Search Toolkit Book for CMultiAlnPrinter

Printer for popular multiple alignmnet formats. More...

#include <objtools/align_format/aln_printer.hpp>

Collaboration diagram for CMultiAlnPrinter:

Public Types
enum	EAlignType { eNotSet = 0 , eNucleotide , eProtein }
	Alignment display type for showing nucleotice or protein-related information. More...

enum	EFormat { eFastaPlusGaps = 0 , eClustal , ePhylipSequential , ePhylipInterleaved , eNexus , ePhylip = ePhylipInterleaved }
	Multiple alignmnet text formats. More...

Public Member Functions
	CMultiAlnPrinter (const CSeq_align &seqalign, CScope &scope, EAlignType type=eNotSet)
	Constructor. More...

void	SetWidth (int width)
	Set text width (number of columns) for alignment output. More...

void	SetFormat (EFormat format)
	Set format for printing alignment. More...

void	SetGapChar (unsigned char gap)
	Set gap character. More...

void	SetEndGapChar (unsigned char gap)
	Set end gap character. More...

void	Print (CNcbiOstream &ostr)
	Print alignment. More...

Protected Member Functions
	CMultiAlnPrinter (const CMultiAlnPrinter &p)
	Forbid copy constructor. More...

CMultiAlnPrinter &	operator= (const CMultiAlnPrinter &p)
	Forbid assignment operator. More...

void	x_PrintFastaPlusGaps (CNcbiOstream &ostr)
	Print alignment in fasta + gaps format. More...

void	x_PrintClustal (CNcbiOstream &ostr)
	Print alignment in ClustalW format. More...

void	x_PrintPhylipSequential (CNcbiOstream &ostr)
	Print alignment in Phylip format with sequetial sequences. More...

void	x_PrintPhylipInterleaved (CNcbiOstream &ostr)
	Print alignment in Phylip format with interleaved sequences. More...

void	x_PrintNexus (CNcbiOstream &ostr)
	Print alignment in Nexus format. More...

Protected Attributes
CRef< CAlnVec >	m_AlnVec
	Alignment manager. More...

EAlignType	m_AlignType
	Alignment type. More...

EFormat	m_Format
	Selected alignment format. More...

int	m_Width
	Selected width of the text field. More...

Detailed Description

Printer for popular multiple alignmnet formats.

Definition at line 50 of file aln_printer.hpp.

Member Enumeration Documentation

◆ EAlignType

enum CMultiAlnPrinter::EAlignType

Alignment display type for showing nucleotice or protein-related information.

Enumerator
eNotSet
eNucleotide
eProtein

Definition at line 56 of file aln_printer.hpp.

◆ EFormat

enum CMultiAlnPrinter::EFormat

Multiple alignmnet text formats.

Enumerator
eFastaPlusGaps
eClustal
ePhylipSequential
ePhylipInterleaved
eNexus
ePhylip

Definition at line 63 of file aln_printer.hpp.

Constructor & Destructor Documentation

◆ CMultiAlnPrinter() [1/2]

CMultiAlnPrinter::CMultiAlnPrinter	(	const CSeq_align &	seqalign,
		CScope &	scope,
		CMultiAlnPrinter::EAlignType	type = `eNotSet`
	)

Constructor.

Parameters

seqalign	Alignment
scope	Scope

Definition at line 94 of file aln_printer.cpp.

References CSeq_data_Base::e_Ncbieaa, m_AlnVec, CAlnVec::SetAaCoding(), CAlnVec::SetEndChar(), and CAlnVec::SetGapChar().

◆ CMultiAlnPrinter() [2/2]

CMultiAlnPrinter::CMultiAlnPrinter ( const CMultiAlnPrinter & p )

protected

Forbid copy constructor.

Member Function Documentation

◆ operator=()

CMultiAlnPrinter& CMultiAlnPrinter::operator= ( const CMultiAlnPrinter & p )

protected

Forbid assignment operator.

◆ Print()

void CMultiAlnPrinter::Print ( CNcbiOstream & ostr )

Print alignment.

Parameters

ostr	Output stream

Definition at line 109 of file aln_printer.cpp.

References eClustal, eFastaPlusGaps, eNexus, ePhylipInterleaved, ePhylipSequential, m_Format, x_PrintClustal(), x_PrintFastaPlusGaps(), x_PrintNexus(), x_PrintPhylipInterleaved(), and x_PrintPhylipSequential().

Referenced by CAlnPrinterFixture::PrintAlignment(), and CMultiApplication::Run().

◆ SetEndGapChar()

void CMultiAlnPrinter::SetEndGapChar ( unsigned char gap )

inline

Set end gap character.

Parameters

End	gap character

Definition at line 99 of file aln_printer.hpp.

Referenced by CMultiApplication::Run().

◆ SetFormat()

void CMultiAlnPrinter::SetFormat ( EFormat format )

inline

Set format for printing alignment.

Parameters

format Format

Definition at line 89 of file aln_printer.hpp.

References format.

Referenced by CAlnPrinterFixture::PrintAlignment(), and CMultiApplication::Run().

◆ SetGapChar()

void CMultiAlnPrinter::SetGapChar ( unsigned char gap )

inline

Set gap character.

Parameters

gap	Gap character

Definition at line 94 of file aln_printer.hpp.

Referenced by CMultiApplication::Run().

◆ SetWidth()

void CMultiAlnPrinter::SetWidth ( int width )

inline

Set text width (number of columns) for alignment output.

Parameters

width Width

Definition at line 84 of file aln_printer.hpp.

Referenced by CAlnPrinterFixture::PrintAlignment(), and CMultiApplication::Run().

◆ x_PrintClustal()

void CMultiAlnPrinter::x_PrintClustal ( CNcbiOstream & ostr )

protected

Print alignment in ClustalW format.

Parameters

ostr	Output stream

Definition at line 188 of file aln_printer.cpp.

References CAlnVecPrinter::ClustalStyle(), m_AlnVec, and m_Width.

Referenced by Print().

◆ x_PrintFastaPlusGaps()

void CMultiAlnPrinter::x_PrintFastaPlusGaps ( CNcbiOstream & ostr )

protected

Print alignment in fasta + gaps format.

Parameters

ostr	Output stream

Definition at line 135 of file aln_printer.cpp.

References CSeq_id::AsFastaString(), CSeq_id::eContent, CScope::eGetBioseq_All, CScope::GetBioseqHandle(), CBioseq_Handle::GetId(), CSeq_id_Base::GetLocal(), CAlnMap::GetNumRows(), CAlnVec::GetScope(), CAlnMap::GetSeqId(), CBioseq_Handle::GetSeqId(), CAlnVec::GetWholeAlnSeqString(), i, int, CObject_id_Base::IsId(), CSeq_id_Base::IsLocal(), ITERATE, label, m_AlnVec, m_Width, NcbiEndl, and s_GetTitle().

Referenced by Print().

◆ x_PrintNexus()

void CMultiAlnPrinter::x_PrintNexus ( CNcbiOstream & ostr )

protected

Print alignment in Nexus format.

Parameters

ostr	Output stream

Definition at line 293 of file aln_printer.cpp.

References eNotSet, eNucleotide, CAlnVec::GetAlnSeqString(), CAlnMap::GetAlnStop(), CAlnVec::GetGapChar(), CAlnMap::GetNumRows(), CAlnMap::GetSeqId(), CSeq_id::GetSeqIdString(), i, m_AlignType, m_AlnVec, m_Width, min(), NCBI_THROW, and NcbiEndl.

Referenced by Print().

◆ x_PrintPhylipInterleaved()

void CMultiAlnPrinter::x_PrintPhylipInterleaved ( CNcbiOstream & ostr )

protected

Print alignment in Phylip format with interleaved sequences.

Parameters

ostr	Output stream

Definition at line 243 of file aln_printer.cpp.

References CScope::eGetBioseq_All, CAlnVec::GetAlnSeqString(), CAlnMap::GetAlnStop(), CScope::GetBioseqHandle(), CAlnMap::GetNumRows(), CAlnVec::GetScope(), CAlnMap::GetSeqId(), i, m_AlnVec, m_Width, min(), NcbiEndl, s_GetLabel(), and s_ReplaceNonAlphaNum().

Referenced by Print().

◆ x_PrintPhylipSequential()

void CMultiAlnPrinter::x_PrintPhylipSequential ( CNcbiOstream & ostr )

protected

Print alignment in Phylip format with sequetial sequences.

Parameters

ostr	Output stream

Definition at line 195 of file aln_printer.cpp.

References CScope::eGetBioseq_All, CScope::GetBioseqHandle(), CAlnMap::GetNumRows(), CAlnVec::GetScope(), CAlnMap::GetSeqId(), CAlnVec::GetWholeAlnSeqString(), i, m_AlnVec, m_Width, NcbiEndl, s_GetLabel(), and s_ReplaceNonAlphaNum().

Referenced by Print().

Member Data Documentation

◆ m_AlignType

EAlignType CMultiAlnPrinter::m_AlignType

protected

Alignment type.

Definition at line 140 of file aln_printer.hpp.

Referenced by x_PrintNexus().

◆ m_AlnVec

CRef<CAlnVec> CMultiAlnPrinter::m_AlnVec

protected

Alignment manager.

Definition at line 137 of file aln_printer.hpp.

Referenced by CMultiAlnPrinter(), x_PrintClustal(), x_PrintFastaPlusGaps(), x_PrintNexus(), x_PrintPhylipInterleaved(), and x_PrintPhylipSequential().

◆ m_Format

EFormat CMultiAlnPrinter::m_Format

protected

Selected alignment format.

Definition at line 143 of file aln_printer.hpp.

Referenced by Print().

◆ m_Width

int CMultiAlnPrinter::m_Width

protected

Selected width of the text field.

Definition at line 146 of file aln_printer.hpp.

Referenced by x_PrintClustal(), x_PrintFastaPlusGaps(), x_PrintNexus(), x_PrintPhylipInterleaved(), and x_PrintPhylipSequential().

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

include/objtools/align_format/aln_printer.hpp
src/objtools/align_format/aln_printer.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ EAlignType

◆ EFormat

Constructor & Destructor Documentation

◆ CMultiAlnPrinter() [1/2]

◆ CMultiAlnPrinter() [2/2]

Member Function Documentation

◆ operator=()

◆ Print()

◆ SetEndGapChar()

◆ SetFormat()

◆ SetGapChar()

◆ SetWidth()

◆ x_PrintClustal()

◆ x_PrintFastaPlusGaps()

◆ x_PrintNexus()

◆ x_PrintPhylipInterleaved()

◆ x_PrintPhylipSequential()

Member Data Documentation

◆ m_AlignType

◆ m_AlnVec

◆ m_Format

◆ m_Width