NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | Static Private Member Functions | Private Attributes | List of all members
CTabularFormatter Class Reference

Search Toolkit Book for CTabularFormatter

Simple tabular alignment formatter This is a replacement for the BLAST tabular formatter that supports a set of custom gpipe extensions and also provides for better performance. More...

#include <algo/align/util/tabular_fmt.hpp>

+ Collaboration diagram for CTabularFormatter:

Classes

class  IFormatter
 

Public Types

typedef map< string, CIRef< IFormatter > > TFormatterMap
 

Public Member Functions

 CTabularFormatter (CNcbiOstream &ostr, objects::CScoreLookup &scores, const string &unavailable_string="")
 
void SetFormat (const string &format)
 
void SetGencoll (CConstRef< objects::CGC_Assembly > gencoll)
 
void RegisterField (const string &field_name, IFormatter *field_formatter)
 
void WriteHeader ()
 
void Format (const objects::CSeq_align &align)
 
const TFormatterMapAvailableFormatters () const
 
const list< CIRef< IFormatter > > & Formatters () const
 

Static Private Member Functions

static void s_RegisterStandardFields (CTabularFormatter &formatter)
 

Private Attributes

list< CIRef< IFormatter > > m_Formatters
 
objects::CScoreLookup * m_Scores
 
CNcbiOstreamm_Ostr
 
TFormatterMap m_FormatterMap
 
string m_UnavailableString
 

Detailed Description

Simple tabular alignment formatter This is a replacement for the BLAST tabular formatter that supports a set of custom gpipe extensions and also provides for better performance.

Definition at line 56 of file tabular_fmt.hpp.

Member Typedef Documentation

◆ TFormatterMap

Definition at line 76 of file tabular_fmt.hpp.

Constructor & Destructor Documentation

◆ CTabularFormatter()

CTabularFormatter::CTabularFormatter ( CNcbiOstream ostr,
objects::CScoreLookup &  scores,
const string unavailable_string = "" 
)

Definition at line 2787 of file tabular_fmt.cpp.

References s_RegisterStandardFields().

Member Function Documentation

◆ AvailableFormatters()

const TFormatterMap& CTabularFormatter::AvailableFormatters ( ) const
inline

Definition at line 92 of file tabular_fmt.hpp.

◆ Format()

void CTabularFormatter::Format ( const objects::CSeq_align &  align)

Definition at line 3175 of file tabular_fmt.cpp.

References i, m_Formatters, m_Ostr, m_Scores, m_UnavailableString, and NON_CONST_ITERATE.

◆ Formatters()

const list< CIRef<IFormatter> >& CTabularFormatter::Formatters ( ) const
inline

Definition at line 95 of file tabular_fmt.hpp.

◆ RegisterField()

void CTabularFormatter::RegisterField ( const string field_name,
IFormatter field_formatter 
)
inline

Definition at line 84 of file tabular_fmt.hpp.

Referenced by s_RegisterStandardFields(), and SetGencoll().

◆ s_RegisterStandardFields()

void CTabularFormatter::s_RegisterStandardFields ( CTabularFormatter formatter)
staticprivate

◆ SetFormat()

void CTabularFormatter::SetFormat ( const string format)

◆ SetGencoll()

void CTabularFormatter::SetGencoll ( CConstRef< objects::CGC_Assembly >  gencoll)

Definition at line 3067 of file tabular_fmt.cpp.

References m_FormatterMap, NON_CONST_ITERATE, and RegisterField().

◆ WriteHeader()

void CTabularFormatter::WriteHeader ( )

Definition at line 3158 of file tabular_fmt.cpp.

References i, m_Formatters, m_Ostr, and NON_CONST_ITERATE.

Member Data Documentation

◆ m_FormatterMap

TFormatterMap CTabularFormatter::m_FormatterMap
private

Definition at line 102 of file tabular_fmt.hpp.

Referenced by SetFormat(), and SetGencoll().

◆ m_Formatters

list< CIRef<IFormatter> > CTabularFormatter::m_Formatters
private

Definition at line 99 of file tabular_fmt.hpp.

Referenced by Format(), SetFormat(), and WriteHeader().

◆ m_Ostr

CNcbiOstream& CTabularFormatter::m_Ostr
private

Definition at line 101 of file tabular_fmt.hpp.

Referenced by Format(), and WriteHeader().

◆ m_Scores

objects::CScoreLookup* CTabularFormatter::m_Scores
private

Definition at line 100 of file tabular_fmt.hpp.

Referenced by Format(), and SetFormat().

◆ m_UnavailableString

string CTabularFormatter::m_UnavailableString
private

Definition at line 103 of file tabular_fmt.hpp.

Referenced by Format().


The documentation for this class was generated from the following files:
Modified on Mon Feb 26 04:00:46 2024 by modify_doxy.py rev. 669887