A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCShortReadFastaInputSource.html below:

NCBI C++ ToolKit: CShortReadFastaInputSource Class Reference

Search Toolkit Book for CShortReadFastaInputSource

#include <algo/blast/blastinput/blast_fasta_input.hpp>

Definition at line 114 of file blast_fasta_input.hpp.

◆ EInputFormat ◆ CShortReadFastaInputSource() [1/3] ◆ CShortReadFastaInputSource() [2/3]

Definition at line 534 of file blast_fasta_input.cpp.

References ILineReader::AtEOF(), eFasta, eFastc, CTempString::empty(), m_Format, m_LineReader, m_SecondLineReader, m_SeqBuffLen, m_Sequence, NCBI_THROW, and CRef< C, Locker >::Reset().

◆ ~CShortReadFastaInputSource() virtual CShortReadFastaInputSource::~CShortReadFastaInputSource ( ) inlinevirtual

Definition at line 133 of file blast_fasta_input.hpp.

◆ CShortReadFastaInputSource() [3/3] ◆ End() virtual bool CShortReadFastaInputSource::End ( void  ) inlinevirtual ◆ GetNextSequence() int CShortReadFastaInputSource::GetNextSequence ( CBioseq_set &  bioseq_set ) virtual

Get one sequence (or a pair for NGS reads)

Parameters
bioseq_set Read sequences will be appended there [in|out]
Returns
Number of bases read

Implements CBlastInputSourceOMF.

Definition at line 582 of file blast_fasta_input.cpp.

References eFasta, eFastc, eFastq, m_BasesAdded, m_Format, m_SecondLineReader, NCBI_THROW, CRef< C, Locker >::NotEmpty(), x_ReadFastaOrFastq(), x_ReadFastc(), and x_ReadFromTwoFiles().

◆ operator=() ◆ SetParseSeqIds() void CShortReadFastaInputSource::SetParseSeqIds ( bool  val ) inline ◆ x_GetNextSeqId() CRef< CSeq_id > CShortReadFastaInputSource::x_GetNextSeqId ( void  ) private ◆ x_ParseDefline() ◆ x_ReadFastaOneSeq()

Read one sequence from a FASTA file.

Definition at line 835 of file blast_fasta_input.cpp.

References ILineReader::AtEOF(), CTempString::data(), CSeq_inst_Base::eMol_na, CTempString::empty(), CSeq_inst_Base::eRepr_raw, CSeq_id::fParse_AnyLocal, CTempString::length(), m_BasesAdded, m_ParseSeqIds, m_SeqBuffLen, m_Sequence, CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetTitle(), tmp, x_GetNextSeqId(), and x_ParseDefline().

Referenced by x_ReadFastaOrFastq(), and x_ReadFromTwoFiles().

◆ x_ReadFastaOrFastq() void CShortReadFastaInputSource::x_ReadFastaOrFastq ( CBioseq_set &  bioseq_set ) private

Read sequences in FASTA or FASTQ format.

Definition at line 642 of file blast_fasta_input.cpp.

References CUser_object::AddField(), eFasta, eFastq, eFirstSegment, eLastSegment, first(), m_Format, m_IsPaired, m_LineReader, NCBI_THROW, CRef< C, Locker >::NotEmpty(), s_SetSeqdescUser(), CBioseq_set_Base::SetSeq_set(), x_ReadFastaOneSeq(), and x_ReadFastqOneSeq().

Referenced by GetNextSequence().

◆ x_ReadFastc() void CShortReadFastaInputSource::x_ReadFastc ( CBioseq_set &  bioseq_set ) private

Read sequences in FASTC format: defline, new line, a pair of sequences on a single line separated by '><'.

Definition at line 704 of file blast_fasta_input.cpp.

References CUser_object::AddField(), ILineReader::AtEOF(), CTempString::data(), eFirstSegment, eLastSegment, CSeq_inst_Base::eMol_na, CTempString::empty(), CSeq_inst_Base::eRepr_raw, CTempString::find(), first(), CSeq_id::fParse_AnyLocal, ILineReader::GetLineNumber(), CTempString::length(), m_BasesAdded, m_LineReader, m_ParseSeqIds, NCBI_THROW, CTempString::npos, NStr::NumericToString(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeqdesc_Base::SetTitle(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), x_GetNextSeqId(), and x_ParseDefline().

Referenced by GetNextSequence().

◆ x_ReadFastqOneSeq()

Read one sequence from a FASTQ file.

Definition at line 905 of file blast_fasta_input.cpp.

References CUser_object::AddField(), ILineReader::AtEOF(), CTempString::data(), CSeq_inst_Base::eMol_na, CTempString::empty(), CSeq_inst_Base::eRepr_raw, CSeq_id::fParse_AnyLocal, ILineReader::GetLineNumber(), CTempString::length(), m_BasesAdded, m_ParseSeqIds, NCBI_THROW, NStr::NumericToString(), s_SetSeqdescUser(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetTitle(), x_GetNextSeqId(), and x_ParseDefline().

Referenced by x_ReadFastaOrFastq(), and x_ReadFromTwoFiles().

◆ x_ReadFromTwoFiles()

Read sequences from two FASTA or FASTQ files (for paired reads)

Definition at line 1013 of file blast_fasta_input.cpp.

References CUser_object::AddField(), eFasta, eFastc, eFirstSegment, eLastSegment, first(), format, m_LineReader, m_SecondLineReader, NCBI_THROW, CRef< C, Locker >::NotEmpty(), s_SetSeqdescUser(), CBioseq_set_Base::SetSeq_set(), x_ReadFastaOneSeq(), and x_ReadFastqOneSeq().

Referenced by GetNextSequence().

◆ m_BasesAdded TSeqPos CShortReadFastaInputSource::m_BasesAdded private ◆ m_Format ◆ m_Id unsigned int CShortReadFastaInputSource::m_Id private ◆ m_IsPaired bool CShortReadFastaInputSource::m_IsPaired private ◆ m_LineReader ◆ m_ParseSeqIds bool CShortReadFastaInputSource::m_ParseSeqIds private ◆ m_SecondLineReader ◆ m_SeqBuffLen TSeqPos CShortReadFastaInputSource::m_SeqBuffLen private ◆ m_Sequence string CShortReadFastaInputSource::m_Sequence private

The documentation for this class was generated from the following files:

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4