protocols::noesy_assign::PeakFileFormat_Base Class Reference

#include <PeakFileFormat.hh>

Inheritance diagram for protocols::noesy_assign::PeakFileFormat_Base:

Public Member Functions
	PeakFileFormat_Base ()
	~PeakFileFormat_Base () override
virtual void	write_peak (std::ostream &, core::Size ct, CrossPeak const &) const =0
virtual void	write_resonances (std::ostream &, CrossPeak const &) const =0
virtual void	write_strength (std::ostream &, CrossPeak const &) const =0
virtual void	write_assignments (std::ostream &, CrossPeak const &, std::string const &first_line_end) const =0
virtual void	read_resonances (std::istream &, CrossPeak &) const =0
virtual void	read_assignments (std::istream &is, std::istream &rest_line, CrossPeak &, std::string &new_peak_line) const =0
virtual void	read_strength (std::istream &, CrossPeak &) const =0
void	set_filename (std::string str)
std::string const &	filename () const
virtual void	set_format_from_peak (CrossPeak const &)=0
virtual void	write_header (std::ostream &)=0
virtual bool	compatible_with_current_format (CrossPeak const &) const =0
virtual CrossPeakOP	read_peak (std::istream &, std::string &next_line) const =0
virtual void	output_diagnosis (std::ostream &) const
virtual void	read_header (std::istream &, std::string &next_line)=0
bool	ignore_assignments () const
void	set_ignore_assignments (bool setting=true)
bool	write_only_highest_VC () const
void	set_write_only_highest_VC (bool setting=true)
core::Real	min_VC_to_write () const
void	set_min_VC_to_write (core::Real setting)
bool	ignore_negative_intensity () const
void	set_ignore_negative_intensity (bool setting=true)
void	set_minimum_peak_intensity (core::Real setting)
core::Real	minimum_peak_intensity () const

Protected Attributes
CrossPeakInfoOP	info1_
CrossPeakInfoOP	info2_
std::string	filename_

Private Attributes
bool	ignore_assignments_
core::Real	min_VC_to_write_
bool	write_only_highest_VC_
bool	ignore_negative_intensity_
core::Real	minimum_peak_intensity_

Constructor & Destructor Documentation

PeakFileFormat_Base()

protocols::noesy_assign::PeakFileFormat_Base::PeakFileFormat_Base ( )

inline

~PeakFileFormat_Base()

protocols::noesy_assign::PeakFileFormat_Base::~PeakFileFormat_Base ( )

inlineoverride

References filename(), info1_, and info2_.

Member Function Documentation

compatible_with_current_format()

virtual bool protocols::noesy_assign::PeakFileFormat_Base::compatible_with_current_format ( CrossPeak const &  ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

filename()

std::string const& protocols::noesy_assign::PeakFileFormat_Base::filename ( ) const

inline

References filename_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::write_header(), and ~PeakFileFormat_Base().

ignore_assignments()

bool protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments ( ) const

inline

References ignore_assignments_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_assignments().

ignore_negative_intensity()

bool protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity ( ) const

inline

References ignore_negative_intensity_.

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream().

min_VC_to_write()

core::Real protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write ( ) const

inline

References min_VC_to_write_.

Referenced by protocols::noesy_assign::PeakFileFormat::write_assignments().

minimum_peak_intensity()

core::Real protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity ( ) const

inline

References minimum_peak_intensity_.

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream().

output_diagnosis()

virtual void protocols::noesy_assign::PeakFileFormat_Base::output_diagnosis ( std::ostream &  ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::PeakFileFormat.

read_assignments()

virtual void protocols::noesy_assign::PeakFileFormat_Base::read_assignments ( std::istream &  is, std::istream &  rest_line, CrossPeak &  , std::string &  new_peak_line  ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

read_header()

virtual void protocols::noesy_assign::PeakFileFormat_Base::read_header ( std::istream &  , std::string &  next_line  )

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

read_peak()

virtual CrossPeakOP protocols::noesy_assign::PeakFileFormat_Base::read_peak ( std::istream &  , std::string &  next_line  ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

read_resonances()

virtual void protocols::noesy_assign::PeakFileFormat_Base::read_resonances ( std::istream &  , CrossPeak &    ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

read_strength()

virtual void protocols::noesy_assign::PeakFileFormat_Base::read_strength ( std::istream &  , CrossPeak &    ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

set_filename()

void protocols::noesy_assign::PeakFileFormat_Base::set_filename ( std::string  str )

inline

References filename_, and protocols::kinmatch::str().

Referenced by protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::NoesyModule::read_input_files(), and protocols::noesy_assign::PeakFileFormat::set_format_from_peak().

set_format_from_peak()

virtual void protocols::noesy_assign::PeakFileFormat_Base::set_format_from_peak ( CrossPeak const &  )

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat_xpk, protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat.

set_ignore_assignments()

void protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments ( bool  setting = true )

inline

References ignore_assignments_.

Referenced by protocols::noesy_assign::NoesyModule::read_input_files().

set_ignore_negative_intensity()

void protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity ( bool  setting = true )

inline

References ignore_negative_intensity_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_header().

set_min_VC_to_write()

void protocols::noesy_assign::PeakFileFormat_Base::set_min_VC_to_write ( core::Real  setting )

inline

References min_VC_to_write_.

set_minimum_peak_intensity()

void protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity ( core::Real  setting )

inline

References minimum_peak_intensity_.

Referenced by protocols::noesy_assign::PeakFileFormat::read_header().

set_write_only_highest_VC()

void protocols::noesy_assign::PeakFileFormat_Base::set_write_only_highest_VC ( bool  setting = true )

inline

References write_only_highest_VC_.

write_assignments()

virtual void protocols::noesy_assign::PeakFileFormat_Base::write_assignments ( std::ostream &  , CrossPeak const &  , std::string const &  first_line_end  ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

write_header()

virtual void protocols::noesy_assign::PeakFileFormat_Base::write_header ( std::ostream &  )

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat_xpk, protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat.

write_only_highest_VC()

bool protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC ( ) const

inline

References write_only_highest_VC_.

Referenced by protocols::noesy_assign::PeakFileFormat::write_assignments().

write_peak()

virtual void protocols::noesy_assign::PeakFileFormat_Base::write_peak ( std::ostream &  , core::Size  ct, CrossPeak const &    ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat_xpk, protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat.

write_resonances()

virtual void protocols::noesy_assign::PeakFileFormat_Base::write_resonances ( std::ostream &  , CrossPeak const &    ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

write_strength()

virtual void protocols::noesy_assign::PeakFileFormat_Base::write_strength ( std::ostream &  , CrossPeak const &    ) const

pure virtual

Implemented in protocols::noesy_assign::PeakFileFormat.

Member Data Documentation

filename_

std::string protocols::noesy_assign::PeakFileFormat_Base::filename_

protected

Referenced by filename(), and set_filename().

ignore_assignments_

bool protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments_

private

Referenced by ignore_assignments(), and set_ignore_assignments().

ignore_negative_intensity_

bool protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity_

private

Referenced by ignore_negative_intensity(), and set_ignore_negative_intensity().

info1_

CrossPeakInfoOP protocols::noesy_assign::PeakFileFormat_Base::info1_

protected

Referenced by protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(), protocols::noesy_assign::PeakFileFormat::output_diagnosis(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::read_peak(), protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and ~PeakFileFormat_Base().

info2_

CrossPeakInfoOP protocols::noesy_assign::PeakFileFormat_Base::info2_

protected

Referenced by protocols::noesy_assign::PeakFileFormat::compatible_with_current_format(), protocols::noesy_assign::PeakFileFormat::output_diagnosis(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::read_peak(), protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and ~PeakFileFormat_Base().

min_VC_to_write_

core::Real protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write_

private

Referenced by min_VC_to_write(), and set_min_VC_to_write().

minimum_peak_intensity_

core::Real protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity_

private

Referenced by minimum_peak_intensity(), and set_minimum_peak_intensity().

write_only_highest_VC_

bool protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC_

private

Referenced by set_write_only_highest_VC(), and write_only_highest_VC().

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

• src/protocols/noesy_assign/PeakFileFormat.hh