NCBI C++ ToolKit
|
Search Toolkit Book for CAdjustForConsensusSpliceSite
#include <gui/objutils/adjust_consensus_splicesite.hpp>
Public Member Functions | |
CAdjustForConsensusSpliceSite (objects::CScope &scope) | |
void | SetScope (objects::CScope &scope) |
CRef< CCmdComposite > | GetCommand (const objects::CSeq_feat &cds) |
AdjustForConsensusSpliceSite Adjust internal intervals of a CDS (and its associated mRNA feature) to position the interval endpoints at consensus splice sites (GT-AG), as long as the repositioning does not alter the contents of the translated protein. More... | |
CRef< CCmdComposite > | GetCommandToAdjustCDSEnds (const objects::CSeq_feat &cds) |
bool | AdjustCDS (objects::CSeq_feat &cds) |
bool | AdjustmRNAToMatchCDS (const objects::CSeq_feat &edit_cds, objects::CSeq_feat &mrna) |
CRef< CCmdComposite > | AdjustmRNAandExonFeatures (const objects::CSeq_feat &new_cds, const objects::CSeq_feat &orig_cds) |
bool | AdjustCDSEnds (objects::CSeq_feat &cds) |
bool | AdjustmRNAToMatchCDSEnds (const objects::CSeq_feat &edit_cds, objects::CSeq_feat &mrna) |
CRef< CCmdComposite > | AdjustmRNAandExonEnds (const objects::CSeq_feat &new_cds, const objects::CSeq_feat &orig_cds) |
Static Public Member Functions | |
static bool | s_IsBioseqGood_Strict (const objects::CBioseq_Handle &bsh) |
static bool | s_IsBioseqGood_Relaxed (const objects::CBioseq_Handle &bsh) |
static bool | s_IsBioseqGood_AdjustEnds (const objects::CBioseq_Handle &bsh) |
static bool | s_IsAdjustedSpliceSitePairOK (const string &seqdata, TSeqPos intron_start, TSeqPos intron_stop) |
Private Types | |
typedef vector< TSeqRange > | TLocs |
Private Member Functions | |
void | x_InitRanges (const objects::CSeq_feat &cds) |
void | x_UpdateMixLocations (const objects::CSeq_loc &orig_loc, objects::CSeq_loc::TLocations &locs) |
void | x_UpdateInterval (objects::CSeq_interval &interval) |
void | x_UpdateIntervals (objects::CSeq_loc::TIntervals &locs) |
CRef< objects::CSeq_loc > | x_UpdateLocation (const objects::CSeq_feat &cds) |
TSeqPos | x_IntronLength (const TSeqRange &rng_prev, const TSeqRange &rng) |
void | x_ShiftExonPairForward (TSeqRange &range_prev, TSeqRange &range, TSeqPos offset) |
void | x_ShiftExonPairBackward (TSeqRange &range_prev, TSeqRange &range, TSeqPos offset) |
CRef< objects::CSeq_loc > | x_CreateNewLocation (const objects::CSeq_feat &cds) |
bool | x_HasProteinChanged (const objects::CSeq_feat &cds, const string &orig_prot_seq) |
bool | x_HasProteinChangedAt5End (objects::CSeq_feat &cds, const string &orig_prot_seq) |
bool | x_HasProteinChangedAt3End (objects::CSeq_feat &cds, const string &orig_prot_seq) |
bool | x_AlsoAdjustmRNA (objects::CSeq_feat &mrna, const objects::CSeq_loc &loc) |
void | x_UpdateExonFeatures (CCmdComposite *cmd, const objects::CSeq_feat &orig_cds, const objects::CSeq_feat &new_cds) |
bool | x_AdjustCDS5End (objects::CSeq_feat &cds, const string &orig_prot_seq) |
bool | x_AdjustCDS3End (objects::CSeq_feat &cds, const string &orig_prot_seq) |
bool | x_ExtendStartOfExon (TSeqRange &range, TSeqPos offset, const objects::CSeq_loc &loc, objects::CBioseq_Handle bsh) |
void | x_TrimStartOfExon (TSeqRange &range, TSeqPos offset) |
bool | x_ExtendStopOfExon (TSeqRange &range, TSeqPos offset, const objects::CSeq_loc &loc, objects::CBioseq_Handle bsh) |
void | x_TrimStopOfExon (TSeqRange &range, TSeqPos offset) |
Private Attributes | |
objects::ENa_strand | m_Strand |
TLocs | m_Orig_Ranges |
TLocs | m_New_Ranges |
bool | m_ProtChanged { false } |
CRef< objects::CScope > | m_Scope |
Definition at line 50 of file adjust_consensus_splicesite.hpp.
|
private |
Definition at line 76 of file adjust_consensus_splicesite.hpp.
|
inline |
Definition at line 53 of file adjust_consensus_splicesite.hpp.
bool CAdjustForConsensusSpliceSite::AdjustCDS | ( | objects::CSeq_feat & | cds | ) |
Definition at line 139 of file adjust_consensus_splicesite.cpp.
References _ASSERT, CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::eCoding_Ncbi, CSeq_loc_CI::eEmpty_Skip, eExtreme_Biological, eNa_strand_minus, eNa_strand_other, CSeq_loc_CI::eOrder_Biological, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CRef< C, Locker >::GetObject(), CSeq_feat_Base::GetProduct(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStrand(), NStr::IsBlank(), CSeqFeatData_Base::IsCdregion(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc_Base::IsPnt(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetProduct(), kEmptyStr, m_New_Ranges, m_Scope, m_Strand, match(), offset, CSeq_feat_Base::ResetLocation(), s_IsAdjustedSpliceSitePairOK(), CSeqVector::SetCoding(), CSeq_feat_Base::SetLocation(), CSeqVector::size(), swap(), x_HasProteinChanged(), x_InitRanges(), x_IntronLength(), x_ShiftExonPairBackward(), x_ShiftExonPairForward(), and x_UpdateLocation().
Referenced by GetCommand().
bool CAdjustForConsensusSpliceSite::AdjustCDSEnds | ( | objects::CSeq_feat & | cds | ) |
Definition at line 846 of file adjust_consensus_splicesite.cpp.
References _ASSERT, CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Ncbi, eExtreme_Biological, eNa_strand_other, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CRef< C, Locker >::GetObject(), CSeq_feat_Base::GetProduct(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStrand(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetProduct(), m_Scope, m_Strand, CSeq_feat_Base::ResetLocation(), CSeqVector::SetCoding(), CSeq_feat_Base::SetLocation(), CSeqVector::size(), x_AdjustCDS3End(), x_AdjustCDS5End(), x_InitRanges(), and x_UpdateLocation().
Referenced by GetCommandToAdjustCDSEnds().
CRef< CCmdComposite > CAdjustForConsensusSpliceSite::AdjustmRNAandExonEnds | ( | const objects::CSeq_feat & | new_cds, |
const objects::CSeq_feat & | orig_cds | ||
) |
Definition at line 1208 of file adjust_consensus_splicesite.cpp.
References _ASSERT, AdjustmRNAToMatchCDSEnds(), CSerialObject::Assign(), cmd, GetmRNAforCDS(), CConstRef< C, Locker >::GetObject(), m_Scope, and x_UpdateExonFeatures().
Referenced by GetCommandToAdjustCDSEnds().
CRef< CCmdComposite > CAdjustForConsensusSpliceSite::AdjustmRNAandExonFeatures | ( | const objects::CSeq_feat & | new_cds, |
const objects::CSeq_feat & | orig_cds | ||
) |
Definition at line 298 of file adjust_consensus_splicesite.cpp.
References _ASSERT, AdjustmRNAToMatchCDS(), CSerialObject::Assign(), cmd, GetmRNAforCDS(), CConstRef< C, Locker >::GetObject(), m_Scope, and x_UpdateExonFeatures().
Referenced by GetCommand().
bool CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDS | ( | const objects::CSeq_feat & | edit_cds, |
objects::CSeq_feat & | mrna | ||
) |
Definition at line 293 of file adjust_consensus_splicesite.cpp.
References CSeq_feat_Base::GetLocation(), and x_AlsoAdjustmRNA().
Referenced by AdjustmRNAandExonFeatures().
bool CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds | ( | const objects::CSeq_feat & | edit_cds, |
objects::CSeq_feat & | mrna | ||
) |
Definition at line 1229 of file adjust_consensus_splicesite.cpp.
References CSeq_loc::Assign(), eExtreme_Biological, eNa_strand_minus, CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStart(), CSeq_loc_CI::GetStrand(), CSeq_loc_I::HasChanges(), CSeq_loc_CI::IsSetStrand(), CSeq_loc_I::MakeSeq_loc(), CSeq_loc_I::SetFrom(), CSeq_feat_Base::SetLocation(), CSeq_loc_CI::SetPos(), and CSeq_loc_I::SetTo().
Referenced by AdjustmRNAandExonEnds().
CRef< CCmdComposite > CAdjustForConsensusSpliceSite::GetCommand | ( | const objects::CSeq_feat & | cds | ) |
AdjustForConsensusSpliceSite Adjust internal intervals of a CDS (and its associated mRNA feature) to position the interval endpoints at consensus splice sites (GT-AG), as long as the repositioning does not alter the contents of the translated protein.
cds | Coding region feature |
scope | The scope in which adjustments are to be made (if necessary) |
Definition at line 55 of file adjust_consensus_splicesite.cpp.
References _ASSERT, AdjustCDS(), AdjustmRNAandExonFeatures(), CSerialObject::Assign(), command, m_Scope, and NULL.
Referenced by CSequenceEditingEventHandler::AdjustForConsensusSpliceSites().
CRef< CCmdComposite > CAdjustForConsensusSpliceSite::GetCommandToAdjustCDSEnds | ( | const objects::CSeq_feat & | cds | ) |
Definition at line 90 of file adjust_consensus_splicesite.cpp.
References _ASSERT, AdjustCDSEnds(), AdjustmRNAandExonEnds(), CSerialObject::Assign(), command, CSeqFeatData_Base::e_Prot, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::GetMol(), CSeq_feat_Base::GetProduct(), CSeq_inst_Base::GetRepr(), m_ProtChanged, m_Scope, NULL, prot, CSeq_inst_Base::SetLength(), CSeq_feat_Base::SetLocation(), and CSeq_inst_Base::SetSeq_data().
Referenced by CSequenceEditingEventHandler::AdjustForConsensusSpliceSites().
|
static |
Definition at line 440 of file adjust_consensus_splicesite.cpp.
References Error(), CException::GetMsg(), LOG_POST, and CException::what().
Referenced by AdjustCDS().
|
static |
Definition at line 397 of file adjust_consensus_splicesite.cpp.
References CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Source, CMolInfo_Base::eBiomol_genomic, CSeq_inst_Base::eMol_dna, CMolInfo_Base::GetBiomol(), CSeqdesc_Base::GetMolinfo(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), COrg_ref::GetTaxId(), IsOrganelle(), CMolInfo_Base::IsSetBiomol(), CBioSource_Base::IsSetOrg(), and ZERO_TAX_ID.
Referenced by CSequenceEditingEventHandler::AdjustForConsensusSpliceSites().
|
static |
Definition at line 382 of file adjust_consensus_splicesite.cpp.
References CSeqdesc_Base::e_Source, CBioSource_Base::eGenome_genomic, CBioSource_Base::eGenome_unknown, CBioSource_Base::GetGenome(), and CSeqdesc_Base::GetSource().
Referenced by CSequenceEditingEventHandler::AdjustForConsensusSpliceSites(), and s_IsBioseqGood_Strict().
|
static |
Definition at line 362 of file adjust_consensus_splicesite.cpp.
References CSeqdesc_Base::e_Source, NStr::FindNoCase(), CBioSource::GetLineage(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), COrg_ref::GetTaxId(), CBioSource::IsSetLineage(), CBioSource_Base::IsSetOrg(), NPOS, s_IsBioseqGood_Relaxed(), and ZERO_TAX_ID.
Referenced by CSequenceEditingEventHandler::AdjustForConsensusSpliceSites().
|
inline |
Definition at line 56 of file adjust_consensus_splicesite.hpp.
References m_Scope, and CRef< C, Locker >::Reset().
|
private |
Definition at line 1084 of file adjust_consensus_splicesite.cpp.
References CBioseq_Handle::eCoding_Iupac, CSeq_loc_CI::eEmpty_Skip, eNa_strand_minus, CSeq_loc_CI::eOrder_Biological, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc_CI::GetSize(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), kEmptyStr, m_New_Ranges, m_Scope, m_Strand, offset, CSeq_loc_CI::SetPos(), swap(), x_ExtendStopOfExon(), x_HasProteinChangedAt3End(), and x_TrimStopOfExon().
Referenced by AdjustCDSEnds().
|
private |
Definition at line 960 of file adjust_consensus_splicesite.cpp.
References CBioseq_Handle::eCoding_Iupac, CSeq_loc_CI::eEmpty_Skip, eNa_strand_minus, CSeq_loc_CI::eOrder_Biological, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), kEmptyStr, m_New_Ranges, m_Scope, m_Strand, offset, swap(), x_ExtendStartOfExon(), x_HasProteinChangedAt5End(), and x_TrimStartOfExon().
Referenced by AdjustCDSEnds().
|
private |
Definition at line 456 of file adjust_consensus_splicesite.cpp.
References CSeq_loc_mix::AddInterval(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc::Assign(), CSeq_loc_CI::eEmpty_Skip, eExtreme_Positional, CSeq_loc_CI::eOrder_Positional, CRange_Base::GetFrom(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CRef< C, Locker >::GetObject(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc_Base::IsPnt(), ITERATE, m_New_Ranges, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().
Referenced by AdjustmRNAToMatchCDS().
|
private |
Definition at line 606 of file adjust_consensus_splicesite.cpp.
References CSeq_loc::Assign(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), x_UpdateInterval(), x_UpdateIntervals(), and x_UpdateMixLocations().
Referenced by x_HasProteinChanged(), x_HasProteinChangedAt3End(), and x_HasProteinChangedAt5End().
|
private |
Definition at line 1054 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, CBioseq_Handle::GetInst_Length(), m_Strand, offset, and compile_time_bits::range().
Referenced by x_AdjustCDS5End().
|
private |
Definition at line 1178 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, CBioseq_Handle::GetInst_Length(), m_Strand, offset, and compile_time_bits::range().
Referenced by x_AdjustCDS3End().
|
private |
Definition at line 627 of file adjust_consensus_splicesite.cpp.
References CSerialObject::Assign(), NStr::EqualNocase(), m_Scope, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::SetLocation(), and x_CreateNewLocation().
Referenced by AdjustCDS().
|
private |
Definition at line 688 of file adjust_consensus_splicesite.cpp.
References CSerialObject::Assign(), NStr::EqualNocase(), m_ProtChanged, m_Scope, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::SetLocation(), and x_CreateNewLocation().
Referenced by x_AdjustCDS3End().
|
private |
Definition at line 639 of file adjust_consensus_splicesite.cpp.
References CSerialObject::Assign(), CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, NStr::EqualNocase(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CCdregion_Base::IsSetFrame(), m_ProtChanged, m_Scope, CSeq_feat_Base::ResetLocation(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and x_CreateNewLocation().
Referenced by x_AdjustCDS5End().
|
private |
Definition at line 596 of file adjust_consensus_splicesite.cpp.
References CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Biological, CSeq_feat_Base::GetLocation(), m_New_Ranges, and m_Orig_Ranges.
Referenced by AdjustCDS(), and AdjustCDSEnds().
|
private |
Definition at line 831 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, CRange_Base::GetFrom(), CRange_Base::GetTo(), and m_Strand.
Referenced by AdjustCDS().
|
private |
Definition at line 818 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, CRange_Base::GetFrom(), CRange_Base::GetTo(), m_Strand, offset, compile_time_bits::range(), CRange_Base::SetFrom(), and CRange_Base::SetTo().
Referenced by AdjustCDS().
|
private |
Definition at line 805 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, CRange_Base::GetFrom(), CRange_Base::GetTo(), m_Strand, offset, compile_time_bits::range(), CRange_Base::SetFrom(), and CRange_Base::SetTo().
Referenced by AdjustCDS().
Definition at line 1074 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, m_Strand, offset, and compile_time_bits::range().
Referenced by x_AdjustCDS5End().
Definition at line 1198 of file adjust_consensus_splicesite.cpp.
References eNa_strand_minus, m_Strand, offset, and compile_time_bits::range().
Referenced by x_AdjustCDS3End().
|
private |
Definition at line 319 of file adjust_consensus_splicesite.cpp.
References CSerialObject::Assign(), cmd, CSeq_loc_CI::eEmpty_Skip, eExtreme_Positional, CSeq_loc_CI::eOrder_Positional, CSeqFeatData::eSubtype_exon, CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetMappedFeature(), CConstRef< C, Locker >::GetObject(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CRange_Base::GetTo(), CSeq_loc_Base::IsInt(), CSeq_feat_Base::IsSetLocation(), m_Scope, and CSeq_feat_Base::SetLocation().
Referenced by AdjustmRNAandExonEnds(), and AdjustmRNAandExonFeatures().
|
private |
Definition at line 770 of file adjust_consensus_splicesite.cpp.
References m_New_Ranges, m_Orig_Ranges, CSeq_interval_Base::SetFrom(), and CSeq_interval_Base::SetTo().
Referenced by x_CreateNewLocation().
|
private |
Definition at line 784 of file adjust_consensus_splicesite.cpp.
References m_New_Ranges, m_Orig_Ranges, CSeq_interval_Base::SetFrom(), and CSeq_interval_Base::SetTo().
Referenced by x_CreateNewLocation().
|
private |
Definition at line 548 of file adjust_consensus_splicesite.cpp.
References CSeq_loc_mix::AddInterval(), CSeq_loc_mix::AddSeqLoc(), CSeq_loc_CI::eEmpty_Skip, eExtreme_Biological, CSeq_loc_CI::eOrder_Biological, CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CRef< C, Locker >::GetObject(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::GetStrand(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc_Base::IsPnt(), m_New_Ranges, m_Orig_Ranges, CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().
Referenced by AdjustCDS(), and AdjustCDSEnds().
|
private |
Definition at line 718 of file adjust_consensus_splicesite.cpp.
References CSeq_id::Assign(), CSeq_loc::Assign(), CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Biological, CSeq_point_Base::GetId(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPnt(), m_New_Ranges, m_Orig_Ranges, m_Strand, CSeq_loc::SetInt(), and CSeq_loc::SetPnt().
Referenced by x_CreateNewLocation().
|
private |
Definition at line 108 of file adjust_consensus_splicesite.hpp.
Referenced by AdjustCDS(), x_AdjustCDS3End(), x_AdjustCDS5End(), x_AlsoAdjustmRNA(), x_InitRanges(), x_UpdateInterval(), x_UpdateIntervals(), x_UpdateLocation(), and x_UpdateMixLocations().
|
private |
Definition at line 106 of file adjust_consensus_splicesite.hpp.
Referenced by x_InitRanges(), x_UpdateInterval(), x_UpdateIntervals(), x_UpdateLocation(), and x_UpdateMixLocations().
Definition at line 112 of file adjust_consensus_splicesite.hpp.
Referenced by GetCommandToAdjustCDSEnds(), x_HasProteinChangedAt3End(), and x_HasProteinChangedAt5End().
|
private |
Definition at line 114 of file adjust_consensus_splicesite.hpp.
Referenced by AdjustCDS(), AdjustCDSEnds(), AdjustmRNAandExonEnds(), AdjustmRNAandExonFeatures(), GetCommand(), GetCommandToAdjustCDSEnds(), SetScope(), x_AdjustCDS3End(), x_AdjustCDS5End(), x_HasProteinChanged(), x_HasProteinChangedAt3End(), x_HasProteinChangedAt5End(), and x_UpdateExonFeatures().
|
private |
Definition at line 104 of file adjust_consensus_splicesite.hpp.
Referenced by AdjustCDS(), AdjustCDSEnds(), x_AdjustCDS3End(), x_AdjustCDS5End(), x_ExtendStartOfExon(), x_ExtendStopOfExon(), x_IntronLength(), x_ShiftExonPairBackward(), x_ShiftExonPairForward(), x_TrimStartOfExon(), x_TrimStopOfExon(), and x_UpdateMixLocations().