oligofar Namespace Reference

Detailed Description

* TODO: replace it in newer version

Classes

class CAligner_SW

class CAligner_HSP

class CAligner_fast

class AOutputFormatter

class CAligner

class CAlignerBase

class CAlignTest

class CApp

class CBatch

class CBitHacks

class CBitmaskAccess

class CBitmaskBase

class CBitmaskBuilder

class CFaDiceApp

class CFeatMap

class CFilter

class CGuideFile

class CGuideSamFile

class CHashAtom

class CHashPopulator

class CHit

class COligoFarApp

class COutputFormatter

class CPermutator8b

class CProgressIndicator

class CQuery

class CQueryHash

class CSamBase

class CSRead

class CContig

class CMappedAlignment

class CSamSource

class CSamFormatter

class CScanCallback

class AScoreWithParam

class CCvtQryNcbi8naEquiv

class CShr

class CShl

class CCvtQryNcbi8naBisulfite

class CCvtSubjNcbi8naFwd

class CCvtSubjNcbi8naRev

class CNcbi8naScore

class CNcbiqnaScore

class CCvtQryNcbipnaEquiv

class CCvtQryNcbipnaBisulfite

class CNcbipnaScore

class CDibaseScore_Base

class CDibaseScore

class CScoreParam

class CScoreTbl

class CScoring

class CScoringFactory

class CSeqBuffer

class CSeqCoding

class CIupacnaBase

class CNcbipnaBase

class CNcbiqnaBase

class CNcbi8naBase

class CNcbi4naBase

class CNcbi2naBase

class CColorTwoBase

class CSeqIds

class CSeqScanner

class CSeqVecProcessor

class IShortReader

class CReaderFactory

class CColFileReader

class CSolexaFileReader

class CFastqFileReader

class CSnpDbBase

class CSnpDbCreator

class CSnpDb

class CSpacialRanges

class CWordHash

class CComplexityMeasure

class IAligner

class INucSeq

class IShortRead

class IMappedAlignment

class IAlignmentMap

class IGuideFile

class IOutputFormatter

class IProgressIndicator

class IScore

class TAligner_fast

class TAligner_HSP

class CAligner_SW_Base

class TAligner_SW

class TAlignerBase

class TSeqRef

class UintH

Namespaces

namespace fourplanes

namespace NUtil

Typedefs

typedef CCvtQryNcbi8naBisulfite<
8, CShr< Uint1, 2 > > CCvtQryNcbi8naTC

typedef CCvtQryNcbi8naBisulfite<
1, CShl< Uint1, 2 > > CCvtQryNcbi8naAG

typedef CCvtQryNcbipnaBisulfite< 3, 1 > CCvtQryNcbipnaTC

typedef CCvtQryNcbipnaBisulfite< 0, 2 > CCvtQryNcbipnaAG

typedef long long huge

typedef UintH THashMask

typedef UintH THashValue

typedef Uint8 TPlaneMask

Functions

std::ostream & operator<< (std::ostream &o, const CAligner::CCell &cell)

ostream & operator<< (ostream &o, const CHashAtom &a)

char * Reverse (char *c, int cnt)

char * ReverseComplement (char *c, int cnt)

char * Reverse (char *c, int cnt, CSeqCoding::EStrand s)

char * ReverseComplement (char *c, int cnt, CSeqCoding::EStrand s)

template<class BaseA, class BaseB>

int ComputeScore (const BaseA &a, const BaseB &b)

int ComputeScore (const CNcbi8naBase &a, const CNcbipnaBase &b)

int ComputeScore (const CNcbipnaBase &b, const CNcbi8naBase &a)

int operator * (const CNcbi2naBase &a, const CNcbi2naBase &b)

template<class iterator>

iterator Split (const string &str, const string &delim, iterator i, bool tokenize=true)

template<class container>

string Join (const string &delim, const container &c)

template<class iterator>

string Join (const string &delim, iterator b, iterator e)

UintH operator * (const UintH &x, const UintH &y)

UintH operator/ (const UintH &n, const Uint8 &d)

ostream & operator<< (ostream &out, const UintH &h)

Typedef Documentation

typedef CCvtQryNcbi8naBisulfite<1,CShl<Uint1,2> > oligofar::CCvtQryNcbi8naAG

Definition at line 49 of file cscore-impl.hpp.

typedef CCvtQryNcbi8naBisulfite<8,CShr<Uint1,2> > oligofar::CCvtQryNcbi8naTC

Definition at line 48 of file cscore-impl.hpp.

typedef CCvtQryNcbipnaBisulfite<0,2> oligofar::CCvtQryNcbipnaAG

Definition at line 129 of file cscore-impl.hpp.

typedef CCvtQryNcbipnaBisulfite<3,1> oligofar::CCvtQryNcbipnaTC

Definition at line 128 of file cscore-impl.hpp.

typedef long long oligofar::huge

Definition at line 11 of file defs.hpp.

typedef UintH oligofar::THashMask

Definition at line 8 of file types.hpp.

typedef UintH oligofar::THashValue

Definition at line 9 of file types.hpp.

typedef Uint8 oligofar::TPlaneMask

Definition at line 10 of file types.hpp.

Function Documentation

int oligofar::ComputeScore ( const CNcbipnaBase & b,

const CNcbi8naBase & a

) [inline]

Definition at line 225 of file cseqcoding.hpp.

int oligofar::ComputeScore ( const CNcbi8naBase & a,

const CNcbipnaBase & b

) [inline]

Definition at line 216 of file cseqcoding.hpp.

template<class BaseA, class BaseB>

int oligofar::ComputeScore ( const BaseA & a,

const BaseB & b

) [inline]

Definition at line 211 of file cseqcoding.hpp.
References bool.

template<class iterator>

string oligofar::Join ( const string & delim,

iterator b,

iterator e

) [inline]

Definition at line 41 of file string-util.hpp.

template<class container>

string oligofar::Join ( const string & delim,

const container & c

) [inline]

Definition at line 29 of file string-util.hpp.
Referenced by oligofar::COligoFarApp::Help(), oligofar::CSpacialRanges::Print(), and oligofar::COligoFarApp::ReportSplices().

UintH oligofar::operator * ( const UintH & x,

const UintH & y

) [inline]

Definition at line 111 of file uinth.hpp.
References oligofar::UintH::GetHi(), and oligofar::UintH::GetLo().

int oligofar::operator * ( const CNcbi2naBase & a,

const CNcbi2naBase & b

) [inline]

Definition at line 234 of file cseqcoding.hpp.

UintH oligofar::operator/ ( const UintH & n,

const Uint8 & d

) [inline]

Definition at line 138 of file uinth.hpp.
References oligofar::UintH::GetHi(), and oligofar::UintH::m_lo.

ostream& oligofar::operator<< ( ostream & out,

const UintH & h

) [inline]

Definition at line 157 of file uinth.hpp.
References oligofar::UintH::GetHi(), and oligofar::UintH::GetLo().

ostream& oligofar::operator<< ( ostream & o,

const CHashAtom & a

) [inline]

Definition at line 161 of file chashatom.hpp.
References oligofar::CHashAtom::PrintDebug().

std::ostream& oligofar::operator<< ( std::ostream & o,

const CAligner::CCell & cell

) [inline]

Definition at line 330 of file caligner.hpp.
References CTrItemPacked< bitst, bitsc >::GetCigar(), CTrItemPacked< bitst, bitsc >::GetCount(), and oligofar::CAligner::CCell::GetScore().

char* oligofar::Reverse ( char * c,

int cnt,

CSeqCoding::EStrand s

) [inline]

Definition at line 329 of file coutputformatter.cpp.
References oligofar::CSeqCoding::eStrand_neg, and Reverse().

char* oligofar::Reverse ( char * c,

int cnt

) [inline]

Definition at line 310 of file coutputformatter.cpp.
References swap().
Referenced by Reverse().

char* oligofar::ReverseComplement ( char * c,

int cnt,

CSeqCoding::EStrand s

) [inline]

Definition at line 333 of file coutputformatter.cpp.
References oligofar::CSeqCoding::eStrand_neg, and ReverseComplement().

char* oligofar::ReverseComplement ( char * c,

int cnt

) [inline]

Definition at line 316 of file coutputformatter.cpp.
References oligofar::CIupacnaBase::Complement().
Referenced by ReverseComplement().

template<class iterator>

iterator oligofar::Split ( const string & str,

const string & delim,

iterator i,

bool tokenize = true

) [inline]

Definition at line 13 of file string-util.hpp.
Referenced by COptArgList< List >::Handle(), COptArgSet< Set >::Handle(), oligofar::CSamSource::IndexFile(), oligofar::CGuideSamFile::NextHit(), oligofar::COligoFarApp::ParseArg(), and oligofar::CSamSource::ParseSamLine().

Generated on Mon Dec 7 16:08:33 2009 for NCBI C++ ToolKit by

1.4.6

Modified on Mon Dec 07 16:24:38 2009 by modify_doxy.py rev. 173732


Classes
class	CAligner_SW
class	CAligner_HSP
class	CAligner_fast
class	AOutputFormatter
class	CAligner
class	CAlignerBase
class	CAlignTest
class	CApp
class	CBatch
class	CBitHacks
class	CBitmaskAccess
class	CBitmaskBase
class	CBitmaskBuilder
class	CFaDiceApp
class	CFeatMap
class	CFilter
class	CGuideFile
class	CGuideSamFile
class	CHashAtom
class	CHashPopulator
class	CHit
class	COligoFarApp
class	COutputFormatter
class	CPermutator8b
class	CProgressIndicator
class	CQuery
class	CQueryHash
class	CSamBase
class	CSRead
class	CContig
class	CMappedAlignment
class	CSamSource
class	CSamFormatter
class	CScanCallback
class	AScoreWithParam
class	CCvtQryNcbi8naEquiv
class	CShr
class	CShl
class	CCvtQryNcbi8naBisulfite
class	CCvtSubjNcbi8naFwd
class	CCvtSubjNcbi8naRev
class	CNcbi8naScore
class	CNcbiqnaScore
class	CCvtQryNcbipnaEquiv
class	CCvtQryNcbipnaBisulfite
class	CNcbipnaScore
class	CDibaseScore_Base
class	CDibaseScore
class	CScoreParam
class	CScoreTbl
class	CScoring
class	CScoringFactory
class	CSeqBuffer
class	CSeqCoding
class	CIupacnaBase
class	CNcbipnaBase
class	CNcbiqnaBase
class	CNcbi8naBase
class	CNcbi4naBase
class	CNcbi2naBase
class	CColorTwoBase
class	CSeqIds
class	CSeqScanner
class	CSeqVecProcessor
class	IShortReader
class	CReaderFactory
class	CColFileReader
class	CSolexaFileReader
class	CFastqFileReader
class	CSnpDbBase
class	CSnpDbCreator
class	CSnpDb
class	CSpacialRanges
class	CWordHash
class	CComplexityMeasure
class	IAligner
class	INucSeq
class	IShortRead
class	IMappedAlignment
class	IAlignmentMap
class	IGuideFile
class	IOutputFormatter
class	IProgressIndicator
class	IScore
class	TAligner_fast
class	TAligner_HSP
class	CAligner_SW_Base
class	TAligner_SW
class	TAlignerBase
class	TSeqRef
class	UintH
Namespaces
namespace	fourplanes
namespace	NUtil
Typedefs
typedef CCvtQryNcbi8naBisulfite< 8, CShr< Uint1, 2 > >	CCvtQryNcbi8naTC
typedef CCvtQryNcbi8naBisulfite< 1, CShl< Uint1, 2 > >	CCvtQryNcbi8naAG
typedef CCvtQryNcbipnaBisulfite< 3, 1 >	CCvtQryNcbipnaTC
typedef CCvtQryNcbipnaBisulfite< 0, 2 >	CCvtQryNcbipnaAG
typedef long long	huge
typedef UintH	THashMask
typedef UintH	THashValue
typedef Uint8	TPlaneMask
Functions
std::ostream &	operator<< (std::ostream &o, const CAligner::CCell &cell)
ostream &	operator<< (ostream &o, const CHashAtom &a)
char *	Reverse (char *c, int cnt)
char *	ReverseComplement (char *c, int cnt)
char *	Reverse (char *c, int cnt, CSeqCoding::EStrand s)
char *	ReverseComplement (char *c, int cnt, CSeqCoding::EStrand s)
template<class BaseA, class BaseB>
int	ComputeScore (const BaseA &a, const BaseB &b)
int	ComputeScore (const CNcbi8naBase &a, const CNcbipnaBase &b)
int	ComputeScore (const CNcbipnaBase &b, const CNcbi8naBase &a)
int	operator * (const CNcbi2naBase &a, const CNcbi2naBase &b)
template<class iterator>
iterator	Split (const string &str, const string &delim, iterator i, bool tokenize=true)
template<class container>
string	Join (const string &delim, const container &c)
template<class iterator>
string	Join (const string &delim, iterator b, iterator e)
UintH	operator * (const UintH &x, const UintH &y)
UintH	operator/ (const UintH &n, const Uint8 &d)
ostream &	operator<< (ostream &out, const UintH &h)