Inheritance diagram for ymir::VDJModelParser:

Public Member Functions
	VDJModelParser (const std::string &model_path, Json::Value config, ModelBehaviour behav)

bool	parseGeneSegments ()

Public Member Functions inherited from ymir::ModelParser
	ModelParser (const std::string &model_path, Json::Value config, ModelBehaviour behav)

bool	parse ()

bool	makeEventProbabilitiesVector ()

void	swap_genes (unique_ptr< VDJRecombinationGenes > &ptr)

void	swap_parameters (unique_ptr< ModelParameterVector > &ptr)

Protected Member Functions
virtual void	createContainers (vector< AbstractTDContainer * > &containers)

virtual void	parseDataContainer (const string &element, AbstractTDContainer container, vector< AbstractTDContainer > &containers)

virtual bool	makeModelParameterVector (vector< AbstractTDContainer * > &containers, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace, vector< seq_len_t > &min_D_len_vec)

Protected Member Functions inherited from ymir::ModelParser
bool	createEventProbabilitiesFromScratch ()

bool	parseEventProbabilitiesFromFiles ()

bool	makeModelParameterVector (vector< AbstractTDContainer * > &containers)

bool	findGenes (const vector< string > &names, const GeneSegmentAlphabet &gsa, string &err_message) const

vector< seg_index_t >	arrangeNames (const vector< string > &names, const GeneSegmentAlphabet &gsa) const

void	addGenes (AbstractTDContainer *container, const GeneSegmentAlphabet &gsa, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace) const

void	addGenes (AbstractTDContainer *container, const GeneSegmentAlphabet &gsa_row, const GeneSegmentAlphabet &gsa_column, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace, seg_index_t prev_class_size) const

void	addDels (AbstractTDContainer *container, const GeneSegmentAlphabet &gsa, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace, seg_index_t prev_class_size) const

void	addDels2D (AbstractTDContainer *container, const GeneSegmentAlphabet &gsa, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace, seg_index_t prev_class_size) const

void	addIns (AbstractTDContainer *container, vector< prob_t > &event_probs, vector< event_ind_t > &event_lengths, vector< event_ind_t > &event_classes, vector< seq_len_t > &event_col_num, vector< prob_t > &laplace, seg_index_t prev_class_size, seq_len_t max_ins_len=0) const

Additional Inherited Members
Protected Attributes inherited from ymir::ModelParser
Json::Value	_config

std::string	_model_path

ModelBehaviour	_behaviour

unique_ptr< VDJRecombinationGenes >	_genes

unique_ptr< ModelParameterVector >	_param_vec

seq_len_t	_min_D_len

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

Ymir/src/model_parser.h

Public Member Functions

Protected Member Functions

Additional Inherited Members