Search Toolkit Book for CVdbFastaExtractor
Class to extract FASTA (as returned by the blast_sra library) from SRA data. More...
Class to extract FASTA (as returned by the blast_sra library) from SRA data.
Inspired by the CSeqFormatter class
Definition at line 114 of file blast_vdb_cmd.cpp.
◆ CVdbFastaExtractor() ◆ DumpAll() void CVdbFastaExtractor::DumpAll ( )Definition at line 268 of file blast_vdb_cmd.cpp.
References BLAST_SEQSRC_EOF, BLAST_SEQSRC_ERROR, BlastSeqSrcIteratorNewEx(), BlastSeqSrcIteratorNext(), CVDBBlastUtil::CreateBioseqFromOid(), CRef< C, Locker >::Empty(), ERR_POST, exit(), CFastaOstream::fKeepGTSigns, CFastaOstream::fNoExpensiveOps, CVDBBlastUtil::GetSRASeqSrc(), m_FastaOnly, m_LineWidth, m_Out, m_VdbBlastDB, BlastSeqSrcGetSeqArg::oid, CFastaOstream::SetAllFlags(), CFastaOstream::SetWidth(), CFastaOstream::Write(), and Write().
Referenced by CBlastVdbCmdApp::x_ProcessSearchRequest().
◆ Write() [1/2]Definition at line 197 of file blast_vdb_cmd.cpp.
References ERR_POST, CSeq_descr_Base::Get(), CAliasBase< TPrim >::Get(), CBioseq_Base::GetDescr(), CBioseq::GetFirstId(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacna(), CVDBBlastUtil::GetOIDFromVDBSeqId(), CSeqdesc_Base::GetTitle(), i, int, CSeq_data_Base::IsIupacna(), CSeq_descr_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetSeq_data(), l(), m_Out, m_ReplTypes, m_Seperators, m_VdbBlastDB, NCBI_THROW, NStr::NumericToString(), si, and t.
◆ Write() [2/2] void CVdbFastaExtractor::Write ( CRef< CSeq_id > seqid )Definition at line 177 of file blast_vdb_cmd.cpp.
References CSeq_id::AsFastaString(), CVDBBlastUtil::CreateBioseqFromVDBSeqId(), CRef< C, Locker >::Empty(), ERR_POST, CFastaOstream::fKeepGTSigns, CFastaOstream::fNoExpensiveOps, m_FastaOnly, m_LineWidth, m_Out, m_VdbBlastDB, CFastaOstream::SetAllFlags(), CFastaOstream::SetWidth(), and CFastaOstream::Write().
Referenced by DumpAll(), and CBlastVdbCmdApp::x_ProcessSearchRequest().
◆ m_FastaOnly bool CVdbFastaExtractor::m_FastaOnly private ◆ m_FmtSpec ◆ m_LineWidth TSeqPos CVdbFastaExtractor::m_LineWidth private ◆ m_LoadSeq bool CVdbFastaExtractor::m_LoadSeq private ◆ m_Out ◆ m_ReplTypes vector<char> CVdbFastaExtractor::m_ReplTypes private ◆ m_Seperators vector<string> CVdbFastaExtractor::m_Seperators private ◆ m_VdbBlastDBThe documentation for this class was generated from the following file:
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