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protocols::jd2::archive::Batch Class Reference

a Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files @detail the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive More...

#include <ArchiveManager.hh>

Public Member Functions

 Batch (utility::options::OptionCollection const &options, bool intermediate_structs, bool has_silent_in, core::Size nstruct)
 
 Batch (core::Size id)
 c'stor More...
 
std::string batch () const
 some useful file- and directory names More...
 
std::string dir () const
 
std::string silent_in () const
 
std::string flag_file () const
 
std::string broker_file () const
 
std::string extra_broker_files () const
 
std::string all_broker_files () const
 
std::string silent_out () const
 
std::string alternative_decoys_out () const
 
std::string score_file () const
 
utility::options::OptionCollection const & user_options () const
 
utility::options::OptionCollection & user_options ()
 
bool has_silent_in () const
 Getters. More...
 
bool intermediate_structs () const
 writes out intermediate decoys More...
 
bool has_finished () const
 batch has finished More...
 
bool is_cancelled () const
 batch has finished More...
 
bool allow_reading_cancelled_decoys () const
 batch has finished More...
 
core::Sizenstruct ()
 nstruct ... More...
 
core::Size nstruct () const
 
core::Size id () const
 batch id More...
 
core::Size decoys_returned () const
 how many structures have been processed by archive already More...
 
void set_has_silent_in (bool setting=true)
 Setters. More...
 
void set_intermediate_structs (bool setting=true)
 
void mark_as_finished ()
 
void mark_as_cancelled (bool allow_reading_of_decoys=true)
 
void mark_as_invalid ()
 
bool valid () const
 
void set_id (core::Size id)
 
void set_decoys_returned (core::Size setting)
 
void show (std::ostream &, bool single_line=false) const
 
void write_info_file () const
 read and write BATCH_INFO ( decoys_returned/ finished etc.. ) More...
 
void read_info_file ()
 

Private Member Functions

 Batch ()=delete
 

Private Attributes

core::Size batch_id_
 
core::Size nstruct_ = 0
 
bool intermediate_structs_ = false
 
bool has_silent_in_ = false
 
bool has_finished_ = false
 
bool is_cancelled_ = false
 
bool allow_reading_cancelled_decoys_ = true
 
bool invalid_ = false
 
utility::options::OptionCollectionOP options_
 
core::Size decoys_returned_to_archive_ = 0
 
std::string rosetta_script_file_
 

Friends

std::ostream & operator<< (std::ostream &, Batch const &)
 
std::istream & operator>> (std::istream &, Batch &)
 

Detailed Description

a Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files @detail the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive

Constructor & Destructor Documentation

◆ Batch() [1/3]

protocols::jd2::archive::Batch::Batch ( )
privatedelete

◆ Batch() [2/3]

protocols::jd2::archive::Batch::Batch ( utility::options::OptionCollection const &  options,
bool  intermediate_structs,
bool  has_silent_in,
core::Size  nstruct 
)

◆ Batch() [3/3]

protocols::jd2::archive::Batch::Batch ( core::Size  id)

c'stor

Member Function Documentation

◆ all_broker_files()

std::string protocols::jd2::archive::Batch::all_broker_files ( ) const
inline

◆ allow_reading_cancelled_decoys()

bool protocols::jd2::archive::Batch::allow_reading_cancelled_decoys ( ) const
inline

◆ alternative_decoys_out()

std::string protocols::jd2::archive::Batch::alternative_decoys_out ( ) const

◆ batch()

std::string protocols::jd2::archive::Batch::batch ( ) const

◆ broker_file()

std::string protocols::jd2::archive::Batch::broker_file ( ) const

◆ decoys_returned()

core::Size protocols::jd2::archive::Batch::decoys_returned ( ) const
inline

◆ dir()

std::string protocols::jd2::archive::Batch::dir ( ) const

◆ extra_broker_files()

std::string protocols::jd2::archive::Batch::extra_broker_files ( ) const

Referenced by all_broker_files().

◆ flag_file()

std::string protocols::jd2::archive::Batch::flag_file ( ) const

◆ has_finished()

bool protocols::jd2::archive::Batch::has_finished ( ) const
inline

◆ has_silent_in()

bool protocols::jd2::archive::Batch::has_silent_in ( ) const
inline

Getters.

has input decoys

References has_silent_in_.

Referenced by protocols::jd2::archive::BaseArchiveManager::finalize_batch(), and show().

◆ id()

core::Size protocols::jd2::archive::Batch::id ( ) const
inline

◆ intermediate_structs()

bool protocols::jd2::archive::Batch::intermediate_structs ( ) const
inline

◆ is_cancelled()

bool protocols::jd2::archive::Batch::is_cancelled ( ) const
inline

◆ mark_as_cancelled()

void protocols::jd2::archive::Batch::mark_as_cancelled ( bool  allow_reading_of_decoys = true)
inline

◆ mark_as_finished()

void protocols::jd2::archive::Batch::mark_as_finished ( )
inline

◆ mark_as_invalid()

void protocols::jd2::archive::Batch::mark_as_invalid ( )
inline

References invalid_.

◆ nstruct() [1/2]

core::Size& protocols::jd2::archive::Batch::nstruct ( )
inline

◆ nstruct() [2/2]

core::Size protocols::jd2::archive::Batch::nstruct ( ) const
inline

References nstruct_.

◆ read_info_file()

void protocols::jd2::archive::Batch::read_info_file ( )

◆ score_file()

std::string protocols::jd2::archive::Batch::score_file ( ) const

◆ set_decoys_returned()

void protocols::jd2::archive::Batch::set_decoys_returned ( core::Size  setting)
inline

◆ set_has_silent_in()

void protocols::jd2::archive::Batch::set_has_silent_in ( bool  setting = true)
inline

◆ set_id()

void protocols::jd2::archive::Batch::set_id ( core::Size  id)
inline

◆ set_intermediate_structs()

void protocols::jd2::archive::Batch::set_intermediate_structs ( bool  setting = true)
inline

◆ show()

void protocols::jd2::archive::Batch::show ( std::ostream &  out,
bool  single_line = false 
) const

◆ silent_in()

std::string protocols::jd2::archive::Batch::silent_in ( ) const

◆ silent_out()

std::string protocols::jd2::archive::Batch::silent_out ( ) const

◆ user_options() [1/2]

utility::options::OptionCollection& protocols::jd2::archive::Batch::user_options ( )
inline

References options_.

◆ user_options() [2/2]

utility::options::OptionCollection const& protocols::jd2::archive::Batch::user_options ( ) const
inline

◆ valid()

bool protocols::jd2::archive::Batch::valid ( ) const
inline

References invalid_.

◆ write_info_file()

void protocols::jd2::archive::Batch::write_info_file ( ) const

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<< ( std::ostream &  out,
Batch const &  batch 
)
friend

◆ operator>>

std::istream& operator>> ( std::istream &  in,
Batch batch 
)
friend

Member Data Documentation

◆ allow_reading_cancelled_decoys_

bool protocols::jd2::archive::Batch::allow_reading_cancelled_decoys_ = true
private

◆ batch_id_

core::Size protocols::jd2::archive::Batch::batch_id_
private

Referenced by id(), and set_id().

◆ decoys_returned_to_archive_

core::Size protocols::jd2::archive::Batch::decoys_returned_to_archive_ = 0
private

◆ has_finished_

bool protocols::jd2::archive::Batch::has_finished_ = false
private

Referenced by has_finished(), and mark_as_finished().

◆ has_silent_in_

bool protocols::jd2::archive::Batch::has_silent_in_ = false
private

Referenced by has_silent_in(), and set_has_silent_in().

◆ intermediate_structs_

bool protocols::jd2::archive::Batch::intermediate_structs_ = false
private

◆ invalid_

bool protocols::jd2::archive::Batch::invalid_ = false
private

Referenced by mark_as_invalid(), and valid().

◆ is_cancelled_

bool protocols::jd2::archive::Batch::is_cancelled_ = false
private

Referenced by is_cancelled(), and mark_as_cancelled().

◆ nstruct_

core::Size protocols::jd2::archive::Batch::nstruct_ = 0
private

Referenced by nstruct().

◆ options_

utility::options::OptionCollectionOP protocols::jd2::archive::Batch::options_
private

Referenced by user_options().

◆ rosetta_script_file_

std::string protocols::jd2::archive::Batch::rosetta_script_file_
private

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