void
Sim4::loadGlimmerModel (char *train_dir)
{
char filename[1000];
if (initGlimmerModel)
return;
/* LLL is this still needed? Yes, since it is initialized in the class Sim4*/
sprintf(filename, "%s/%s", train_dir, Glimmer_posDonModelPath);
readModel (&donor_pos_model, filename);
sprintf(filename, "%s/%s", train_dir, Glimmer_negDonModelPath);
readModel (&donor_neg_model, filename);
sprintf(filename, "%s/%s", train_dir, Glimmer_posAccModelPath);
readModel (&acceptor_pos_model, filename);
sprintf(filename, "%s/%s", train_dir, Glimmer_negAccModelPath);
readModel (&acceptor_neg_model, filename);
donor_pos_model_len = getModelLength (donor_pos_model);
donor_neg_model_len = getModelLength (donor_neg_model);
acceptor_pos_model_len = getModelLength (acceptor_pos_model);
acceptor_neg_model_len = getModelLength (acceptor_neg_model);
if (donor_pos_model_len!=donor_neg_model_len)
fatal ("ERROR: Positive and negative donor model lengths differ\n");
if (acceptor_pos_model_len!=acceptor_neg_model_len)
fatal ("ERROR: Positive and negative acceptor model lengths differ\n");
initGlimmerModel = 1;
}
const U2AssemblyCoverageStat &AssemblyModel::getCoverageStat(U2OpStatus & os) {
QMutexLocker mutexLocker(&mutex);
Q_UNUSED(mutexLocker);
if(cachedCoverageStat.isEmpty()) {
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(NULL != attributeDbi) {
U2ByteArrayAttribute attr = U2AttributeUtils::findByteArrayAttribute(attributeDbi, assembly.id, COVERAGE_STAT_ATTRIBUTE_NAME, os);
if(!os.isCoR()) {
if(attr.hasValidId()) {
// TODO: check version
U2AssemblyUtils::deserializeCoverageStat(attr.value, cachedCoverageStat, os);
} else {
qint64 length = getModelLength(os);
if(!os.isCoR()) {
static const qint64 MAX_COVERAGE_CACHE_SIZE = 1000*1000;
int coverageCacheSize = (int)qMin(MAX_COVERAGE_CACHE_SIZE, length);
cachedCoverageStat.resize(coverageCacheSize);
calculateCoverageStat(U2Region(0, length), cachedCoverageStat, os);
if(!os.isCoR()) {
U2ByteArrayAttribute attribute;
attribute.objectId = assembly.id;
attribute.name = COVERAGE_STAT_ATTRIBUTE_NAME;
attribute.value = U2AssemblyUtils::serializeCoverageStat(cachedCoverageStat);
attribute.version = assembly.version;
U2OpStatusImpl opStatus;
attributeDbi->createByteArrayAttribute(attribute, opStatus);
LOG_OP(opStatus);
}
}
}
}
} else {
os.setError("Attribute DBI is not supported");
}
}
return cachedCoverageStat;
}
qint64 AssemblyModel::getModelHeight(U2OpStatus & os) {
if(NO_VAL == cachedModelHeight) {
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(attributeDbi != NULL) {
U2IntegerAttribute attr = U2AttributeUtils::findIntegerAttribute(attributeDbi, assembly.id, U2BaseAttributeName::max_prow, os);
LOG_OP(os);
if(attr.hasValidId()) {
if(attr.version == assembly.version) {
cachedModelHeight = attr.value;
} else if(checkPermissions(QFile::WriteUser,false)) {
U2AttributeUtils::removeAttribute(attributeDbi, attr.id, os);
LOG_OP(os);
}
}
}
if(cachedModelHeight == NO_VAL) {
// if could not get value from attribute, recompute the value...
cachedModelHeight = assemblyDbi->getMaxPackedRow(assembly.id, U2Region(0, getModelLength(os)), os);
LOG_OP(os);
if(! os.isCoR()) {
// ...and store it in a new attribure
U2IntegerAttribute attr;
U2AttributeUtils::init(attr, assembly, U2BaseAttributeName::max_prow);
attr.value = cachedModelHeight;
attributeDbi->createIntegerAttribute(attr, os);
}
}
if(cachedModelHeight == NO_VAL){
os.setError("Can't get model height, database is corrupted");
LOG_OP(os);
}
}
return cachedModelHeight;
}
U2Region AssemblyModel::getGlobalRegion() {
U2OpStatusImpl os;
return U2Region(0, getModelLength(os));
}
