Esempio n. 1
0
void CandidateSet::recomputeLoglOfAllTrees(IQTree &treeObject) {
    vector<string> allTreeStrings = getBestTreeStrings();
    for (vector<string>:: iterator it = allTreeStrings.begin(); it != allTreeStrings.end(); it++) {
        treeObject.readTreeString(*it);
        double score = treeObject.optimizeAllBranches(1);
        update(treeObject.getTreeString(), score);
    }
}
void RateMeyerHaeseler::runIterativeProc(Params &params, IQTree &tree) {
	int i;
	if (verbose_mode >= VB_MED) {
		ofstream out("x");
		out.close();
	}
	setTree(&tree);
	RateHeterogeneity *backup_rate = tree.getRate();
	if (backup_rate->getGammaShape() > 0 ) {
		IntVector pattern_cat;
		backup_rate->computePatternRates(*this, pattern_cat);
		double sum = 0.0;
		for (i = 0; i < size(); i++)
			sum += at(i) * phylo_tree->aln->at(i).frequency;
		sum /=  phylo_tree->aln->getNSite();
		if (fabs(sum - 1.0) > 0.0001) {
			if (verbose_mode >= VB_MED)
				cout << "Normalizing Gamma rates (" << sum << ")" << endl;
			for (i = 0; i < size(); i++)
				at(i) /= sum;
		}
	}
	tree.getModelFactory()->site_rate = this;
	tree.setRate(this);

	
	//if  (empty()) initializeRates();

	//setRates(prev_rates);
	//string rate_file = params.out_prefix;
	//rate_file += ".mhrate";
	double prev_lh = tree.getCurScore();
	string dist_file = params.out_prefix;
	dist_file += ".tdist";
	tree.getModelFactory()->stopStoringTransMatrix();

	for (i = 2; i < 100; i++) {
		//DoubleVector prev_rates;
		//getRates(prev_rates);
		//writeSiteRates(prev_rates, rate_file.c_str());
		tree.setCurScore(optimizeParameters(0.0));
		//phylo_tree->aln->printDist(dist_file.c_str(), dist_mat);
		tree.setCurScore(tree.optimizeAllBranches(i));
		cout << "Current Log-likelihood: " << tree.getCurScore() << endl;
		if (tree.getCurScore() <= prev_lh + 1e-4) {
			break;
		}
		prev_lh = tree.getCurScore();
	}
	cout << "Optimization took " << i-1 << " rounds to finish" << endl;
	tree.getModelFactory()->startStoringTransMatrix();
	//tree.getModelFactory()->site_rate = backup_rate;
	//tree.setRate(backup_rate);
}