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CAdjustForConsensusSpliceSite Class Reference

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#include <gui/objutils/adjust_consensus_splicesite.hpp>

+ Collaboration diagram for CAdjustForConsensusSpliceSite:

Public Member Functions

 CAdjustForConsensusSpliceSite (objects::CScope &scope)
 
void SetScope (objects::CScope &scope)
 
CRef< CCmdCompositeGetCommand (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< CCmdCompositeGetCommandToAdjustCDSEnds (const objects::CSeq_feat &cds)
 
bool AdjustCDS (objects::CSeq_feat &cds)
 
bool AdjustmRNAToMatchCDS (const objects::CSeq_feat &edit_cds, objects::CSeq_feat &mrna)
 
CRef< CCmdCompositeAdjustmRNAandExonFeatures (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< CCmdCompositeAdjustmRNAandExonEnds (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< TSeqRangeTLocs
 

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
 

Detailed Description

Definition at line 50 of file adjust_consensus_splicesite.hpp.

Member Typedef Documentation

◆ TLocs

Definition at line 76 of file adjust_consensus_splicesite.hpp.

Constructor & Destructor Documentation

◆ CAdjustForConsensusSpliceSite()

CAdjustForConsensusSpliceSite::CAdjustForConsensusSpliceSite ( objects::CScope &  scope)
inline

Definition at line 53 of file adjust_consensus_splicesite.hpp.

Member Function Documentation

◆ AdjustCDS()

bool CAdjustForConsensusSpliceSite::AdjustCDS ( objects::CSeq_feat &  cds)

◆ AdjustCDSEnds()

bool CAdjustForConsensusSpliceSite::AdjustCDSEnds ( objects::CSeq_feat &  cds)

◆ AdjustmRNAandExonEnds()

CRef< CCmdComposite > CAdjustForConsensusSpliceSite::AdjustmRNAandExonEnds ( const objects::CSeq_feat &  new_cds,
const objects::CSeq_feat &  orig_cds 
)

◆ AdjustmRNAandExonFeatures()

CRef< CCmdComposite > CAdjustForConsensusSpliceSite::AdjustmRNAandExonFeatures ( const objects::CSeq_feat &  new_cds,
const objects::CSeq_feat &  orig_cds 
)

◆ AdjustmRNAToMatchCDS()

bool CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDS ( const objects::CSeq_feat &  edit_cds,
objects::CSeq_feat &  mrna 
)

◆ AdjustmRNAToMatchCDSEnds()

bool CAdjustForConsensusSpliceSite::AdjustmRNAToMatchCDSEnds ( const objects::CSeq_feat &  edit_cds,
objects::CSeq_feat &  mrna 
)

◆ GetCommand()

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.

Parameters
cdsCoding region feature
scopeThe 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().

◆ GetCommandToAdjustCDSEnds()

CRef< CCmdComposite > CAdjustForConsensusSpliceSite::GetCommandToAdjustCDSEnds ( const objects::CSeq_feat &  cds)

◆ s_IsAdjustedSpliceSitePairOK()

bool CAdjustForConsensusSpliceSite::s_IsAdjustedSpliceSitePairOK ( const string seqdata,
TSeqPos  intron_start,
TSeqPos  intron_stop 
)
static

Definition at line 440 of file adjust_consensus_splicesite.cpp.

References Error(), CException::GetMsg(), LOG_POST, and CException::what().

Referenced by AdjustCDS().

◆ s_IsBioseqGood_AdjustEnds()

bool CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds ( const objects::CBioseq_Handle &  bsh)
static

◆ s_IsBioseqGood_Relaxed()

bool CAdjustForConsensusSpliceSite::s_IsBioseqGood_Relaxed ( const objects::CBioseq_Handle &  bsh)
static

◆ s_IsBioseqGood_Strict()

bool CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict ( const objects::CBioseq_Handle &  bsh)
static

◆ SetScope()

void CAdjustForConsensusSpliceSite::SetScope ( objects::CScope &  scope)
inline

Definition at line 56 of file adjust_consensus_splicesite.hpp.

References m_Scope, and CRef< C, Locker >::Reset().

◆ x_AdjustCDS3End()

bool CAdjustForConsensusSpliceSite::x_AdjustCDS3End ( objects::CSeq_feat &  cds,
const string orig_prot_seq 
)
private

◆ x_AdjustCDS5End()

bool CAdjustForConsensusSpliceSite::x_AdjustCDS5End ( objects::CSeq_feat &  cds,
const string orig_prot_seq 
)
private

◆ x_AlsoAdjustmRNA()

bool CAdjustForConsensusSpliceSite::x_AlsoAdjustmRNA ( objects::CSeq_feat &  mrna,
const objects::CSeq_loc &  loc 
)
private

◆ x_CreateNewLocation()

CRef< objects::CSeq_loc > CAdjustForConsensusSpliceSite::x_CreateNewLocation ( const objects::CSeq_feat &  cds)
private

◆ x_ExtendStartOfExon()

bool CAdjustForConsensusSpliceSite::x_ExtendStartOfExon ( TSeqRange range,
TSeqPos  offset,
const objects::CSeq_loc &  loc,
objects::CBioseq_Handle  bsh 
)
private

◆ x_ExtendStopOfExon()

bool CAdjustForConsensusSpliceSite::x_ExtendStopOfExon ( TSeqRange range,
TSeqPos  offset,
const objects::CSeq_loc &  loc,
objects::CBioseq_Handle  bsh 
)
private

◆ x_HasProteinChanged()

bool CAdjustForConsensusSpliceSite::x_HasProteinChanged ( const objects::CSeq_feat &  cds,
const string orig_prot_seq 
)
private

◆ x_HasProteinChangedAt3End()

bool CAdjustForConsensusSpliceSite::x_HasProteinChangedAt3End ( objects::CSeq_feat &  cds,
const string orig_prot_seq 
)
private

◆ x_HasProteinChangedAt5End()

bool CAdjustForConsensusSpliceSite::x_HasProteinChangedAt5End ( objects::CSeq_feat &  cds,
const string orig_prot_seq 
)
private

◆ x_InitRanges()

void CAdjustForConsensusSpliceSite::x_InitRanges ( const objects::CSeq_feat &  cds)
private

◆ x_IntronLength()

TSeqPos CAdjustForConsensusSpliceSite::x_IntronLength ( const TSeqRange rng_prev,
const TSeqRange rng 
)
private

◆ x_ShiftExonPairBackward()

void CAdjustForConsensusSpliceSite::x_ShiftExonPairBackward ( TSeqRange range_prev,
TSeqRange range,
TSeqPos  offset 
)
private

◆ x_ShiftExonPairForward()

void CAdjustForConsensusSpliceSite::x_ShiftExonPairForward ( TSeqRange range_prev,
TSeqRange range,
TSeqPos  offset 
)
private

◆ x_TrimStartOfExon()

void CAdjustForConsensusSpliceSite::x_TrimStartOfExon ( TSeqRange range,
TSeqPos  offset 
)
private

◆ x_TrimStopOfExon()

void CAdjustForConsensusSpliceSite::x_TrimStopOfExon ( TSeqRange range,
TSeqPos  offset 
)
private

◆ x_UpdateExonFeatures()

void CAdjustForConsensusSpliceSite::x_UpdateExonFeatures ( CCmdComposite cmd,
const objects::CSeq_feat &  orig_cds,
const objects::CSeq_feat &  new_cds 
)
private

◆ x_UpdateInterval()

void CAdjustForConsensusSpliceSite::x_UpdateInterval ( objects::CSeq_interval &  interval)
private

◆ x_UpdateIntervals()

void CAdjustForConsensusSpliceSite::x_UpdateIntervals ( objects::CSeq_loc::TIntervals &  locs)
private

◆ x_UpdateLocation()

CRef< CSeq_loc > CAdjustForConsensusSpliceSite::x_UpdateLocation ( const objects::CSeq_feat &  cds)
private

◆ x_UpdateMixLocations()

void CAdjustForConsensusSpliceSite::x_UpdateMixLocations ( const objects::CSeq_loc &  orig_loc,
objects::CSeq_loc::TLocations &  locs 
)
private

Member Data Documentation

◆ m_New_Ranges

TLocs CAdjustForConsensusSpliceSite::m_New_Ranges
private

◆ m_Orig_Ranges

TLocs CAdjustForConsensusSpliceSite::m_Orig_Ranges
private

◆ m_ProtChanged

bool CAdjustForConsensusSpliceSite::m_ProtChanged { false }
private

◆ m_Scope

CRef<objects::CScope> CAdjustForConsensusSpliceSite::m_Scope
private

◆ m_Strand

objects::ENa_strand CAdjustForConsensusSpliceSite::m_Strand
private

The documentation for this class was generated from the following files:
Modified on Mon Mar 04 05:13:52 2024 by modify_doxy.py rev. 669887