#include <corelib/ncbi_limits.hpp>#include <algorithm>#include <sstream>#include "NSeq.hpp"#include "PSeq.hpp"#include "BackAlignInfo.hpp"#include "scoring.hpp"#include <objects/seqfeat/Genetic_code_table.hpp>#include <algo/align/prosplign/prosplign_exception.hpp>
Include dependency graph for nucprot.hpp:
This graph shows which files directly or indirectly include this file:
Go to the source code of this file.
Go to the SVN repository for this file.
Classes | |
| struct | CBMode |
| class | CTranslationTable |
| class | CSubstMatrix |
| Substitution Matrix for Scoring Amino-Acid Alignments. More... | |
| class | CFastIScore |
| class | CProSplignInterrupt |
Enumerations | |
| enum | EWMode { eD , eV , eH , eH1 , eH2 , eH3 , eFV , eFH , eS } |
Enumeration Type Documentation
◆ EWMode
| enum EWMode |
| Enumerator | |
|---|---|
| eD | |
| eV | |
| eH | |
| eH1 | |
| eH2 | |
| eH3 | |
| eFV | |
| eFH | |
| eS | |
Definition at line 54 of file nucprot.hpp.
Function Documentation
◆ AlignFNog()
| int AlignFNog | ( | const CProSplignInterrupt & | interrupt, |
| CTBackAlignInfo< CBMode > & | bi, | ||
| const PSEQ & | pseq, | ||
| const CNSeq & | nseq, | ||
| const CProSplignScaledScoring & | scoring, | ||
| const CSubstMatrix & | matrix | ||
| ) |
Definition at line 937 of file nucprot.cpp.
References CTBackAlignInfo< T >::b, bb, ch1, ch2, ch3, CProSplignInterrupt::CheckUserInterrupt(), f, g(), CFIntron::GetH1len(), CFIntron::GetH2len(), CFIntron::GetH3len(), CFastIScore::GetScore(), CFIntron::GetVlen(), CFIntron::GetW1len(), CFIntron::GetW2len(), CFIntron::GetWlen(), CAlignRow::h1, CBestI::h1, CAlignRow::h2, CBestI::h2, CAlignRow::h3, CBestI::h3, i, infinity, CFastIScore::Init(), CFIntron::InitRowScores(), int, CAlignRow::m_w, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, pb, CFastIScore::SetAmin(), CNSeq::size(), CProSplignScaledScoring::sm_If, CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, CFIntron::Step(), swap(), CAlignRow::v, CBestI::v, v2, CAlignRow::w, CBestI::w, CBestI::w1, and CBestI::w2.
Referenced by COneStage::stage1().
◆ BackAlignNog()
| void BackAlignNog | ( | CTBackAlignInfo< CBMode > & | bi, |
| CAli & | ali | ||
| ) |
Definition at line 1143 of file nucprot.cpp.
References CAliCreator::Add(), CTBackAlignInfo< T >::b, eD, eH1, eH2, eH3, eHP, eMP, eSP, eV, eVP, CAliCreator::Fini(), i, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, and NCBI_THROW.
Referenced by COneStage::stage2().
◆ FindFGapIntronNog()
| int FindFGapIntronNog | ( | const CProSplignInterrupt & | interrupt, |
| vector< pair< int, int > > & | igi, | ||
| const PSEQ & | pseq, | ||
| const CNSeq & | nseq, | ||
| bool & | left_gap, | ||
| bool & | right_gap, | ||
| const CProSplignScaledScoring & | scoring, | ||
| const CSubstMatrix & | matrix | ||
| ) |
Definition at line 260 of file nucprot.cpp.
References _ASSERT, ch1, ch2, ch3, CProSplignInterrupt::CheckUserInterrupt(), CIgapIntronChain::Clear(), CFindGapIntronRow::ClearIIC(), CIgapIntronChain::Copy(), CIgapIntronChain::Creat(), CIgapIntronChain::Expand(), f, g(), CFIntron::GetH1len(), CFIntron::GetH2len(), CFIntron::GetH3len(), CFastIScore::GetScore(), CFIntron::GetVlen(), CFIntron::GetW1len(), CFIntron::GetW2len(), CFIntron::GetWlen(), CAlignRow::h1, CBestI::h1, CFindGapIntronRow::h1is, CAlignRow::h2, CBestI::h2, CFindGapIntronRow::h2is, CAlignRow::h3, CBestI::h3, CFindGapIntronRow::h3is, i, infinity, CFastIScore::Init(), CFIntron::InitRowScores(), int, len, CIgapIntronChain::m_Top, CAlignRow::m_w, max(), CFastIScore::SetAmin(), CIgapIntronChain::SetPool(), CNSeq::size(), CProSplignScaledScoring::sm_If, CProSplignScaledScoring::sm_Ig, CProSplignScaledScoring::sm_Ine, CFIntron::Step(), swap(), tmp, CAlignRow::v, CBestI::v, v2, CFindGapIntronRow::vis, CAlignRow::w, CBestI::w, CBestI::w1, CBestI::w2, and CFindGapIntronRow::wis.
Referenced by CTwoStageNew::stage1().
◆ FindIGapIntrons()
| int FindIGapIntrons | ( | const CProSplignInterrupt & | interrupt, |
| vector< pair< int, int > > & | igi, | ||
| const PSEQ & | pseq, | ||
| const CNSeq & | nseq, | ||
| int | g, | ||
| int | e, | ||
| int | f, | ||
| const CProSplignScaledScoring & | scoring, | ||
| const CSubstMatrix & | matrix | ||
| ) |
Definition at line 508 of file nucprot.cpp.
References CProSplignInterrupt::CheckUserInterrupt(), CAlignInfo::ClearIIC(), CIgapIntronChain::Copy(), CIgapIntronChain::Creat(), CIgapIntronChain::Expand(), f, CAlignInfo::fh, CAlignInfo::fhis, CAlignInfo::fv, CAlignInfo::fvis, g(), CBestIntron::Getfh000(), CBestIntron::Getfv000(), CBestIntron::Getfv111(), CBestIntron::Geth000(), CBestIntron::Geth012(), CBestIntron::Geth021(), CBestIntron::Getv000(), CBestIntron::Getw000(), CBestIntron::Getw012(), CBestIntron::Getw021(), CBestIntron::GetW1(), CBestIntron::Getw111(), CBestIntron::GetW2(), CAlignInfo::h, CAlignInfo::his, i, infinity, int, CIgapIntronChain::m_Top, max(), CSubstMatrix::MultScore(), CBestIntron::NucStep(), CNSeq::size(), swap(), tmp, CAlignInfo::v, v2, CAlignInfo::vis, CAlignInfo::w, and CAlignInfo::wis.
Referenced by CTwoStageOld::stage1().
◆ FrAlign()
| int FrAlign | ( | const CProSplignInterrupt & | interrupt, |
| CBackAlignInfo & | bi, | ||
| const PSEQ & | pseq, | ||
| const CNSeq & | nseq, | ||
| int | g, | ||
| int | e, | ||
| int | f, | ||
| const CProSplignScaledScoring & | scoring, | ||
| const CSubstMatrix & | matrix | ||
| ) |
Definition at line 171 of file nucprot.cpp.
References CTBackAlignInfo< T >::b, b, CProSplignInterrupt::CheckUserInterrupt(), f, g(), i, CTBackAlignInfo< T >::ilen, infinity, int, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, CSubstMatrix::MultScore(), CNSeq::size(), swap(), CFrAlignRow::v, v2, and CFrAlignRow::w.
Referenced by CIntronlessOld::stage1(), and CTwoStageOld::stage2().
◆ FrAlignFNog1()
| int FrAlignFNog1 | ( | const CProSplignInterrupt & | interrupt, |
| CBackAlignInfo & | bi, | ||
| const PSEQ & | pseq, | ||
| const CNSeq & | nseq, | ||
| const CProSplignScaledScoring & | scoring, | ||
| const CSubstMatrix & | matrix, | ||
| bool | left_gap = false, |
||
| bool | right_gap = false |
||
| ) |
Definition at line 774 of file nucprot.cpp.
References _ASSERT, CTBackAlignInfo< T >::b, b, bb, CProSplignInterrupt::CheckUserInterrupt(), f, g(), CProSplignScoring::GetFrameshiftOpeningCost(), CProSplignScoring::GetGapExtensionCost(), CProSplignScoring::GetGapOpeningCost(), CFastIScore::GetScore(), i, infinity, CFastIScore::Init(), int, max(), CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, CSubstMatrix::MultScore(), pb, CFastIScore::SetAmin(), CNSeq::size(), swap(), CFrAlignRow::v, v2, and CFrAlignRow::w.
Referenced by CIntronlessNew::stage1(), and CTwoStageNew::stage2().
◆ FrBackAlign()
| void FrBackAlign | ( | CBackAlignInfo & | bi, |
| CAli & | ali | ||
| ) |
Definition at line 684 of file nucprot.cpp.
References CAliCreator::Add(), CTBackAlignInfo< T >::b, b, eD, eH, eH1, eH2, eH3, eHP, eMP, eV, eVP, CAliCreator::Fini(), i, CTBackAlignInfo< T >::ilen, CTBackAlignInfo< T >::jlen, CTBackAlignInfo< T >::maxi, CTBackAlignInfo< T >::maxj, and NCBI_THROW.
Referenced by CTwoStageOld::stage2(), CTwoStageNew::stage2(), and CIntronless::stage2().
