#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
#include "nucprot.hpp"
#include "intron.hpp"
#include "Info.hpp"
#include "BackAlignInfo.hpp"
#include "Ali.hpp"
#include "AlignInfo.hpp"
#include "scoring.hpp"
#include <util/tables/raw_scoremat.h>
Include dependency graph for nucprot.cpp:
Go to the source code of this file.
Functions | |
| int | FrAlign (CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) |
| int | FindFGapIntronNog (vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, bool &left_gap, bool &right_gap, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) |
| int | FindIGapIntrons (vector< pair< int, int > > &igi, const PSEQ &pseq, const CNSeq &nseq, int g, int e, int f, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) |
| void | FrBackAlign (CBackAlignInfo &bi, CAli &ali) |
| int | FrAlignFNog1 (CBackAlignInfo &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix, bool left_gap, bool right_gap) |
| int | AlignFNog (CTBackAlignInfo< CBMode > &bi, const PSEQ &pseq, const CNSeq &nseq, const CProSplignScaledScoring &scoring, const CSubstMatrix &matrix) |
| void | BackAlignNog (CTBackAlignInfo< CBMode > &bi, CAli &ali) |
Variables | |
| const int | infinity = numeric_limits<int>::min()/3 |
|
||||||||||||||||||||||||
|
Definition at line 930 of file nucprot.cpp. References infinity, CFastIScore::Init(), CNSeq::size(), CAlignRow::v, and CAlignRow::w. Referenced by COneStage::stage1(). |
|
||||||||||||
|
Definition at line 1135 of file nucprot.cpp. References CAliCreator::Add(), CTBackAlignInfo< T >::b, eD, eH1, eH2, eH3, eHP, eMP, eSP, eV, eVP, CBMode::h1len, CBMode::h2len, CBMode::h3len, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, NCBI_THROW, CBMode::vlen, CBMode::wlen, and CBMode::wmode. Referenced by COneStage::stage2(). |
|
||||||||||||||||||||||||||||||||
|
Definition at line 256 of file nucprot.cpp. References ch1, ch2, ch3, CIgapIntronChain::Creat(), CIgapIntronChain::Expand(), f(), g(), infinity, CFastIScore::Init(), CIgapIntronChain::SetPool(), CNSeq::size(), CProSplignScaledScoring::sm_If, CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, CAlignRow::v, CAlignRow::w, and CFindGapIntronRow::wis. Referenced by CTwoStageNew::stage1(). |
|
||||||||||||||||||||||||||||||||||||
|
Definition at line 503 of file nucprot.cpp. References CIgapIntronChain::Creat(), CAlignInfo::fv, infinity, CNSeq::size(), CAlignInfo::v, CAlignInfo::w, and CAlignInfo::wis. Referenced by CTwoStageOld::stage1(). |
|
||||||||||||||||||||||||||||||||||||
|
Definition at line 168 of file nucprot.cpp. References infinity, CNSeq::size(), CFrAlignRow::v, and CFrAlignRow::w. Referenced by CIntronlessOld::stage1(), and CTwoStageOld::stage2(). |
|
||||||||||||||||||||||||||||||||
|
Definition at line 768 of file nucprot.cpp. References f(), g(), CProSplignScoring::GetFrameshiftOpeningCost(), CProSplignScoring::GetGapExtensionCost(), CProSplignScoring::GetGapOpeningCost(), infinity, CFastIScore::Init(), CNSeq::size(), CFrAlignRow::v, and CFrAlignRow::w. Referenced by CIntronlessNew::stage1(), and CTwoStageNew::stage2(). |
|
||||||||||||
|
Definition at line 678 of file nucprot.cpp. References CAliCreator::Add(), CTBackAlignInfo< T >::b, eD, eH, eH1, eH2, eH3, eHP, eMP, eV, eVP, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, and NCBI_THROW. Referenced by CIntronless::stage2(), CTwoStageNew::stage2(), and CTwoStageOld::stage2(). |
|
|
Definition at line 52 of file nucprot.cpp. Referenced by AlignFNog(), CAlignRow::CAlignRow(), FindFGapIntronNog(), FindIGapIntrons(), FrAlign(), FrAlignFNog1(), CFIntronDon::Reset(), and CFloatTextValidator::Validate(). |
1.4.6
Modified on Wed Dec 09 08:18:29 2009 by modify_doxy.py rev. 173732