonIdentDrop(

)

;

SetTestType(

&

);

GetTestType(

)

;

SetScoringType(EScoringType

);

EScoringType s_GetDefaultScoringType(

);

EScoringType GetScoringType(

)

;

SetMatchScore(

score);

s_GetDefaultMatchScore(

);

GetMatchScore(

)

;

SetMismatchScore(

score);

s_GetDefaultMismatchScore(

);

GetMismatchScore(

)

;

SetGapOpeningScore(

score);

s_GetDefaultGapOpeningScore(

);

GetGapOpeningScore(

)

;

SetGapExtensionScore(

score);

s_GetDefaultGapExtensionScore(

);

GetGapExtensionScore(

)

;

SetGtAgSpliceScore(

score);

s_GetDefaultGtAgSpliceScore(

);

GetGtAgSpliceScore(

)

;

SetGcAgSpliceScore(

score);

s_GetDefaultGcAgSpliceScore(

);

GetGcAgSpliceScore(

)

;

SetAtAcSpliceScore(

score);

s_GetDefaultAtAcSpliceScore(

);

GetAtAcSpliceScore(

)

;

SetNonConsensusSpliceScore(

score);

s_GetDefaultNonConsensusSpliceScore(

);

GetNonConsensusSpliceScore(

)

;

m_model_id = model_id - 1;

m_model_id + 1;

SetMaxCompsPerQuery(

m);

GetMaxCompsPerQuery(

)

;

m_MaskMap[idh] = mask_ranges;

m_Status(eStatus_Empty),

m_Cds_start(0), m_Cds_stop(0),

m_Status(eStatus_Empty),

m_Cds_start(0), m_Cds_stop(0),

GetIdentity(

)

;

GetBox(

* box)

;

AlignSingleCompartment(

* hitrefs,

SAlignedCompartment*

);

SAlignedCompartment*

);

ClearMem(

);

pair<size_t,size_t>

;

s_TestPolyA(

* seq,

dim,

cds_stop = 0);

IsPolyA(

* seq,

polya_start,

dim);

eCS_InframeMatches = 20,

eCS_InframeIdentity = 22,

eCS_CombinationIdentity = 32

eSF_BasicNonCds = 1 << 0,

eSF_BasicCds = 1 << 1

s_ComputeStats(

embed_scoreset =

,

x_Run(

* seq1,

* seq2);

x_SplitQualifyingHits(

* phitrefs);

x_SetPattern(

* hitrefs);

x_ProcessTermSegm(

** term_segs,

side)

;

x_GetGenomicExtent(

query_extent,

max_ext = 0)

;

x_LoadSequence(vector<char>* seq,

objects::CSeq_id& seqid,

retain,

is_genomic =

,

genomic_strand =

);

x_MaskSequence(vector<char>* seq,

x_IsInGap(

pos);

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

map< string, TOrfPair > TStrIdToOrfs

CSplign(const CSplign &)

forbidden

void SetHardMaskRanges(objects::CSeq_id_Handle idh, const TSeqRangeColl &mask_ranges)

int m_NonConsensusSpliceScore

list< CRef< objects::CScore_set > > TScoreSets

size_t m_MinSingletonIdtyBps

pair< size_t, size_t > m_BoundingRange

vector< size_t > m_pattern

pair< size_t, size_t > TOrf

CConstRef< objects::CSeqMap > m_GenomicSeqMap

EScoringType m_ScoringType

CSplign & operator=(const CSplign &)

vector< char > m_mrna_polya

size_t m_MaxCompsPerQuery

const TResults & GetResult(void) const

void SetStartModelId(size_t model_id)

double m_MinSingletonIdty

CRef< objects::CScope > m_Scope

size_t GetNextModelId(void) const

vector< SAlignedCompartment > TResults

vector< THitRef > THitRefs

double m_MinCompartmentIdty

map< objects::CSeq_id_Handle, TSeqRangeColl > TSIHToMaskRanges

double m_MaxPartExonIdentDrop

size_t m_MinPatternHitLength

TSIHToMaskRanges m_MaskMap

CRangeCollection< TSeqPos > TSeqRangeColl

vector< TSegment > TSegments

double m_CompartmentPenalty

pair< TOrf, TOrf > TOrfPair

objects::CBioseq_Handle m_mrna_bio_handle

CRef< TAligner > m_aligner

CNWFormatter::SSegment TSegment

vector< SAlnMapElem > m_alnmap

CSplign::THitRefs THitRefs

Include a standard set of the NCBI C++ Toolkit most basic headers.

static void test_type(TDSSOCKET *tds, TDSCOLUMN *col)

unsigned int TSeqPos

Type for sequence locations and lengths.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed 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

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

const string kTestType_20_28

const string kTestType_20_28_plus

const string kTestType_production_default

ECompartmentStatus m_Status

vector< char > TNetCacheBuffer

SAlignedCompartment(void)

SAlignedCompartment(size_t id, const char *msg)

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