void DetectabilitySimulation::predictDetectabilities(vector<String>& peptides_vector, vector<DoubleReal>& labels,
vector<DoubleReal>& detectabilities)
{
// The support vector machine
SVMWrapper svm;
// initialize support vector machine
LibSVMEncoder encoder;
UInt k_mer_length = 0;
DoubleReal sigma = 0.0;
UInt border_length = 0;
if (File::readable(dt_model_file_))
{
svm.loadModel(dt_model_file_);
}
else
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation got invalid parameter. 'dt_model_file' " + dt_model_file_ + " is not readable");
}
// load additional parameters
if (svm.getIntParameter(SVMWrapper::KERNEL_TYPE) == SVMWrapper::OLIGO)
{
String add_paramfile = dt_model_file_ + "_additional_parameters";
if (!File::readable(add_paramfile))
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation: SVM parameter file " + add_paramfile + " is not readable");
}
Param additional_parameters;
ParamXMLFile paramFile;
paramFile.load(add_paramfile, additional_parameters);
if (additional_parameters.getValue("border_length") == DataValue::EMPTY
&& svm.getIntParameter(SVMWrapper::KERNEL_TYPE) == SVMWrapper::OLIGO)
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation: No border length defined in additional parameters file.");
}
border_length = ((String)additional_parameters.getValue("border_length")).toInt();
if (additional_parameters.getValue("k_mer_length") == DataValue::EMPTY
&& svm.getIntParameter(SVMWrapper::KERNEL_TYPE) == SVMWrapper::OLIGO)
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation: No k-mer length defined in additional parameters file.");
}
k_mer_length = ((String)additional_parameters.getValue("k_mer_length")).toInt();
if (additional_parameters.getValue("sigma") == DataValue::EMPTY
&& svm.getIntParameter(SVMWrapper::KERNEL_TYPE) == SVMWrapper::OLIGO)
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation: No sigma defined in additional parameters file.");
}
sigma = ((String)additional_parameters.getValue("sigma")).toFloat();
}
if (File::readable(dt_model_file_))
{
svm.setParameter(SVMWrapper::BORDER_LENGTH, (Int) border_length);
svm.setParameter(SVMWrapper::SIGMA, sigma);
// to obtain probabilities
svm.setParameter(SVMWrapper::PROBABILITY, 1);
}
// loading training data
String sample_file = dt_model_file_ + "_samples";
svm_problem* training_data = NULL;
if (File::readable(sample_file))
{
training_data = encoder.loadLibSVMProblem(sample_file);
svm.setTrainingSample(training_data);
}
else
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "DetectibilitySimulation: SVM sample file " + sample_file + " is not readable");
}
LOG_INFO << "Predicting peptide detectabilities.. " << endl;
String allowed_amino_acid_characters = "ACDEFGHIKLMNPQRSTVWY";
// Encoding test data
vector<DoubleReal> probs;
probs.resize(peptides_vector.size(), 0);
svm_problem* prediction_data = encoder.encodeLibSVMProblemWithOligoBorderVectors(peptides_vector, probs,
k_mer_length,
allowed_amino_acid_characters,
svm.getIntParameter(SVMWrapper::BORDER_LENGTH));
svm.getSVCProbabilities(prediction_data, detectabilities, labels);
// clean up when finished with prediction
delete prediction_data;
delete training_data;
}
