#include <stdio.h>
#include <common/ncbi_export.h>

Include dependency graph for thrddecl.h:

This graph shows which files directly or indirectly include this file:

Functions
int	atd (Fld_Mtf mtf, Cor_Def cdf, Qry_Seq qsq, Rcx_Ptl pmf, Gib_Scd gsp, Thd_Tbl ttb, Seq_Mtf psm, float trg, int zscs, double ScalingFactor, float PSSM_Weight)

void	cprl (Fld_Mtf mtf, Cor_Def cdf, Rcx_Ptl pmf, Cxl_Los *cpr, int ct)

void	ttb0 (Thd_Tbl *ttb)

void	sgoi (int is, int it, Rnd_Smp pvl, Seg_Ord sgo)

int	slo0 (Fld_Mtf mtf, Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, int cs, int ct, int mn, int mx)

int	rsmp (Rnd_Smp *pvl)

float	Rand01 (int *idum)

int	sal0 (Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, Cur_Aln sai, int cs, int mn, int mx)

int	spci (Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, Cur_Aln sai, int n, Seg_Cmp *spc)

void	spni (Cxl_Los *cpl, Cur_Loc sli, int n, Seg_Nsm *spn)

void	cxei (Seg_Nsm spn, Seg_Cmp spc, Rcx_Ptl pmf, Cur_Loc sli, Seq_Mtf psm, Cor_Def cdf, Thd_Cxe *cxe)

void	cpll (Cor_Def cdf, Rcx_Ptl pmf, Qry_Seq qsq, Cxl_Los cpr, Cur_Aln sai, Cxl_Los **cpl)

void	spel (Cxl_Los *cpl, Cur_Aln sai, Cur_Loc sli, int cs, Seg_Gsm spe, Cor_Def cdf, Seq_Mtf psm, Seg_Cmp *spc)

int	ttbi (Cur_Aln sai, Cur_Loc sli, Thd_Gsm tdg, Thd_Tbl ttb, int nrs, int o)

void	cpal (Rcx_Ptl pmf, Cxl_Los cpr, Cur_Loc sli, Cxl_Als **cpa)

void	spea (Cor_Def cdf, Cxl_Als cpa, Cur_Aln sai, Cur_Loc sli, int n, int h, Seg_Gsm spe, Seq_Mtf psm, Seg_Cmp spc)

int	salr (Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, Cur_Aln sai, int cs, int mn, int mx)

void	salu (Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, int cs, int al, Cur_Aln sai)

int	algs (Rnd_Smp *pvl, int tm)

int	slor (Fld_Mtf mtf, Cor_Def cdf, Qry_Seq qsq, Cur_Loc sli, Cur_Aln sai, int cs, int ct, int mn, int *mx)

void	slou (Fld_Mtf mtf, Cor_Def cdf, int cs, int ct, int of, Cur_Loc sli, Cur_Aln sai, Qry_Seq *qsq)

void	bwfi (Thd_Tbl ttb, Gib_Scd gsp, Thd_Tst *tts)

void	zsc (Thd_Tbl ttb, Seq_Mtf psm, Qry_Seq qsq, Cxl_Los cpr, Cor_Def cdf, Rcx_Ptl pmf, Seg_Gsm spe, Cur_Aln sai, Rnd_Smp pvl, double ScalingFactor)

int	g (Seg_Gsm spe, Seq_Mtf psm, Thd_Gsm *tdg)

float	g0 (Seg_Nsm spn, Thd_Cxe cxe)

float	dgri (Seg_Gsm spe, Seg_Nsm spn, Thd_Cxe cxe, Thd_Gsm tdg, Seq_Mtf psm, Seg_Cmp spc)

Cor_Def *	NewCorDef (int NumBlocks)

Cor_Def *	FreeCorDef (Cor_Def *cdf)

void	PrintCorDef (Cor_Def cdf, FILE pFile)

Seq_Mtf *	NewSeqMtf (int NumResidues, int AlphabetSize)

Seq_Mtf *	FreeSeqMtf (Seq_Mtf *psm)

void	PrintSeqMtf (Seq_Mtf psm, FILE pFile)

Qry_Seq *	NewQrySeq (int NumResidues, int NumBlocks)

Qry_Seq *	FreeQrySeq (Qry_Seq *qsq)

void	PrintQrySeq (Qry_Seq qsq, FILE pFile)

Rcx_Ptl *	NewRcxPtl (int NumResTypes, int NumDistances, int PeptideIndex)

Rcx_Ptl *	FreeRcxPtl (Rcx_Ptl *pmf)

Gib_Scd *	NewGibScd (int NumTempSteps)

Gib_Scd *	FreeGibScd (Gib_Scd *gsp)

Fld_Mtf *	NewFldMtf (int NumResidues, int NumResResContacts, int NumResPepContacts)

Fld_Mtf *	FreeFldMtf (Fld_Mtf *mtf)

void	PrintFldMtf (Fld_Mtf mtf, FILE pFile)

Thd_Tbl *	NewThdTbl (int NumResults, int NumCoreElements)

Thd_Tbl *	FreeThdTbl (Thd_Tbl *ttb)

void	OrderThdTbl (Thd_Tbl *pResults)

int	CopyResult (Thd_Tbl pFromResults, Thd_Tbl pToResults, int from, int to)

void	PrintThdTbl (Thd_Tbl ttb, FILE pFile)

void	ScaleThdTbl (Thd_Tbl *ttb, double ScalingFactor)

int	ThrdRound (double Num)

Function Documentation

◆ algs()

int algs	(	Rnd_Smp *	pvl,
		int	tm
	)

Definition at line 45 of file thrdalgs.c.

References b, _Rnd_Smp::e, g(), i, _Rnd_Smp::n, _Rnd_Smp::p, and rsmp().

Referenced by atd().

◆ atd()

int atd	(	Fld_Mtf *	mtf,
		Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Rcx_Ptl *	pmf,
		Gib_Scd *	gsp,
		Thd_Tbl *	ttb,
		Seq_Mtf *	psm,
		float *	trg,
		int	zscs,
		double	ScalingFactor,
		float	PSSM_Weight
	)

Definition at line 68 of file thrdatd.c.

References _Cur_Aln::al, algs(), _Gib_Scd::als, _Rnd_Smp::aqi, BIGNEG, _Thd_Tst::bw, bwfi(), calloc(), _Cur_Aln::cf, _Gib_Scd::cfm, _Cur_Loc::co, _Cor_Def::comn, _Cor_Def::comx, cpal(), cpll(), cprl(), _Cur_Loc::cr, _Gib_Scd::crs, _Seg_Gsm::cs, _Gib_Scd::csm, cxei(), _Cxl_Los::d, _Thd_Gsm::dg, dgri(), _Cxl_Als::e, _Cxl_Los::e, _Rnd_Smp::e, free(), _Seg_Nsm::frf, _Thd_Tst::gb, _Seg_Gsm::gs, _Seg_Gsm::gss, i, _Thd_Tst::ib, int, _Gib_Scd::isl, _Gib_Scd::iso, _Gib_Scd::ito, _Cor_Def::lll, _Cor_Def::llmx, _Thd_Tst::lm, _Gib_Scd::lmf, _Gib_Scd::lms, _Gib_Scd::lmw, _Cur_Loc::lp, _Seg_Cmp::lrt, _Seg_Gsm::ls, _Rnd_Smp::lsg, _Fld_Mtf::mll, _Qry_Seq::mn, _Thd_Tbl::mn, _Seg_Gsm::ms, _Thd_Tbl::mx, _Fld_Mtf::n, _Cor_Def::n, _Qry_Seq::n, _Thd_Tbl::n, _Cxl_Los::n, _Rnd_Smp::n, n, _Gib_Scd::nac, _Thd_Tst::nb, _Rcx_Ptl::ndi, _Seg_Nsm::ndi, _Thd_Cxe::ndi, _Gib_Scd::nlc, _Cur_Loc::nlp, _Seg_Cmp::nlp, _Cur_Loc::nmt, _Cur_Aln::nmt, _Cur_Loc::no, _Cor_Def::nomn, _Cor_Def::nomx, _Seg_Nsm::nrf, _Seg_Nsm::nrp, _Seg_Nsm::nrr, _Gib_Scd::nrs, _Rcx_Ptl::nrt, _Seg_Nsm::nrt, _Seg_Cmp::nrt, _Thd_Cxe::nrt, _Cur_Loc::nsc, _Cur_Aln::nsc, _Seg_Nsm::nsc, _Seg_Cmp::nsc, _Seg_Gsm::nsc, _Seg_Ord::nsc, _Gib_Scd::nti, _Gib_Scd::nts, _Thd_Tst::nw, _Thd_Tbl::nx, _Rnd_Smp::o, OrderThdTbl(), _Rnd_Smp::p, _Cxl_Los::p2, _Thd_Tbl::pr, _Cxl_Als::r, _Rnd_Smp::r, _Cxl_Als::r1, _Cxl_Los::r1, _Cxl_Als::r2, _Cxl_Los::r2, Rand01(), _Cxl_Los::rf, _Thd_Cxe::rfe, _Cor_Def::rfpt, _Thd_Cxe::rp, _Cxl_Los::rp, _Thd_Cxe::rpe, _Cxl_Als::rr, _Cxl_Los::rr, _Thd_Cxe::rre, _Thd_Cxe::rrp, _Gib_Scd::rsd, rsmp(), _Seg_Cmp::rt, _Seg_Cmp::rto, _Seg_Gsm::s0, _Qry_Seq::sac, sal0(), salr(), salu(), ScaleThdTbl(), sgoi(), _Seg_Ord::si, _Cor_Def::sll, slo0(), slor(), slou(), _Seg_Ord::so, spci(), spea(), spel(), spni(), _Qry_Seq::sq, _Cur_Aln::sq, _Rnd_Smp::sq, _Seg_Nsm::srf, _Seg_Nsm::srp, _Seg_Nsm::srr, _Seg_Cmp::srt, _Cxl_Los::t2, _Thd_Tbl::tf, _Thd_Tst::tf, _Thd_Tbl::tg, _Gib_Scd::tma, _Gib_Scd::tml, tmp, _Seg_Ord::to, _Gib_Scd::trg, _Thd_Tst::ts, ttb0(), ttbi(), and zsc().

Referenced by Threader::Realign().

◆ bwfi()

void bwfi	(	Thd_Tbl *	ttb,
		Gib_Scd *	gsp,
		Thd_Tst *	tts
	)

Definition at line 43 of file thrdbwfi.c.

References b, _Thd_Tst::bw, _Gib_Scd::cef, _Gib_Scd::cet, g(), i, _Thd_Tbl::mx, n, NERZRO, _Thd_Tbl::nx, _Thd_Tbl::tf, _Thd_Tst::tf, _Thd_Tbl::tg, _Thd_Tbl::ts, and _Thd_Tst::ts.

Referenced by atd().

◆ CopyResult()

int CopyResult	(	Thd_Tbl *	pFromResults,
		Thd_Tbl *	pToResults,
		int	from,
		int	to
	)

Definition at line 1789 of file thrdatd.c.

References _Thd_Tbl::al, _Thd_Tbl::co, _Thd_Tbl::cs, _Thd_Tbl::errm, _Thd_Tbl::errp, _Thd_Tbl::g0, i, _Thd_Tbl::lps, _Thd_Tbl::ls, _Thd_Tbl::m0, _Thd_Tbl::ms, _Thd_Tbl::no, _Thd_Tbl::nsc, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Tbl::tf, _Thd_Tbl::tg, _Thd_Tbl::ts, and _Thd_Tbl::zsc.

Referenced by OrderThdTbl().

◆ cpal()

void cpal	(	Rcx_Ptl *	pmf,
		Cxl_Los **	cpr,
		Cur_Loc *	sli,
		Cxl_Als **	cpa
	)

Definition at line 57 of file thrdcpal.c.

References _Cur_Loc::cr, _Cxl_Los::d, _Cxl_Als::e, i, l(), _Cxl_Als::n, _Cxl_Los::n, n, _Cur_Loc::nmt, _Rcx_Ptl::nrt, _Cur_Loc::nsc, _Cxl_Los::p2, _Rcx_Ptl::ppi, _Cxl_Als::r, _Cxl_Als::r1, _Cxl_Los::r1, r1, _Cxl_Als::r2, _Cxl_Los::r2, r2, _Rcx_Ptl::re, _Cxl_Los::rf, _Cxl_Los::rp, _Cxl_Als::rr, _Cxl_Los::rr, _Rcx_Ptl::rre, _Rcx_Ptl::rrt, and _Cxl_Los::t2.

Referenced by atd().

◆ cpll()

void cpll	(	Cor_Def *	cdf,
		Rcx_Ptl *	pmf,
		Qry_Seq *	qsq,
		Cxl_Los **	cpr,
		Cur_Aln *	sai,
		Cxl_Los **	cpl
	)

Definition at line 49 of file thrdcpll.c.

References _Cur_Aln::al, _Cur_Aln::cf, _Cor_Def::comn, _Cor_Def::comx, _Cxl_Los::d, _Cxl_Los::e, i, la(), le(), _Cor_Def::lll, _Cor_Def::llmn, _Qry_Seq::n, _Cxl_Los::n, _Cur_Aln::nmt, _Cor_Def::nomn, _Cor_Def::nomx, _Cur_Aln::nsc, _Cxl_Los::p2, _Rcx_Ptl::ppi, _Cxl_Los::r1, r1, _Cxl_Los::r2, r2, _Cxl_Los::rf, _Cor_Def::rfpt, _Cxl_Los::rp, _Cxl_Los::rr, _Rcx_Ptl::rrt, _Cor_Def::sll, _Qry_Seq::sq, and _Cxl_Los::t2.

Referenced by atd().

◆ cprl()

void cprl	(	Fld_Mtf *	mtf,
		Cor_Def *	cdf,
		Rcx_Ptl *	pmf,
		Cxl_Los **	cpr,
		int	ct
	)

Definition at line 53 of file thrdcprl.c.

References calloc(), _Cor_Def::comx, _Cor_Def::ct, _Fld_Mtf::d, _Cxl_Los::d, _Cor_Def::fll, free(), i, _Fld_Mtf::n, _Cor_Def::n, _Cxl_Los::n, _Cor_Def::nomx, _Cor_Def::nt, _Fld_Mtf::p2, _Cxl_Los::p2, _Rcx_Ptl::ppi, _Fld_Mtf::r1, _Cxl_Los::r1, r1, _Fld_Mtf::r2, _Cxl_Los::r2, r2, _Cxl_Los::rf, _Cor_Def::rfpt, _Cxl_Los::rp, _Fld_Mtf::rpc, _Cxl_Los::rr, _Fld_Mtf::rrc, _Cor_Def::sll, _Cor_Def::sq, and _Cxl_Los::t2.

Referenced by atd().

◆ cxei()

void cxei	(	Seg_Nsm *	spn,
		Seg_Cmp *	spc,
		Rcx_Ptl *	pmf,
		Cur_Loc *	sli,
		Seq_Mtf *	psm,
		Cor_Def *	cdf,
		Thd_Cxe *	cxe
	)

Definition at line 50 of file thrdcxei.c.

References _Cur_Loc::co, _Seg_Nsm::frf, i, _Thd_Cxe::ndi, _Cur_Loc::no, _Seg_Cmp::nrt, _Thd_Cxe::nrt, _Seg_Cmp::nsc, _Rcx_Ptl::ppi, _Thd_Cxe::rfe, _Cor_Def::rfpt, _Thd_Cxe::rp, _Thd_Cxe::rpe, _Thd_Cxe::rre, _Thd_Cxe::rrp, _Rcx_Ptl::rrt, _Seg_Cmp::rt, _Cor_Def::sll, _Seg_Nsm::srf, _Seg_Nsm::srp, _Seg_Nsm::srr, _Seq_Mtf::ww, and _Seq_Mtf::ww0.

Referenced by atd().

◆ dgri()

float dgri	(	Seg_Gsm *	spe,
		Seg_Nsm *	spn,
		Thd_Cxe *	cxe,
		Thd_Gsm *	tdg,
		Seq_Mtf *	psm,
		Seg_Cmp *	spc
	)

Definition at line 121 of file thrddgri.c.

References _Thd_Gsm::cs, _Thd_Gsm::dg, _Thd_Gsm::g, g(), _Thd_Gsm::g0, g0(), _Thd_Gsm::ls, _Thd_Gsm::ms, and _Thd_Gsm::ps.

Referenced by atd().

◆ FreeCorDef()

Cor_Def* FreeCorDef ( Cor_Def * cdf )

Definition at line 1313 of file thrdatd.c.

References _Cor_Def::comn, _Cor_Def::comx, free(), _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cor_Def::lrfs, _Cor_Def::nomn, _Cor_Def::nomx, NULL, _Cor_Def::rfpt, and _Cor_Def::sll.

Referenced by Threader::Realign().

◆ FreeFldMtf()

Fld_Mtf* FreeFldMtf ( Fld_Mtf * mtf )

Definition at line 1615 of file thrdatd.c.

References _Fld_Mtf::d, free(), i, _Fld_Mtf::mll, _Fld_Mtf::n, NULL, _Fld_Mtf::p2, _Fld_Mtf::r1, _Fld_Mtf::r2, _Fld_Mtf::rpc, and _Fld_Mtf::rrc.

Referenced by Threader::~Threader().

◆ FreeGibScd()

Gib_Scd* FreeGibScd ( Gib_Scd * gsp )

Definition at line 1573 of file thrdatd.c.

References free(), _Gib_Scd::lmf, _Gib_Scd::lms, _Gib_Scd::lmw, _Gib_Scd::nac, _Gib_Scd::nlc, _Gib_Scd::nti, NULL, _Gib_Scd::tma, and _Gib_Scd::tml.

Referenced by Threader::Realign().

◆ FreeQrySeq()

Qry_Seq* FreeQrySeq ( Qry_Seq * qsq )

Definition at line 1456 of file thrdatd.c.

References free(), _Qry_Seq::mn, _Qry_Seq::mx, NULL, _Qry_Seq::sac, and _Qry_Seq::sq.

Referenced by Threader::Realign().

◆ FreeRcxPtl()

Rcx_Ptl* FreeRcxPtl ( Rcx_Ptl * pmf )

Definition at line 1530 of file thrdatd.c.

References free(), i, _Rcx_Ptl::ndi, _Rcx_Ptl::nrt, NULL, _Rcx_Ptl::re, _Rcx_Ptl::rre, and _Rcx_Ptl::rrt.

Referenced by Threader::CalculateScores(), Threader::CreateRcxPtl(), and Threader::Realign().

◆ FreeSeqMtf()

Seq_Mtf* FreeSeqMtf ( Seq_Mtf * psm )

Definition at line 1381 of file thrdatd.c.

References free(), _Seq_Mtf::freqs, i, _Seq_Mtf::n, NULL, and _Seq_Mtf::ww.

Referenced by Threader::CalculateScores(), and Threader::Realign().

◆ FreeThdTbl()

Thd_Tbl* FreeThdTbl ( Thd_Tbl * ttb )

Definition at line 1702 of file thrdatd.c.

References _Thd_Tbl::al, _Thd_Tbl::co, _Thd_Tbl::cs, _Thd_Tbl::errm, _Thd_Tbl::errp, free(), _Thd_Tbl::g0, i, _Thd_Tbl::lps, _Thd_Tbl::ls, _Thd_Tbl::m0, _Thd_Tbl::ms, _Thd_Tbl::no, _Thd_Tbl::nsc, NULL, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Tbl::tf, _Thd_Tbl::tg, _Thd_Tbl::ts, and _Thd_Tbl::zsc.

Referenced by OrderThdTbl(), and Threader::Realign().

◆ g()

int g	(	Seg_Gsm *	spe,
		Seq_Mtf *	psm,
		Thd_Gsm *	tdg
	)

Definition at line 44 of file thrddgri.c.

References _Seg_Gsm::cs, _Thd_Gsm::cs, _Seg_Gsm::gs, _Seg_Gsm::gss, i, _Seg_Gsm::ls, _Thd_Gsm::ls, _Thd_Gsm::m0, _Seg_Gsm::ms, _Thd_Gsm::ms, ms(), _Seg_Gsm::nsc, and _Seq_Mtf::ww0.

Referenced by _sse2neon_vmull_p64(), PeriodicTableClass::AddElement(), CGlModel2D::AddGeomObject(), CWorkerNodeCleanup::AddListener(), CAutoDefModifierCombo::AddSource(), CSplignTrim::AdjustGaps(), algs(), AlignFNog(), CAutoDefModifierCombo::AreFeatureClausesUnique(), BalWFext(), BLAST_Gdb3(), BOOST_AUTO_TEST_CASE(), BvectorBulkSetTest(), bwfi(), CalcMD5(), calcUpAverages(), CAlignModel::CAlignModel(), CWorkerNodeCleanup::CallEventHandlers(), CWorkerNodeJobCleanup::CallEventHandlers(), NTweakExon::CanCreateNonframeshiftingGap(), CDataType::ClassName(), CAlignCollapser::CleanSelfTranscript(), CTable2AsnValidator::Clear(), CTable2AsnValidator::CollectDiscrepancies(), CMsvcPrjFilesCollector::CollectExtra(), CGlState::Color3d(), IRender::Color3d(), CGlState::Color3f(), IRender::Color3f(), CGlState::Color4d(), IRender::Color4d(), CGlRenderDebug::Color4f(), CGlState::Color4f(), IRender::Color4f(), OpenGLRenderer::ConstructLogo(), CreateMimeFromBiostruc(), CRgbaColor::CRgbaColor(), CSeqIdList::CSeqIdList(), SNetServerInPool::DeleteThis(), dgri(), CStrWithURLRenderer::Draw(), CRgbaGradColorTable::FillGradient(), fillTableUp(), FindFGapIntronNog(), FindIGapIntrons(), CCleanup::FixGeneXrefSkew(), FrAlign(), FrAlignFNog1(), SPSG_StatsCounters::SReport::Func(), generate_string_set(), GetAverage(), CBaseCountItem::GetCounts(), CSNPDbSeqIterator::GetCoverageAnnot(), CSNPDbSeqIterator::GetCoverageGraph(), CSNPDbSeqIterator::GetEntry(), CSNPDbSeqIterator::GetOverviewAnnot(), CSNPDbSeqIterator::GetOverviewGraph(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), GL2Matrix(), DeBruijn::HistogramRange(), huft_build(), CValidError_imp::InitializeSourceQualTags(), CGeneModel::InsertTrustedmRNA(), CGeneModel::InsertTrustedProt(), InvertInto(), CCleanup::IsGeneXrefUnnecessary(), CMsvcSite::IsLibOk(), limitedFillTableUp(), makeOLSAveragesTable(), Matrix2GL(), CSimpleRebalanceStrategy::NeedRebalance(), NlmKarlinLambdaNR(), OLSext(), CwxTableListCtrl::OnGetItemAttr(), CSimpleRebalanceStrategy::OnResourceRequested(), CSeqGraphicWidget::OnSetSeqMarkerDlg(), CSeqGraphicWidget::OnSetSeqMarkerForSelDlg(), SNetScheduleAPIImpl::SServerParamsSync::operator()(), CLockerGuard::operator=(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::Populate(), bm::print_svector_stat(), CCommandArgDescriptions::PrintUsageXml(), CTbl2AsnApp::ProcessSingleEntry(), OpenGLRenderer::PushMatrix(), CWorkerNodeCleanup::RemoveListener(), CWorkerNodeCleanup::RemoveListeners(), CAutoDefSourceGroup::RemoveNonMatchingDescriptions(), CThreadedApp::Run(), CDemoApp::Run(), s_AddProjItemToDll(), s_ValidateExon(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CODBC_CursorCmd::SendDataCmd(), CODBC_CursorCmdExpl::SendDataCmd(), CRgbaColor::Set(), CGLCanvas::SetClearColor(), CPhyloNodeData::SetEdgeColorGradient(), CMagicBlastOptionsHandle::SetGapExtensionCost(), CBlastNucleotideOptionsHandle::SetGapOpeningCost(), CBlastOptions::SetGapOpeningCost(), CBlastProteinOptionsHandle::SetGapOpeningCost(), CMagicBlastOptionsHandle::SetGapOpeningCost(), CBlastOptionsLocal::SetGapOpeningCost(), CBlastOptions::SetGapTrigger(), CBlastOptionsHandle::SetGapTrigger(), CBlastOptionsLocal::SetGapTrigger(), CRgbaColor::SetGreen(), CStdCmdLineArgs::SetGzipEnabled(), CGraphTrack::SetLayout(), CStdCmdLineArgs::SetSRAaccessionEnabled(), CAutoDefSourceGroup::SplitGroup(), string_hash_function(), TestCompressSparseGather(), TestCompressSparseSignedVector(), TestCompressSparseVector(), TestSignedSparseSort(), TestSparseSort(), TestStrSparseSort(), CODBC_CursorCmd::UpdateBlob(), CODBC_CursorCmdExpl::UpdateBlob(), CTable2AsnValidator::ValCollect(), CTable2AsnValidator::Validate(), CTable2AsnValidator::ValReportErrors(), CTable2AsnValidator::ValReportErrorStats(), CTable2AsnValidator::ValTotalErrors(), WFext(), CGraphTrack::x_CollectAllGraphs(), x_CollectCoverageGraph(), x_CollectOverviewGraph(), CSGAlignStatJob::x_CreatePileUpGraphs(), SBaseStats::x_finish_add(), CCommandArgDescriptions::x_GetCommandGroupIndex(), CValidErrorFormat::x_GetLocusTag(), CThreadedApp::x_InitializeDelayedStart(), CThreadedApp::x_InitializeThreadGroups(), CID2SNPProcessor_Impl::x_LoadBlob(), CBamRefSeqInfo::x_LoadRangesCov(), CCSRARefSeqInfo::x_LoadRangesStat(), CThreadedApp::x_PrintThreadGroups(), CSplign::x_Run(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CBedImportData::xInitializeRgb(), CRgbaColor::YuvToRgb(), and zsc().

◆ g0()

float g0	(	Seg_Nsm *	spn,
		Thd_Cxe *	cxe
	)

Definition at line 90 of file thrddgri.c.

References i, _Seg_Nsm::ndi, _Thd_Cxe::rfe, _Thd_Cxe::rpe, _Thd_Cxe::rre, _Seg_Nsm::srf, _Seg_Nsm::srp, and _Seg_Nsm::srr.

Referenced by dgri(), SFeatByPos::operator()(), TestSignedSparseVectorScan(), and TestSparseVectorScan().

◆ NewCorDef()

Cor_Def* NewCorDef ( int NumBlocks )

Definition at line 1292 of file thrdatd.c.

References calloc(), _Cor_Def::comn, _Cor_Def::comx, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cor_Def::lrfs, _Cor_Def::n, _Cor_Def::nomn, _Cor_Def::nomx, _Cor_Def::rfpt, and _Cor_Def::sll.

Referenced by Threader::CreateCorDef().

◆ NewFldMtf()

Fld_Mtf* NewFldMtf	(	int	NumResidues,
		int	NumResResContacts,
		int	NumResPepContacts
	)

Definition at line 1590 of file thrdatd.c.

References calloc(), _Fld_Mtf::d, i, _Fld_Mtf::mll, _Fld_Mtf::n, _Fld_Mtf::p2, _Fld_Mtf::r1, _Fld_Mtf::r2, _Fld_Mtf::rpc, and _Fld_Mtf::rrc.

Referenced by Threader::CreateFldMtf().

◆ NewGibScd()

Gib_Scd* NewGibScd ( int NumTempSteps )

Definition at line 1553 of file thrdatd.c.

References calloc(), _Gib_Scd::lmf, _Gib_Scd::lms, _Gib_Scd::lmw, _Gib_Scd::nac, _Gib_Scd::nlc, _Gib_Scd::nti, _Gib_Scd::nts, _Gib_Scd::tma, and _Gib_Scd::tml.

Referenced by Threader::CreateGibScd().

◆ NewQrySeq()

Qry_Seq* NewQrySeq	(	int	NumResidues,
		int	NumBlocks
	)

Definition at line 1433 of file thrdatd.c.

References calloc(), i, _Qry_Seq::mn, _Qry_Seq::mx, _Qry_Seq::n, _Qry_Seq::sac, and _Qry_Seq::sq.

Referenced by Threader::CreateQrySeq().

◆ NewRcxPtl()

Rcx_Ptl* NewRcxPtl	(	int	NumResTypes,
		int	NumDistances,
		int	PeptideIndex
	)

Definition at line 1503 of file thrdatd.c.

References calloc(), i, _Rcx_Ptl::ndi, _Rcx_Ptl::nrt, _Rcx_Ptl::ppi, _Rcx_Ptl::re, _Rcx_Ptl::rre, and _Rcx_Ptl::rrt.

Referenced by Threader::CreateRcxPtl().

◆ NewSeqMtf()

Seq_Mtf* NewSeqMtf	(	int	NumResidues,
		int	AlphabetSize
	)

Definition at line 1361 of file thrdatd.c.

References _Seq_Mtf::AlphabetSize, calloc(), _Seq_Mtf::freqs, i, _Seq_Mtf::n, and _Seq_Mtf::ww.

Referenced by Threader::CreateSeqMtf().

◆ NewThdTbl()

Thd_Tbl* NewThdTbl	(	int	NumResults,
		int	NumCoreElements
	)

Definition at line 1665 of file thrdatd.c.

References _Thd_Tbl::al, calloc(), _Thd_Tbl::co, _Thd_Tbl::cs, _Thd_Tbl::errm, _Thd_Tbl::errp, _Thd_Tbl::g0, i, _Thd_Tbl::lps, _Thd_Tbl::ls, _Thd_Tbl::m0, _Thd_Tbl::ms, _Thd_Tbl::n, _Thd_Tbl::no, _Thd_Tbl::nsc, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Tbl::tf, _Thd_Tbl::tg, _Thd_Tbl::ts, and _Thd_Tbl::zsc.

Referenced by OrderThdTbl(), and Threader::Realign().

◆ OrderThdTbl()

void OrderThdTbl ( Thd_Tbl * pResults )

Definition at line 1819 of file thrdatd.c.

References calloc(), CopyResult(), FALSE, free(), FreeThdTbl(), i, _Thd_Tbl::mn, _Thd_Tbl::mx, _Thd_Tbl::n, NewThdTbl(), _Thd_Tbl::nsc, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::tg, and TRUE.

Referenced by atd().

◆ PrintCorDef()

void PrintCorDef	(	Cor_Def *	cdf,
		FILE *	pFile
	)

Definition at line 1330 of file thrdatd.c.

References _Cor_Def::comn, _Cor_Def::comx, _Cor_Def::ct, FALSE, _Cor_Def::fll, i, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cor_Def::lrfs, _Cor_Def::n, _Cor_Def::nomn, _Cor_Def::nomx, _Cor_Def::nt, _Cor_Def::rfpt, _Cor_Def::sll, _Cor_Def::sq, and TRUE.

Referenced by Threader::Realign().

◆ PrintFldMtf()

void PrintFldMtf	(	Fld_Mtf *	mtf,
		FILE *	pFile
	)

Definition at line 1636 of file thrdatd.c.

References _Fld_Mtf::d, i, _Fld_Mtf::mll, _Fld_Mtf::n, _Fld_Mtf::p2, _Fld_Mtf::r1, _Fld_Mtf::r2, _Fld_Mtf::rpc, and _Fld_Mtf::rrc.

Referenced by Threader::Realign().

◆ PrintQrySeq()

void PrintQrySeq	(	Qry_Seq *	qsq,
		FILE *	pFile
	)

Definition at line 1468 of file thrdatd.c.

References i, _Qry_Seq::mn, _Qry_Seq::mx, _Qry_Seq::n, _Qry_Seq::sac, and _Qry_Seq::sq.

Referenced by Threader::Realign().

◆ PrintSeqMtf()

void PrintSeqMtf	(	Seq_Mtf *	psm,
		FILE *	pFile
	)

Definition at line 1398 of file thrdatd.c.

References _Seq_Mtf::freqs, i, _Seq_Mtf::n, and _Seq_Mtf::ww.

Referenced by Threader::Realign().

◆ PrintThdTbl()

void PrintThdTbl	(	Thd_Tbl *	ttb,
		FILE *	pFile
	)

Definition at line 1736 of file thrdatd.c.

References _Thd_Tbl::al, _Thd_Tbl::co, _Thd_Tbl::cs, _Thd_Tbl::errm, _Thd_Tbl::errp, _Thd_Tbl::g0, i, _Thd_Tbl::lps, _Thd_Tbl::ls, _Thd_Tbl::m0, _Thd_Tbl::mn, _Thd_Tbl::ms, _Thd_Tbl::mx, _Thd_Tbl::n, _Thd_Tbl::no, _Thd_Tbl::nsc, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Tbl::tf, _Thd_Tbl::tg, _Thd_Tbl::ts, and _Thd_Tbl::zsc.

Referenced by Threader::Realign().

◆ Rand01()

float Rand01 ( int * idum )

Definition at line 87 of file thrdrsmp.c.

References IA1, IA2, IA3, IC1, IC2, IC3, M1, M2, M3, r(), RM1, and RM2.

Referenced by atd(), and rsmp().

◆ rsmp()

int rsmp ( Rnd_Smp * pvl )

Definition at line 48 of file thrdrsmp.c.

References i, _Rnd_Smp::n, _Rnd_Smp::p, r(), and Rand01().

Referenced by algs(), atd(), and sgoi().

◆ sal0()

int sal0	(	Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		Cur_Aln *	sai,
		int	cs,
		int *	mn,
		int *	mx
	)

Definition at line 55 of file thrdsal0.c.

References _Cur_Aln::al, _Cur_Loc::co, i, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cur_Loc::lp, _Qry_Seq::mn, _Qry_Seq::mx, _Cor_Def::n, _Qry_Seq::n, _Cur_Loc::no, _Qry_Seq::sac, and _Cor_Def::sll.

Referenced by atd().

◆ salr()

int salr	(	Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		Cur_Aln *	sai,
		int	cs,
		int *	mn,
		int *	mx
	)

Definition at line 48 of file thrdsalr.c.

References _Cur_Aln::al, _Cur_Loc::co, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Cur_Loc::lp, _Qry_Seq::mn, _Qry_Seq::mx, _Cor_Def::n, _Qry_Seq::n, _Cur_Loc::no, _Qry_Seq::sac, and _Cor_Def::sll.

Referenced by atd().

◆ salu()

void salu	(	Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		int	cs,
		int	al,
		Cur_Aln *	sai
	)

Definition at line 44 of file thrdsalu.c.

References _Cur_Aln::al, _Cur_Loc::co, _Cur_Loc::no, _Cor_Def::rfpt, si, _Cor_Def::sll, _Qry_Seq::sq, and _Cur_Aln::sq.

Referenced by atd().

◆ ScaleThdTbl()

void ScaleThdTbl	(	Thd_Tbl *	ttb,
		double	ScalingFactor
	)

Definition at line 1889 of file thrdatd.c.

References _Thd_Tbl::cs, _Thd_Tbl::errm, _Thd_Tbl::errp, _Thd_Tbl::g0, i, _Thd_Tbl::lps, _Thd_Tbl::m0, _Thd_Tbl::ms, _Thd_Tbl::n, _Thd_Tbl::ps, _Thd_Tbl::tg, and _Thd_Tbl::zsc.

Referenced by atd().

◆ sgoi()

void sgoi	(	int	is,
		int	it,
		Rnd_Smp *	pvl,
		Seg_Ord *	sgo
	)

Definition at line 44 of file thrdsgoi.c.

References i, _Rnd_Smp::n, _Seg_Ord::nsc, _Rnd_Smp::p, rsmp(), _Seg_Ord::si, si, _Seg_Ord::so, and _Seg_Ord::to.

Referenced by atd().

◆ slo0()

int slo0	(	Fld_Mtf *	mtf,
		Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		int	cs,
		int	ct,
		int *	mn,
		int *	mx
	)

Definition at line 63 of file thrdslo0.c.

References calloc(), _Cur_Loc::co, _Cor_Def::comn, _Cor_Def::comx, free(), i, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Fld_Mtf::mll, _Qry_Seq::mn, _Qry_Seq::mx, _Cor_Def::n, _Qry_Seq::n, _Cur_Loc::no, _Cor_Def::nomn, _Cor_Def::nomx, _Cor_Def::rfpt, _Qry_Seq::sac, and _Cor_Def::sll.

Referenced by atd().

◆ slor()

int slor	(	Fld_Mtf *	mtf,
		Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		Cur_Aln *	sai,
		int	cs,
		int	ct,
		int *	mn,
		int *	mx
	)

Definition at line 60 of file thrdslor.c.

References _Cur_Aln::al, _Cur_Loc::co, _Cor_Def::comn, _Cor_Def::comx, i, _Cor_Def::lll, _Cor_Def::llmn, _Cor_Def::llmx, _Fld_Mtf::mll, _Cor_Def::n, _Qry_Seq::n, _Cur_Loc::no, _Cor_Def::nomn, _Cor_Def::nomx, nr(), NULL, _Cor_Def::rfpt, and _Cor_Def::sll.

Referenced by atd().

◆ slou()

void slou	(	Fld_Mtf *	mtf,
		Cor_Def *	cdf,
		int	cs,
		int	ct,
		int	of,
		Cur_Loc *	sli,
		Cur_Aln *	sai,
		Qry_Seq *	qsq
	)

Definition at line 44 of file thrdslou.c.

References _Cur_Aln::al, _Cur_Loc::co, _Cur_Loc::cr, i, _Cur_Loc::lp, _Fld_Mtf::mll, _Cor_Def::n, _Cur_Loc::no, _Cor_Def::rfpt, si, _Cor_Def::sll, _Qry_Seq::sq, and _Cur_Aln::sq.

Referenced by atd().

◆ spci()

int spci	(	Cor_Def *	cdf,
		Qry_Seq *	qsq,
		Cur_Loc *	sli,
		Cur_Aln *	sai,
		int	n,
		Seg_Cmp *	spc
	)

Definition at line 51 of file thrdspci.c.

References _Cur_Aln::al, _Cur_Loc::co, i, _Cor_Def::lll, _Cor_Def::lrfs, _Seg_Cmp::lrt, _Qry_Seq::n, n, _Seg_Cmp::nlp, _Cur_Loc::no, _Seg_Cmp::nrt, _Seg_Cmp::nsc, r(), _Seg_Cmp::rt, _Seg_Cmp::rto, _Qry_Seq::sq, and _Seg_Cmp::srt.

Referenced by atd().

◆ spea()

void spea	(	Cor_Def *	cdf,
		Cxl_Als **	cpa,
		Cur_Aln *	sai,
		Cur_Loc *	sli,
		int	n,
		int	h,
		Seg_Gsm *	spe,
		Seq_Mtf *	psm,
		Seg_Cmp *	spc
	)

Definition at line 50 of file thrdspea.c.

References _Cur_Loc::co, _Cur_Loc::cr, _Cxl_Als::e, _Seg_Gsm::gs, _Seg_Gsm::gss, i, _Seg_Gsm::ms, ms(), _Cxl_Als::n, n, _Cur_Loc::no, _Cur_Aln::nsc, _Cxl_Als::r, _Cxl_Als::r1, r1, _Cxl_Als::r2, r2, _Cor_Def::rfpt, _Cxl_Als::rr, _Cor_Def::sll, _Cur_Aln::sq, and _Seq_Mtf::ww.

Referenced by atd().

◆ spel()

void spel	(	Cxl_Los **	cpl,
		Cur_Aln *	sai,
		Cur_Loc *	sli,
		int	cs,
		Seg_Gsm *	spe,
		Cor_Def *	cdf,
		Seq_Mtf *	psm,
		Seg_Cmp *	spc
	)

Definition at line 48 of file thrdspel.c.

References _Cur_Loc::co, _Cur_Loc::cr, _Seg_Gsm::cs, _Cxl_Los::e, _Seg_Gsm::gs, _Seg_Gsm::gss, i, _Seg_Gsm::ls, _Seg_Gsm::ms, ms(), _Cxl_Los::n, _Cur_Loc::no, _Cur_Aln::nsc, _Cxl_Los::p2, _Cxl_Los::r1, _Cxl_Los::r2, _Cxl_Los::rf, _Cor_Def::rfpt, _Cxl_Los::rp, _Cxl_Los::rr, _Seg_Gsm::s0, _Cor_Def::sll, _Cur_Aln::sq, and _Seq_Mtf::ww.

Referenced by atd().

◆ spni()

void spni	(	Cxl_Los **	cpl,
		Cur_Loc *	sli,
		int	n,
		Seg_Nsm *	spn
	)

Definition at line 45 of file thrdspni.c.

References _Cur_Loc::cr, _Cxl_Los::d, _Seg_Nsm::frf, i, _Cxl_Los::n, n, _Seg_Nsm::ndi, _Seg_Nsm::nrf, _Seg_Nsm::nrp, _Seg_Nsm::nrr, _Seg_Nsm::nrt, _Seg_Nsm::nsc, _Cxl_Los::p2, _Cxl_Los::r1, _Cxl_Los::r2, _Cxl_Los::rf, _Cxl_Los::rp, _Cxl_Los::rr, _Seg_Nsm::srf, _Seg_Nsm::srp, _Seg_Nsm::srr, _Cxl_Los::t2, and _Seg_Nsm::trf.

Referenced by atd().

◆ ThrdRound()

int ThrdRound ( double Num )

Definition at line 1913 of file thrdatd.c.

Referenced by Threader::CreateRcxPtl(), and Threader::CreateSeqMtf().

◆ ttb0()

void ttb0 ( Thd_Tbl * ttb )

Definition at line 45 of file thrdttb0.c.

References BIGNEG, _Thd_Tbl::cs, i, _Thd_Tbl::lps, _Thd_Tbl::mn, _Thd_Tbl::ms, _Thd_Tbl::mx, _Thd_Tbl::n, n, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Tbl::tf, _Thd_Tbl::tg, and _Thd_Tbl::ts.

Referenced by atd().

◆ ttbi()

int ttbi	(	Cur_Aln *	sai,
		Cur_Loc *	sli,
		Thd_Gsm *	tdg,
		Thd_Tbl *	ttb,
		int	nrs,
		int	o
	)

Definition at line 53 of file thrdttbi.c.

References _Thd_Tbl::al, _Cur_Aln::al, _Thd_Tbl::co, _Cur_Loc::co, _Thd_Tbl::cs, _Thd_Gsm::cs, _Thd_Gsm::dg, fabs, i, in(), le(), _Thd_Tbl::lps, _Thd_Tbl::ls, _Thd_Gsm::ls, _Thd_Tbl::m0, _Thd_Gsm::m0, _Thd_Tbl::mn, _Thd_Tbl::ms, _Thd_Gsm::ms, _Thd_Tbl::mx, _Thd_Tbl::n, _Thd_Tbl::no, _Cur_Loc::no, _Cur_Loc::nsc, _Thd_Tbl::nx, _Thd_Tbl::pr, _Thd_Tbl::ps, _Thd_Gsm::ps, SIGDIF, _Thd_Tbl::tf, _Thd_Tbl::tg, and _Thd_Tbl::ts.

Referenced by atd().

◆ zsc()

void zsc	(	Thd_Tbl *	ttb,
		Seq_Mtf *	psm,
		Qry_Seq *	qsq,
		Cxl_Los **	cpr,
		Cor_Def *	cdf,
		Rcx_Ptl *	pmf,
		Seg_Gsm *	spe,
		Cur_Aln *	sai,
		Rnd_Smp *	pvl,
		double	ScalingFactor
	)

Definition at line 64 of file thrdzsc.cpp.

References _Thd_Tbl::al, _Rnd_Smp::aqi, _Cur_Aln::cf, _Thd_Tbl::co, _Seg_Gsm::cs, _Cxl_Los::d, _Thd_Tbl::errm, _Thd_Tbl::errp, g(), _Thd_Tbl::g0, _Seg_Gsm::gs, _Seg_Gsm::gss, i, _Cor_Def::lll, _Cor_Def::lrfs, _Seg_Gsm::ls, _Rnd_Smp::lsg, _Thd_Tbl::m0, _Seg_Gsm::ms, ms(), _Thd_Tbl::mx, _Cor_Def::n, _Qry_Seq::n, _Cxl_Los::n, _Seq_Mtf::n, _Thd_Tbl::no, _Thd_Tbl::nx, _Rnd_Smp::o, _Cxl_Los::p2, _Rcx_Ptl::ppi, _Rnd_Smp::r, r(), _Cxl_Los::r1, r1, _Cxl_Los::r2, r2, RandomNum(), RandomSeed(), _Cxl_Los::rf, _Cor_Def::rfpt, _Cxl_Los::rp, _Cxl_Los::rr, _Rcx_Ptl::rrt, _Cor_Def::sll, _Qry_Seq::sq, _Rnd_Smp::sq, _Cxl_Los::t2, _Seq_Mtf::ww, and _Thd_Tbl::zsc.

Referenced by atd().

Functions

Function Documentation

◆ algs()

◆ atd()

◆ bwfi()

◆ CopyResult()

◆ cpal()

◆ cpll()

◆ cprl()

◆ cxei()

◆ dgri()

◆ FreeCorDef()

◆ FreeFldMtf()

◆ FreeGibScd()

◆ FreeQrySeq()

◆ FreeRcxPtl()

◆ FreeSeqMtf()

◆ FreeThdTbl()

◆ g()

◆ g0()

◆ NewCorDef()

◆ NewFldMtf()

◆ NewGibScd()

◆ NewQrySeq()

◆ NewRcxPtl()

◆ NewSeqMtf()

◆ NewThdTbl()

◆ OrderThdTbl()

◆ PrintCorDef()

◆ PrintFldMtf()

◆ PrintQrySeq()

◆ PrintSeqMtf()

◆ PrintThdTbl()

◆ Rand01()

◆ rsmp()

◆ sal0()

◆ salr()

◆ salu()

◆ ScaleThdTbl()

◆ sgoi()

◆ slo0()

◆ slor()

◆ slou()

◆ spci()

◆ spea()

◆ spel()

◆ spni()

◆ ThrdRound()

◆ ttb0()

◆ ttbi()

◆ zsc()