bool LibarchivePlugin::list()
{
qCDebug(ARK) << "Listing archive contents";
if (!initializeReader()) {
return false;
}
qDebug(ARK) << "Detected compression filter:" << archive_filter_name(m_archiveReader.data(), 0);
QString compMethod = convertCompressionName(QString::fromUtf8(archive_filter_name(m_archiveReader.data(), 0)));
if (!compMethod.isEmpty()) {
emit compressionMethodFound(compMethod);
}
m_cachedArchiveEntryCount = 0;
m_extractedFilesSize = 0;
m_numberOfEntries = 0;
auto compressedArchiveSize = QFileInfo(filename()).size();
struct archive_entry *aentry;
int result = ARCHIVE_RETRY;
bool firstEntry = true;
while (!QThread::currentThread()->isInterruptionRequested() && (result = archive_read_next_header(m_archiveReader.data(), &aentry)) == ARCHIVE_OK) {
if (firstEntry) {
qDebug(ARK) << "Detected format for first entry:" << archive_format_name(m_archiveReader.data());
firstEntry = false;
}
if (!m_emitNoEntries) {
emitEntryFromArchiveEntry(aentry);
}
m_extractedFilesSize += (qlonglong)archive_entry_size(aentry);
emit progress(float(archive_filter_bytes(m_archiveReader.data(), -1))/float(compressedArchiveSize));
m_cachedArchiveEntryCount++;
archive_read_data_skip(m_archiveReader.data());
}
if (result != ARCHIVE_EOF) {
qCWarning(ARK) << "Could not read until the end of the archive:" << QLatin1String(archive_error_string(m_archiveReader.data()));
return false;
}
return archive_read_close(m_archiveReader.data()) == ARCHIVE_OK;
}
/**
* Retrieve data from files, prep data.
*
* Only called if this is not a slave.
*/
void Bagging::init(){
bag_param->read_parameters(param_reader->get_engine_specific_params());
initializeReader(); // defined in engine.h
this->outstream.open(this->param_reader->get_out_file().c_str() );
if(!this->outstream.is_open()){
cerr << "Unable to open file " << this->param_reader->get_out_file() << endl;
exit(1);
}
reader->process(data->getDataObject(), param_reader);
data->getDataObject()->prep_data(param_reader);
data->make_categorical(-1,1);
data->getDataObject()->remove_haplotype();
}
/**
* Performs several functions, not all documented here.
*
* Main tasks: get engine specific parameters and read and prep data.
*
* Param checks:
* map file present (does not currently exit)
*
*/
void Dandelion::init(){
ld_param->read_parameters(param_reader->get_engine_specific_params());
initializeReader(); // defined in engine.h
if(param_reader->get_linkage_map_file().compare("none") == 0){
cerr << "Dandelion requires that you enter a map file. Aborting." << endl;
//exit(0);
}
reader->process(data->getDataObject(), param_reader);
numInitSNPs = data->geno_size();
numInitPhen = data->pheno_size();
data->getDataObject()->remove_phenotype(numeric_limits<double>::max());
data->getDataObject()->remove_covariate(numeric_limits<double>::max());
data->getDataObject()->remove_phenotype(0);
data->getDataObject()->prep_data(param_reader);
try{
data->make_categorical(1,2);
}catch(DataException d){
cerr << "Data Exception with message: " << endl << d.message << endl;
exit(0);
}catch(...){
cerr << "Exception making categorical." << endl;
}
delete reader; // No longer needed.
// This removes any individuals that are missing a value at any of the SNPs.
// We don't want to use this if we are windowing.
//data->getDataObject()->remove_indiv_with_snp_value(0);
if(data->pheno_size() == 0){
cerr << "Error: there are no individuals. Program halting." << endl;
exit(0);
}
numFinalPhen = data->pheno_size();
}
/*
* Get data and populate the parameter holder.
*/
void QSnpgwa::init(){
snp_param->read_parameters(param_reader->get_engine_specific_params());
initializeReader(); // defined in engine.h
if(param_reader->get_linkage_map_file().compare("none") == 0){
cerr << "QSNPGWA requires that you enter a map file. Aborting." << endl;
exit(0);
}
Logger::Instance()->init(param_reader->get_out_file() + ".log");
reader->process(data->getDataObject(), param_reader);
numInitSNPs = data->geno_size();
numInitPhen = data->pheno_size();
delete reader; // No longer needed.
data->getDataObject()->remove_phenotype(numeric_limits<double>::max());
data->getDataObject()->remove_covariate(numeric_limits<double>::max());
data->getDataObject()->prep_data(param_reader);
}
/** init()
*
* Set up the reader and input all data.
* Call the data checker in the snp_data method.
*
*/
void ADTree::init(){
ad_param->read_parameters(param_reader->get_engine_specific_params());
initializeReader(); // defined in engine.h
reader->process(data->getDataObject(), param_reader);
data->getDataObject()->prep_data(param_reader);
try{
data->make_categorical(-1,1);
}catch(DataException d){
cerr << "Data Exception with message: " << endl << d.message << endl;
exit(0);
}catch(...){
cerr << "Exception making categorical." << endl;
}
data->getDataObject()->remove_haplotype();
//data->getDataObject()->pass_through_bootstrap();
delete reader; // No longer needed.
}
