bpp-seq3  3.0.0
Public Member Functions | Protected Attributes | List of all members
bpp::BppSequenceApplication Class Reference

#include <Bpp/Seq/App/BppSequenceApplication.h>

+ Inheritance diagram for bpp::BppSequenceApplication:
+ Collaboration diagram for bpp::BppSequenceApplication:

Public Member Functions

 BppSequenceApplication (int argc, char *argv[], const std::string &name)
 
virtual std::shared_ptr< Alphabet > getAlphabet (const string &suffix="", bool suffixIsOptional=true, bool allowGeneric=false) const
 
virtual std::shared_ptr< GeneticCode > getGeneticCode (std::shared_ptr< const Alphabet > &alphabet, const string &suffix="", bool suffixIsOptional=true) const
 
virtual std::map< size_t, std::unique_ptr< AlignmentDataInterface > > getAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const
 
virtual std::map< size_t, std::unique_ptr< const AlignmentDataInterface > > getConstAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const
 
virtual void startTimer ()
 
virtual void done ()
 
virtual const std::map< std::string, std::string > & getParams () const
 
virtual std::map< std::string, std::string > & getParams ()
 
virtual const std::string & getParam (const std::string &name) const
 
virtual std::string & getParam (const std::string &name)
 
virtual bool isVerbose () const
 
virtual int getWarningLevel () const
 
virtual void help (const std::string &program) const
 

Protected Attributes

std::string appName_
 
std::map< std::string, std::string > params_
 
bool timerStarted_
 
bool verbose_
 
int warn_
 

Detailed Description

Definition at line 27 of file BppSequenceApplication.h.

Constructor & Destructor Documentation

◆ BppSequenceApplication()

bpp::BppSequenceApplication::BppSequenceApplication ( int  argc,
char *  argv[],
const std::string &  name 
)
inline

Definition at line 31 of file BppSequenceApplication.h.

Member Function Documentation

◆ getAlignmentsMap()

map< size_t, unique_ptr< AlignmentDataInterface > > BppSequenceApplication::getAlignmentsMap ( std::shared_ptr< const Alphabet > &  alphabet,
bool  changeGapsToUnknownCharacters = true,
bool  optionalData = false,
const std::string &  prefix = "input.",
const std::string &  suffix = "",
bool  suffixIsOptional = true 
) const
virtual

Definition at line 55 of file BppSequenceApplication.cpp.

◆ getAlphabet()

shared_ptr< Alphabet > BppSequenceApplication::getAlphabet ( const string &  suffix = "",
bool  suffixIsOptional = true,
bool  allowGeneric = false 
) const
virtual

Definition at line 20 of file BppSequenceApplication.cpp.

◆ getConstAlignmentsMap()

map< size_t, unique_ptr< const AlignmentDataInterface > > BppSequenceApplication::getConstAlignmentsMap ( std::shared_ptr< const Alphabet > &  alphabet,
bool  changeGapsToUnknownCharacters = true,
bool  optionalData = false,
const std::string &  prefix = "input.",
const std::string &  suffix = "",
bool  suffixIsOptional = true 
) const
virtual

Definition at line 124 of file BppSequenceApplication.cpp.

◆ getGeneticCode()

shared_ptr< GeneticCode > BppSequenceApplication::getGeneticCode ( std::shared_ptr< const Alphabet > &  alphabet,
const string &  suffix = "",
bool  suffixIsOptional = true 
) const
virtual

Definition at line 28 of file BppSequenceApplication.cpp.

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