Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Generic manager for reading arguments of the program and run the calculations
More...
#include <Morse_theory_based_analyzer_module.hpp>
Static Public Member Functions | |
static boost::program_options::options_description *& | get_options (void) |
Access to the options' description of the module. More... | |
Other Types | |
typedef SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< Graph, Get_weight > | Morse_Smale_Witten_chain_complex_builder |
typedef Morse_Smale_Witten_chain_complex_builder::Morse_function | Morse_function |
typedef Morse_Smale_Witten_chain_complex_builder::Morse_Smale_Witten_chain_complex | Morse_Smale_Witten_chain_complex |
typedef T_Morse_theory_based_analyzer_module< ModuleTraits, Morse_Smale_Witten_chain_complex > | Base |
Other Types | |
typedef SBL::GT::T_Morse_theory_based_analyzer< Morse_Smale_Witten_chain_complex > | Morse_theory_based_analyzer |
typedef Morse_theory_based_analyzer::Point | Point |
typedef Morse_theory_based_analyzer::FT | FT |
typedef Morse_theory_based_analyzer::Persistence_diagram | Persistence_diagram |
typedef std::vector< std::pair< FT, FT > > | Persistence_intervals_container |
typedef Morse_theory_based_analyzer::Disconnectivity_forest | Disconnectivity_forest |
typedef Morse_theory_based_analyzer::Stable_manifold_partition | Stable_manifold_partition |
typedef Morse_theory_based_analyzer::Sublevelsets_connected_components | Sublevelsets_connected_components |
Input Accessors | |
Graph *& | get_weighted_graph (void) |
Morse_function *& | get_Morse_function (void) |
Mandatory Requirements | |
void | run (unsigned verbose, std::ostream &out) override |
Runs the module following the input options. More... | |
bool | is_runnable (void) const override |
Checks that all the input options were set. More... | |
std::string | get_name (void) const override |
Returns the name of the package. More... | |
Optional Requirements | |
void | report (const std::string &prefix) override |
Reports the output and statistics in output files. More... | |
Input Accessors | |
Morse_Smale_Witten_chain_complex *& | get_Morse_Smale_Witten_chain_complex (void) |
static const std::string & | get_Morse_Smale_Witten_chain_complex_filename (void) |
Output Accessors | |
const Morse_theory_based_analyzer & | get_Morse_theory_based_analyzer (void) const |
Morse_theory_based_analyzer & | get_Morse_theory_based_analyzer (void) |
Mandatory Requirements | |
void | statistics (std::ostream &out) override |
Reports high-level statistics on the module. More... | |
Optional Requirements | |
boost::program_options::options_description | add_options (void) override |
Virtual method for adding options to the module. More... | |
bool | check_options (std::string &message) const override |
Checks that the input options' values are coherent. More... | |
std::string | get_output_prefix (void) const override |
Returns a prefix that concatains the input line options used when running the module. More... | |
Modules Management | |
void | set_module_instance_name (const std::string &module_instance_name) |
Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More... | |
const std::string & | get_module_instance_name (void) const |
Get the name of this instance of this module. More... | |
void | set_report_mode (std::ios_base::openmode report_mode) |
Set a report mode, that is open or append modes. More... | |
void | set_report_mode (std::ios_base::openmode &report_mode) |
Set a report mode, that is open or append modes. More... | |
const std::ios_base::openmode | get_report_mode (void) const |
Get the report mode to be used when reporting. More... | |
Optional Requirements | |
void | check_filesystem_directory_exists (const std::string &output_prefix) |
To avoid later crash: check filesystem / existence of directory / directory exists. More... | |
Others | |
template<class Self_ > | |
Self_ * | clone (const Self_ *s) const |
Clones the object using the copy constructor. More... | |
virtual bool | is_logical_module (void) const |
Checks that this module defines a logical operator. More... | |
virtual bool | is_condition_module (void) const |
Checks that this module defines a condition operator. More... | |
virtual bool | operator() (void) |
Only for condition modules, for returning the predicate value. More... | |
virtual bool | is_modules_collection (void) const |
Checks that this module defines a collection of modules. More... | |
Parameters | |
static bool & | get_show_diagrams (void) |
Generic manager for reading arguments of the program and run the calculations
ModuleTraits | Model of a traits class defining the types used in the manager (see T_Conformational_clustering_traits). |
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inlineoverridevirtualinherited |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
To avoid later crash: check filesystem / existence of directory / directory exists.
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inlineoverridevirtualinherited |
Checks that the input options' values are coherent.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Clones the object using the copy constructor.
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inlineinherited |
Get the name of this instance of this module.
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inlineoverridevirtual |
Returns the name of the package.
Reimplemented from Module_base.
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inlinestaticinherited |
Access to the options' description of the module.
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inlineoverridevirtualinherited |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Get the report mode to be used when reporting.
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inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a collection of modules.
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inlineoverridevirtual |
Checks that all the input options were set.
Reimplemented from Module_base.
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
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inlineoverridevirtual |
Reports the output and statistics in output files.
Reimplemented from Module_base.
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inlineoverridevirtual |
Runs the module following the input options.
Implements Module_base.
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inlineinherited |
Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineoverridevirtualinherited |
Reports high-level statistics on the module.
Reimplemented from Module_base.