Ymir  .9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ymir::ModelParser Class Referenceabstract
Inheritance diagram for ymir::ModelParser:
ymir::VDJModelParser ymir::VJModelParser

Public Member Functions

 ModelParser (const std::string &model_path, Json::Value config, ModelBehaviour behav)
 
bool parse ()
 
virtual bool parseGeneSegments ()=0
 
bool makeEventProbabilitiesVector ()
 
void swap_genes (unique_ptr< VDJRecombinationGenes > &ptr)
 
void swap_parameters (unique_ptr< ModelParameterVector > &ptr)
 

Protected Member Functions

bool createEventProbabilitiesFromScratch ()
 
virtual void createContainers (vector< AbstractTDContainer * > &containers)=0
 
bool parseEventProbabilitiesFromFiles ()
 
virtual void parseDataContainer (const string &element, AbstractTDContainer *container, vector< AbstractTDContainer * > &containers)=0
 
bool makeModelParameterVector (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)=0
 
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
 

Protected Attributes

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: