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NCBI C++ ToolKit: src/app/agp_validate/AgpFastaComparator.hpp Source File

(

std::list<std::string> & files,

pair<string, TSeqPos>

;

std::list<std::string> & agpFiles );

CTmpSeqVecStorage *temp_dir );

CTmpSeqVecStorage *temp_dir );

(

objects::CSeq_entry_Handle seh,

* in_out_pUniqueBioseqsLoaded,

* in_out_pBioseqsSkipped,

objects::CSeq_id_Handle & idh,

CTmpSeqVecStorage & temp_dir );

void WriteData(EType type, objects::CSeq_entry_Handle seh)

string GetFileName(EType type, objects::CSeq_id_Handle idh)

EFileType x_GuessFileType(const string &filename)

bool x_GetCompAndObjSeqIds(TSeqIdSet &out_compSeqIds, TSeqIdSet &out_objSeqIds, const std::list< std::string > &agpFiles)

void x_CheckForDups(TUniqueSeqs &unique_ids, const string &file_type)

CAgpFastaComparator(void)

EResult Run(const std::list< std::string > &files, const std::string &loadlog, const std::string &agp_as_fasta_file, TDiffsToHide diffsToHide, int diffs_to_find)

void x_Process(const objects::CSeq_entry_Handle seh, TUniqueSeqs &seqs, int *in_out_pUniqueBioseqsLoaded, int *in_out_pBioseqsSkipped, CNcbiOfstream *pDataOutFile)

unique_ptr< CNcbiOfstream > m_pLoadLogFile

void x_ProcessObjects(const list< string > &filenames, TUniqueSeqs &fasta_ids, CTmpSeqVecStorage *temp_dir)

void x_ProcessAgps(const list< string > &filenames, TUniqueSeqs &agp_ids, CTmpSeqVecStorage *temp_dir)

@ fDiffsToHide_ObjfileOnly

pair< string, TSeqPos > TKey

void x_OutputSeqDifferences(int diffs_to_find, const TSeqIdSet &seqIdIntersection, CTmpSeqVecStorage &temp_dir)

void x_PrintDetailsOfLengthIssue(objects::CBioseq_Handle bioseq_h)

bool x_IsLogFileOpen(void)

void x_OutputDifferingSeqIds(const TSeqIdSet &vSeqIdFASTAOnly, const TSeqIdSet &vSeqIdAGPOnly, TDiffsToHide diffs_to_hide, TSeqIdSet &out_seqIdIntersection)

void x_SetBinaryVsText(CNcbiIstream &file_istrm, CFormatGuess::EFormat guess_format)

void x_WriteDataAsFasta(CNcbiOfstream &dataOutFile, const objects::CSeq_id_Handle &idh, const std::string &data)

map< TKey, TSeqIdSet > TUniqueSeqs

set< objects::CSeq_id_Handle > TSeqIdSet

unique_ptr< CNcbiOfstream > m_pAgpAsFastaFile

EFormat

The formats are checked in the same order as declared here.

Include a standard set of the NCBI C++ Toolkit most basic headers.

EFileType

enumerated file type information

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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