void EvaluateBaseContentTask::run() {
if (_obj->getGObjectType() == GObjectTypes::SEQUENCE) {
U2SequenceObject* dnaObj = qobject_cast<U2SequenceObject*>(_obj);
alp = dnaObj->getAlphabet();
DNASequenceGenerator::evaluateBaseContent(dnaObj->getWholeSequence(stateInfo), result);
} else if (_obj->getGObjectType() == GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT) {
MultipleSequenceAlignmentObject* maObj = qobject_cast<MultipleSequenceAlignmentObject*>(_obj);
alp = maObj->getAlphabet();
DNASequenceGenerator::evaluateBaseContent(maObj->getMultipleAlignment(), result);
} else {
stateInfo.setError(tr("Base content can be evaluated for sequence or sequence alignment"));
}
}
void uHMMPlugin::sl_search() {
//to select a sequence
//1. check that annotated DNA view is active
//2. if not -> check that DNASequence object is selected in project view
U2SequenceObject* obj = NULL;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(ov);
if (av!=NULL) {
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
obj = seqCtx->getSequenceObject();
}
}
}
if (obj == NULL) {
ProjectView* pv = AppContext::getProjectView();
if (pv!=NULL) {
const GObjectSelection* sel = pv->getGObjectSelection();
GObject* o = sel->getSelectedObjects().size() == 1 ? sel->getSelectedObjects().first() : NULL;
obj = qobject_cast<U2SequenceObject*>(o);
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
if (obj == NULL) {
QMessageBox::critical(p, tr("Error"), tr("Error! Select sequence in Project view or open sequence view."));
return;
}
U2OpStatusImpl os;
DNASequence sequence = obj->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, obj, p);
d->exec();
}
void GTest_UHMM3Search::setAndCheckArgs() {
assert( !stateInfo.hasError() );
if( hmmFilename.isEmpty() ) {
stateInfo.setError( "hmm_filename_is_empty" );
return;
}
hmmFilename = env->getVar( "COMMON_DATA_DIR" ) + "/" + hmmFilename;
if( searchTaskCtxName.isEmpty() ) {
stateInfo.setError( "task_ctx_name_is_empty" );
return;
}
if( seqDocCtxName.isEmpty() ) {
stateInfo.setError( "sequence_document_ctx_name_is_empty" );
return;
}
if( UNKNOWN_SEARCH == algo ) {
stateInfo.setError( "unknown_algorithm_type" );
return;
}
Document* seqDoc = getContext<Document>( this, seqDocCtxName );
if( NULL == seqDoc ) {
stateInfo.setError( QString( "context %1 not found" ).arg( seqDocCtxName ) );
return;
}
QList< GObject* > objsList = seqDoc->findGObjectByType( GObjectTypes::SEQUENCE );
CHECK_EXT(!objsList.isEmpty(),setError("No sequence objects found!"), );
U2SequenceObject* seqObj = qobject_cast< U2SequenceObject* >( objsList.first() );
sequence = seqObj->getWholeSequence(stateInfo);
CHECK_OP(stateInfo, );
CHECK_EXT(sequence.length() > 0, setError(tr("Sequence is empty")), );
if( !machinePath.isEmpty() ) {
machinePath = env->getVar( "COMMON_DATA_DIR" ) + "/" + machinePath;
}
}
void GTest_uHMMERSearch::prepare() {
Document* doc = getContext<Document>(this, seqDocCtxName);
if (doc == NULL) {
stateInfo.setError( QString("context not found %1").arg(seqDocCtxName) );
return;
}
QList<GObject*> list = doc->findGObjectByType(GObjectTypes::SEQUENCE);
if (list.size() == 0) {
stateInfo.setError( QString("container of object with type \"%1\" is empty").arg(GObjectTypes::SEQUENCE) );
return;
}
GObject *obj = list.first();
if(obj==NULL){
stateInfo.setError( QString("object with type \"%1\" not found").arg(GObjectTypes::SEQUENCE) );
return;
}
assert(obj!=NULL);
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError( QString("error can't cast to sequence from GObject") );
return;
}
UHMMSearchSettings s;
if (expertOptions){
s.globE = evalueCutoff;
s.eValueNSeqs = number_of_seq;
s.domE = domEvalueCutoff;
s.domT = minScoreCutoff;
}
QString env_algo = env->getVar(ENV_HMMSEARCH_ALGORITHM_NAME);
if( !env_algo.isEmpty() ) {
if( ENV_HMMSEARCH_ALGORITHM_SSE == env_algo ) {
#if !defined(HMMER_BUILD_WITH_SSE2)
stateInfo.setError( QString("SSE2 was not enabled in this build") );
return;
#endif
s.alg = HMMSearchAlgo_SSEOptimized;
} else if( ENV_HMMSEARCH_ALGORITHM_CELL == env_algo ) {
#if !defined UGENE_CELL
stateInfo.setError( QString("HMMER-Cell was not enabled in this build") );
return;
#endif
s.alg = HMMSearchAlgo_CellOptimized;
} else {
stateInfo.setError( QString("unknown hmmsearch algorithm is selected") );
return;
}
}
if(customHmmSearchChunk) {
s.searchChunkSize = hmmSearchChunk;
}
QString annotationName = "hmm_signal";
QString url = env->getVar("TEMP_DATA_DIR")+"/uhmmsearch/"+resultDocName;
IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(url));
DocumentFormat* df = AppContext::getDocumentFormatRegistry()->getFormatById(BaseDocumentFormats::PLAIN_GENBANK);
assert(aDoc == NULL);
aDoc = df->createNewLoadedDocument(iof, url, stateInfo);
CHECK_OP(stateInfo, );
AnnotationTableObject *ao = new AnnotationTableObject( "Annotations", aDoc->getDbiRef( ) );
aDoc->addObject(ao);
DNASequence dnaSequence = mySequence->getWholeSequence(stateInfo);
CHECK_OP(stateInfo, );
searchTask = new HMMSearchToAnnotationsTask(env->getVar("COMMON_DATA_DIR")+"/"+hmmFileName, dnaSequence, ao, annotationName, "", U2FeatureTypes::MiscSignal, annotationName, s);
addSubTask(searchTask);
}
