NCBI C++ ToolKit
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CGff3FlybaseWriter Class Reference

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#include <objtools/writers/gff3flybase_writer.hpp>

+ Inheritance diagram for CGff3FlybaseWriter:
+ Collaboration diagram for CGff3FlybaseWriter:

Public Member Functions

 CGff3FlybaseWriter (objects::CScope &scope, CNcbiOstream &ostr, bool sortAlignments=false)
 
virtual bool WriteHeader () override
 

Protected Member Functions

virtual bool xWriteAlignDisc (const CSeq_align &, const string &="") override
 
virtual bool xAssignAlignmentSplicedLocation (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override
 
virtual bool xAssignAlignmentSplicedTarget (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override
 
virtual bool xAssignAlignmentSplicedGap (CGffAlignRecord &record, const CSpliced_seg &spliced, const CSpliced_exon &exon) override
 
virtual bool xAssignAlignmentSplicedSeqId (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override
 
virtual bool xAssignAlignmentSplicedScores (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override
 
virtual bool xAssignAlignmentDensegSeqId (CGffAlignRecord &, const CAlnMap &, unsigned int) override
 
virtual bool xAssignAlignmentDensegTarget (CGffAlignRecord &, const CAlnMap &, unsigned int) override
 
virtual bool xAssignAlignmentDensegLocation (CGffAlignRecord &, const CAlnMap &, unsigned int) override
 
virtual bool xAssignAlignmentDensegScores (CGffAlignRecord &, const CAlnMap &, unsigned int) override
 
virtual bool xAssignAlignmentScores (CGffAlignRecord &, const CSeq_align &) override
 
virtual void x_SortAlignments (TAlignCache &alignCache, CScope &scope) override
 
bool xAssignTaxid (CBioseq_Handle, CGffAlignRecord &)
 
bool xAssignDefline (CBioseq_Handle, CGffAlignRecord &)
 
bool xIsNeededScore (const std::string &, const CScore &) const
 

Protected Attributes

map< string, stringmTaxidMap
 
map< string, stringmDeflineMap
 
string mCurrentIdForAttributes
 

Detailed Description

Definition at line 41 of file gff3flybase_writer.hpp.

Constructor & Destructor Documentation

◆ CGff3FlybaseWriter()

CGff3FlybaseWriter::CGff3FlybaseWriter ( objects::CScope &  scope,
CNcbiOstream ostr,
bool  sortAlignments = false 
)
inline

Definition at line 45 of file gff3flybase_writer.hpp.

Member Function Documentation

◆ WriteHeader()

bool CGff3FlybaseWriter::WriteHeader ( void  )
overridevirtual

Definition at line 170 of file gff3flybase_writer.cpp.

Referenced by sRunTest(), and sUpdateCase().

◆ x_SortAlignments()

void CGff3FlybaseWriter::x_SortAlignments ( TAlignCache &  alignCache,
CScope scope 
)
overrideprotectedvirtual

Definition at line 604 of file gff3flybase_writer.cpp.

◆ xAssignAlignmentDensegLocation()

bool CGff3FlybaseWriter::xAssignAlignmentDensegLocation ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int   
)
overrideprotectedvirtual

◆ xAssignAlignmentDensegScores()

bool CGff3FlybaseWriter::xAssignAlignmentDensegScores ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
overrideprotectedvirtual

◆ xAssignAlignmentDensegSeqId()

bool CGff3FlybaseWriter::xAssignAlignmentDensegSeqId ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
overrideprotectedvirtual

◆ xAssignAlignmentDensegTarget()

bool CGff3FlybaseWriter::xAssignAlignmentDensegTarget ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
overrideprotectedvirtual

◆ xAssignAlignmentScores()

bool CGff3FlybaseWriter::xAssignAlignmentScores ( CGffAlignRecord record,
const CSeq_align align 
)
overrideprotectedvirtual

◆ xAssignAlignmentSplicedGap()

bool CGff3FlybaseWriter::xAssignAlignmentSplicedGap ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
overrideprotectedvirtual

◆ xAssignAlignmentSplicedLocation()

bool CGff3FlybaseWriter::xAssignAlignmentSplicedLocation ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
overrideprotectedvirtual

◆ xAssignAlignmentSplicedScores()

bool CGff3FlybaseWriter::xAssignAlignmentSplicedScores ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
overrideprotectedvirtual

◆ xAssignAlignmentSplicedSeqId()

bool CGff3FlybaseWriter::xAssignAlignmentSplicedSeqId ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
overrideprotectedvirtual

◆ xAssignAlignmentSplicedTarget()

bool CGff3FlybaseWriter::xAssignAlignmentSplicedTarget ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
overrideprotectedvirtual

◆ xAssignDefline()

bool CGff3FlybaseWriter::xAssignDefline ( CBioseq_Handle  bsh,
CGffAlignRecord record 
)
protected

◆ xAssignTaxid()

bool CGff3FlybaseWriter::xAssignTaxid ( CBioseq_Handle  bsh,
CGffAlignRecord record 
)
protected

◆ xIsNeededScore()

bool CGff3FlybaseWriter::xIsNeededScore ( const std::string ,
const CScore  
) const
protected

◆ xWriteAlignDisc()

bool CGff3FlybaseWriter::xWriteAlignDisc ( const CSeq_align align,
const string aid = "" 
)
overrideprotectedvirtual

Definition at line 187 of file gff3flybase_writer.cpp.

References CGff3Writer::xWriteAlignDisc().

Member Data Documentation

◆ mCurrentIdForAttributes

string CGff3FlybaseWriter::mCurrentIdForAttributes
protected

Definition at line 126 of file gff3flybase_writer.hpp.

Referenced by xAssignAlignmentScores().

◆ mDeflineMap

map<string, string> CGff3FlybaseWriter::mDeflineMap
protected

Definition at line 125 of file gff3flybase_writer.hpp.

Referenced by xAssignDefline().

◆ mTaxidMap

map<string, string> CGff3FlybaseWriter::mTaxidMap
protected

Definition at line 124 of file gff3flybase_writer.hpp.

Referenced by xAssignTaxid().


The documentation for this class was generated from the following files:
Modified on Fri Sep 20 14:58:15 2024 by modify_doxy.py rev. 669887