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CReportTrim Class Reference

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#include <gui/objutils/report_trim.hpp>

+ Inheritance diagram for CReportTrim:
+ Collaboration diagram for CReportTrim:

Public Member Functions

 CReportTrim (EMeaningOfAmbig eMeaningOfAmbig, TFlags fFlags=0, const TTrimRuleVec &vecTrimRules=GetDefaultTrimRules(), TSignedSeqPos uMinSeqLen=50)
 
virtual ~CReportTrim ()
 
virtual EResult Trim (objects::CBioseq_Handle &bioseq_handle, TSignedSeqPos &left, TSignedSeqPos &right)
 
void AdjustAndTranslate (objects::CBioseq_Handle bsh, int length, int from, int to, CRef< CCmdComposite > command, objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)
 
void TrimAlignments (CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to)
 
void TrimSeqGraphs (CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to, int length)
 

Private Member Functions

void x_AdjustCdregionFrame (CRef< objects::CSeq_feat > feat, int diff)
 
void x_RetranslateCDS (objects::CScope &scope, CRef< CCmdComposite > command, CRef< objects::CSeq_feat > cds, const objects::CSeq_feat &old_cds)
 
bool x_AdjustLocation (objects::CSeq_loc &loc, int length, int from, int to, int &diff)
 
bool x_AdjustLocation (objects::CSeq_loc &loc, int length, int from, int to)
 
void x_AdjustInt (int &begin, int &end, int from, int to, int length, int &diff, objects::ENa_strand strand)
 
void x_UpdateVariation (objects::CVariation_ref &var, int length, int from, int to)
 
bool x_IsProtLocation (const objects::CSeq_loc &loc, objects::CBioseq_Handle bsh, objects::CScope &scope)
 
void x_AdjustDensegAlignment (CRef< objects::CSeq_align > align, objects::CDense_seg::TDim row, TSeqPos cut_from, TSeqPos cut_to)
 
void x_CutDensegSegment (CRef< objects::CSeq_align > align, objects::CDense_seg::TDim row, TSeqPos pos)
 
bool x_FindSegment (const objects::CDense_seg &denseg, objects::CDense_seg::TDim row, TSeqPos pos, objects::CDense_seg::TNumseg &seg, TSeqPos &seg_start) const
 
bool x_UpdateSeqGraphLoc (CRef< objects::CSeq_graph > new_graph, TSeqPos from, TSeqPos to, int length, const CRef< objects::CSeq_id > seqid)
 
bool x_TrimSeqGraphData (CRef< objects::CSeq_graph > new_graph, const objects::CMappedGraph &orig_graph, TSeqPos trim_start, TSeqPos trim_stop, int length, const CRef< objects::CSeq_id > seqid)
 
bool x_IsThereGapNotAtTheEnd (objects::CBioseq_Handle bsh, TSignedSeqPos from, TSignedSeqPos to, int length)
 

Detailed Description

Definition at line 44 of file report_trim.hpp.

Constructor & Destructor Documentation

◆ CReportTrim()

CReportTrim::CReportTrim ( EMeaningOfAmbig  eMeaningOfAmbig,
TFlags  fFlags = 0,
const TTrimRuleVec &  vecTrimRules = GetDefaultTrimRules(),
TSignedSeqPos  uMinSeqLen = 50 
)
inline

Definition at line 47 of file report_trim.hpp.

◆ ~CReportTrim()

virtual CReportTrim::~CReportTrim ( )
inlinevirtual

Definition at line 49 of file report_trim.hpp.

Member Function Documentation

◆ AdjustAndTranslate()

void CReportTrim::AdjustAndTranslate ( objects::CBioseq_Handle  bsh,
int  length,
int  from,
int  to,
CRef< CCmdComposite command,
objects::CScope &  scope,
map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &  product_to_cds 
)

◆ Trim()

CSequenceAmbigTrimmer::EResult CReportTrim::Trim ( objects::CBioseq_Handle &  bioseq_handle,
TSignedSeqPos left,
TSignedSeqPos right 
)
virtual

◆ TrimAlignments()

void CReportTrim::TrimAlignments ( CRef< CCmdComposite command,
objects::CBioseq_Handle  bsh,
const objects::CBioseq::TId &  seqids,
TSeqPos  from,
TSeqPos  to 
)

◆ TrimSeqGraphs()

void CReportTrim::TrimSeqGraphs ( CRef< CCmdComposite command,
objects::CBioseq_Handle  bsh,
const objects::CBioseq::TId &  seqids,
TSeqPos  from,
TSeqPos  to,
int  length 
)

◆ x_AdjustCdregionFrame()

void CReportTrim::x_AdjustCdregionFrame ( CRef< objects::CSeq_feat >  feat,
int  diff 
)
private

◆ x_AdjustDensegAlignment()

void CReportTrim::x_AdjustDensegAlignment ( CRef< objects::CSeq_align >  align,
objects::CDense_seg::TDim  row,
TSeqPos  cut_from,
TSeqPos  cut_to 
)
private

◆ x_AdjustInt()

void CReportTrim::x_AdjustInt ( int begin,
int end,
int  from,
int  to,
int  length,
int diff,
objects::ENa_strand  strand 
)
private

Definition at line 200 of file report_trim.cpp.

References eNa_strand_minus.

◆ x_AdjustLocation() [1/2]

bool CReportTrim::x_AdjustLocation ( objects::CSeq_loc &  loc,
int  length,
int  from,
int  to 
)
private

◆ x_AdjustLocation() [2/2]

bool CReportTrim::x_AdjustLocation ( objects::CSeq_loc &  loc,
int  length,
int  from,
int  to,
int diff 
)
private

◆ x_CutDensegSegment()

void CReportTrim::x_CutDensegSegment ( CRef< objects::CSeq_align >  align,
objects::CDense_seg::TDim  row,
TSeqPos  pos 
)
private

◆ x_FindSegment()

bool CReportTrim::x_FindSegment ( const objects::CDense_seg &  denseg,
objects::CDense_seg::TDim  row,
TSeqPos  pos,
objects::CDense_seg::TNumseg &  seg,
TSeqPos seg_start 
) const
private

◆ x_IsProtLocation()

bool CReportTrim::x_IsProtLocation ( const objects::CSeq_loc &  loc,
objects::CBioseq_Handle  bsh,
objects::CScope &  scope 
)
private

Definition at line 191 of file report_trim.cpp.

References CScope::GetBioseqHandle(), and CBioseq_Handle::IsAa().

◆ x_IsThereGapNotAtTheEnd()

bool CReportTrim::x_IsThereGapNotAtTheEnd ( objects::CBioseq_Handle  bsh,
TSignedSeqPos  from,
TSignedSeqPos  to,
int  length 
)
private

◆ x_RetranslateCDS()

void CReportTrim::x_RetranslateCDS ( objects::CScope &  scope,
CRef< CCmdComposite command,
CRef< objects::CSeq_feat >  cds,
const objects::CSeq_feat &  old_cds 
)
private

◆ x_TrimSeqGraphData()

bool CReportTrim::x_TrimSeqGraphData ( CRef< objects::CSeq_graph >  new_graph,
const objects::CMappedGraph &  orig_graph,
TSeqPos  trim_start,
TSeqPos  trim_stop,
int  length,
const CRef< objects::CSeq_id >  seqid 
)
private

◆ x_UpdateSeqGraphLoc()

bool CReportTrim::x_UpdateSeqGraphLoc ( CRef< objects::CSeq_graph >  new_graph,
TSeqPos  from,
TSeqPos  to,
int  length,
const CRef< objects::CSeq_id >  seqid 
)
private

◆ x_UpdateVariation()

void CReportTrim::x_UpdateVariation ( objects::CVariation_ref &  var,
int  length,
int  from,
int  to 
)
private

The documentation for this class was generated from the following files:
Modified on Tue Jun 25 13:33:17 2024 by modify_doxy.py rev. 669887