data/simulator/alisimulatorinvar.cpp

//
//  alisimulatorinvar.cpp
//  model
//
//  Created by Nhan Ly-Trong on 23/03/2021.
//

#include "alisimulatorinvar.h"

AliSimulatorInvar::AliSimulatorInvar(Params *params, double invar_prop) :
AliSimulator(params) {
    invariant_proportion = invar_prop;
}

AliSimulatorInvar::AliSimulatorInvar(AliSimulator *alisimulator, double invar_prop){
    tree = alisimulator->tree;
    params = alisimulator->params;
    num_sites_per_state = alisimulator->num_sites_per_state;
    length_ratio = alisimulator->length_ratio;
    inverse_length_ratio = alisimulator->inverse_length_ratio;
    expected_num_sites = alisimulator->expected_num_sites;
    partition_rate = alisimulator->partition_rate;
    invariant_proportion = invar_prop;
    max_length_taxa_name = alisimulator->max_length_taxa_name;
    fundi_items = alisimulator->fundi_items;
    STATE_UNKNOWN = alisimulator->STATE_UNKNOWN;
    max_num_states = alisimulator->max_num_states;
    seq_length_indels = alisimulator->seq_length_indels;
    map_seqname_node = alisimulator->map_seqname_node;
    latest_insertion = alisimulator->latest_insertion;
    first_insertion = alisimulator->first_insertion;
    starting_pos = alisimulator->starting_pos;
    output_line_length = alisimulator->output_line_length;
    num_threads = alisimulator->num_threads;
    force_output_PHYLIP = alisimulator->force_output_PHYLIP;
}

/**
    simulate a sequence for a node from a specific branch after all variables has been initializing
*/
void AliSimulatorInvar::simulateASequenceFromBranchAfterInitVariables(int segment_start, ModelSubst *model, double *trans_matrix, vector<short int> &dad_seq_chunk, vector<short int> &node_seq_chunk, Node *node, NeighborVec::iterator it, int* rstream, string lengths)
{
    // rescale ratio due to invariant sites
    double scale = 1.0 / (1 - invariant_proportion);
    
    // compute the transition probability matrix
    model->computeTransMatrix(partition_rate * params->alisim_branch_scale * (*it)->length * scale, trans_matrix);
    
    // convert the probability matrix into an accumulated probability matrix
    convertProMatrixIntoAccumulatedProMatrix(trans_matrix, max_num_states, max_num_states);
    
    // estimate the sequence for the current neighbor
    for (int i = 0; i < node_seq_chunk.size(); i++)
    {
        
        // if this site is invariant or the parent's state is a gap -> preserve the dad's state
        if (site_specific_rates[segment_start + i] == 0 || dad_seq_chunk[i] == STATE_UNKNOWN)
            node_seq_chunk[i] = dad_seq_chunk[i];
        else // otherwise, randomly select the state, considering it's dad states, and the transition_probability_matrix
        {
            // NHANLT: potential improvement
            // cache parent_state * max_num_states
            int parent_state = dad_seq_chunk[i];
            node_seq_chunk[i] = getRandomItemWithAccumulatedProbMatrixMaxProbFirst(trans_matrix, parent_state * max_num_states, max_num_states, parent_state, rstream);
        }
    }
}

/**
    initialize variables (e.g., site-specific rate)
*/
void AliSimulatorInvar::initVariablesRateHeterogeneity(int sequence_length, default_random_engine& generator, bool regenerate_root_sequence)
{
    initSiteSpecificRates(site_specific_rates, sequence_length);
}

/**
  initialize site_specific_rate
*/
void AliSimulatorInvar::initSiteSpecificRates(vector<double> &site_specific_rates, int sequence_length)
{
    site_specific_rates.resize(sequence_length, 1);
    for (int i = 0; i < sequence_length; i++)
    {
        // if this site is invariant -> preserve the dad's state
        if (random_double() <= invariant_proportion)
            site_specific_rates[i] = 0;
        else
            site_specific_rates[i] = 1;
    }
}

/**
*  insert a new sequence into the current sequence
*
*/
void AliSimulatorInvar::insertNewSequenceForInsertionEvent(vector<short int> &indel_sequence, int position, vector<short int> &new_sequence, default_random_engine& generator)
{
    // initialize new_site_specific_rates for new sequence
    vector<double> new_site_specific_rates;
    initSiteSpecificRates(new_site_specific_rates, new_sequence.size());
    
    // insert new_site_specific_rates into site_specific_rates
    site_specific_rates.insert(site_specific_rates.begin()+position, new_site_specific_rates.begin(), new_site_specific_rates.end());
    
    // insert new_sequence into the current sequence
    AliSimulator::insertNewSequenceForInsertionEvent(indel_sequence, position, new_sequence, generator);
}