void MafftAddToAlignmentTask::prepare() {
algoLog.info(tr("Align sequences to an existing alignment by MAFFT started"));
MSAUtils::removeColumnsWithGaps(inputMsa, inputMsa->getNumRows());
tmpDirUrl = ExternalToolSupportUtils::createTmpDir("add_to_alignment", stateInfo);
QString tmpAddedUrl = generateTmpFileUrl(tmpDirUrl + QDir::separator() + "XXXXXXXXXXXXXXXX_add.fa");;
DocumentFormatRegistry *dfr = AppContext::getDocumentFormatRegistry();
DocumentFormat *dfd = dfr->getFormatById(BaseDocumentFormats::FASTA);
Document* tempDocument = dfd->createNewLoadedDocument(IOAdapterUtils::get(BaseIOAdapters::LOCAL_FILE), GUrl(tmpAddedUrl), stateInfo);
QListIterator<QString> namesIterator(settings.addedSequencesNames);
int currentRowNumber = inputMsa->getNumRows();
foreach(const U2EntityRef& sequenceRef, settings.addedSequencesRefs) {
uniqueIdsToNames[QString::number(currentRowNumber)] = namesIterator.next();
U2SequenceObject seqObject(QString::number(currentRowNumber), sequenceRef);
GObject* cloned = seqObject.clone(tempDocument->getDbiRef(), stateInfo);
CHECK_OP(stateInfo, );
cloned->setGObjectName(QString::number(currentRowNumber));
tempDocument->addObject(cloned);
currentRowNumber++;
}
saveSequencesDocumentTask = new SaveDocumentTask(tempDocument, tempDocument->getIOAdapterFactory(), tmpAddedUrl, SaveDocFlags(SaveDoc_Roll) | SaveDoc_DestroyAfter | SaveDoc_ReduceLoggingLevel);
addSubTask(saveSequencesDocumentTask);
QString tmpExistingAlignmentUrl = generateTmpFileUrl(tmpDirUrl + QDir::separator() + "XXXXXXXXXXXXXXXX.fa");
saveAlignmentDocumentTask = new SaveMSA2SequencesTask(inputMsa, tmpExistingAlignmentUrl, false, BaseDocumentFormats::FASTA);
addSubTask(saveAlignmentDocumentTask);
}
QList<Task*> DefaultConvertFileTask::onSubTaskFinished(Task *subTask) {
QList<Task*> result;
CHECK(!subTask->hasError() && !subTask->isCanceled(), result);
CHECK(!hasError() && !isCanceled(), result);
if (saveTask == subTask) {
return result;
}
SAFE_POINT_EXT(loadTask == subTask, setError("Unknown subtask"), result);
bool mainThread = false;
Document *srcDoc = loadTask->getDocument(mainThread);
SAFE_POINT_EXT(NULL != srcDoc, setError("NULL document"), result);
DocumentFormatRegistry *dfr = AppContext::getDocumentFormatRegistry();
DocumentFormat *df = dfr->getFormatById(targetFormat);
SAFE_POINT_EXT(NULL != df, setError("NULL document format"), result);
QSet<GObjectType> selectedFormatObjectsTypes = df->getSupportedObjectTypes();
QSet<GObjectType> inputFormatObjectTypes;
QListIterator<GObject*> objectsIterator(srcDoc->getObjects());
while (objectsIterator.hasNext()) {
GObject *obj = objectsIterator.next();
inputFormatObjectTypes << obj->getGObjectType();
}
inputFormatObjectTypes.intersect(selectedFormatObjectsTypes);
if (inputFormatObjectTypes.empty()) {
setError(tr("The formats are not compatible: %1 and %2").arg(srcDoc->getDocumentFormatId()).arg(targetFormat));
return result;
}
QString ext = targetFormat;
if (!df->getSupportedDocumentFileExtensions().isEmpty()) {
ext = df->getSupportedDocumentFileExtensions().first();
}
if (targetUrl.isEmpty()) {
QString fileName = srcDoc->getName() + "." + ext;
targetUrl = GUrlUtils::rollFileName(workingDir + fileName, QSet<QString>());
} else {
if (QFileInfo(targetFormat).suffix() != ext) {
targetUrl += "." + ext;
}
targetUrl = GUrlUtils::rollFileName(targetUrl, QSet<QString>());
}
IOAdapterFactory *iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(srcDoc->getURL()));
Document *dstDoc = srcDoc->getSimpleCopy(df, iof, srcDoc->getURL());
saveTask = new SaveDocumentTask(dstDoc, iof, targetUrl);
result << saveTask;
return result;
}
void ExportAlignmentTask::run() {
DocumentFormatRegistry* r = AppContext::getDocumentFormatRegistry();
DocumentFormat* f = r->getFormatById(format);
IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(fileName));
resultDocument = f->createNewLoadedDocument(iof, fileName, stateInfo);
CHECK_OP(stateInfo, );
MultipleSequenceAlignmentObject* obj = MultipleSequenceAlignmentImporter::createAlignment(resultDocument->getDbiRef(), ma, stateInfo);
CHECK_OP(stateInfo, );
resultDocument->addObject(obj);
f->storeDocument(resultDocument, stateInfo);
}
void ExportMSA2SequencesTask::run() {
DocumentFormatRegistry* r = AppContext::getDocumentFormatRegistry();
DocumentFormat* f = r->getFormatById(format);
IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(url));
resultDocument = f->createNewLoadedDocument(iof, url, stateInfo);
CHECK_OP(stateInfo, );
QList<DNASequence> lst = MSAUtils::ma2seq(ma, trimAli);
QSet<QString> usedNames;
foreach(DNASequence s, lst) {
QString name = s.getName();
if (usedNames.contains(name)) {
name = TextUtils::variate(name, " ", usedNames, false, 1);
s.setName(name);
}
U2EntityRef seqRef = U2SequenceUtils::import(stateInfo, resultDocument->getDbiRef(), s);
CHECK_OP(stateInfo, );
resultDocument->addObject(new U2SequenceObject(name, seqRef));
usedNames.insert(name);
}