Task::ReportResult GTest_DNASequenceQualityScores::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("Can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAQuality& quality = mySequence->getQuality();
if (quality.isEmpty()) {
stateInfo.setError("Sequence doesn't have quality scores");
return ReportResult_Finished;
}
if (quality.qualCodes != qualityScores) {
stateInfo.setError( QString("Quality scores are not valid! The score is %1, expected %2").arg(quality.qualCodes.constData()).arg(qualityScores.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequencePart::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * objSequence = qobject_cast<U2SequenceObject*>(obj);
if (objSequence==NULL) {
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if (objSequence->getSequenceLength() < startPos + subseq.length()) {
stateInfo.setError(QString("sequence size is less that region end: size=%1, region-end=%2, objectName=%3").arg(objSequence->getSequenceLength()).arg(startPos + subseq.length()).arg(obj->getGObjectName()));
return ReportResult_Finished;
}
QByteArray objSubSeq = objSequence->getSequenceData(U2Region(startPos, subseq.length()));
if (!objSequence->getAlphabet()->isCaseSensitive()) {
subseq = subseq.toUpper();
}
if (objSubSeq != subseq){
stateInfo.setError(QString("region not matched: %1, expected %2").arg(objSubSeq.constData()).arg(subseq.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequenceQualityValue::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("Can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAQuality& quality = mySequence->getQuality();
if ( (pos < 0) || (pos > quality.qualCodes.count() - 1 ) ) {
stateInfo.setError(QString("Quality scores doesn't have position %1").arg(pos));
return ReportResult_Finished;
}
int val = quality.getValue(pos);
if (val != expectedVal) {
stateInfo.setError( QString("Quality score values do not match! The score is %1, expected %2").arg(val).arg(expectedVal));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
void DotPlotDialog::sl_loadTaskStateChanged(Task* t){
DotPlotLoadDocumentsTask *loadTask = qobject_cast<DotPlotLoadDocumentsTask*>(t);
if (!loadTask || !loadTask->isFinished()) {
if(t->isFinished()){
if(curURL == ""){
return;
}
GUrl URL(curURL);
Project *project = AppContext::getProject();
SAFE_POINT(project, "project is NULL", );
Document *doc = project->findDocumentByURL(URL);
if (!doc || !doc->isLoaded()) {
return;
}
QList<GObject*> docObjects = doc->getObjects();
foreach (GObject* obj, docObjects) {
U2SequenceObject* seqObj = qobject_cast<U2SequenceObject*>(obj);
if (seqObj != NULL){
QString name = seqObj->getGObjectName();
xAxisCombo->addItem(name);
yAxisCombo->addItem(name);
sequences << seqObj;
}
}
curURL = "";
}
return;
}
void EnzymesPlugin::sl_onOpenCreateFragmentDialog() {
GObjectViewWindow* w = GObjectViewUtils::getActiveObjectViewWindow();
if (w == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
AnnotatedDNAView* view = qobject_cast<AnnotatedDNAView*>(w->getObjectView());
if (view == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
U2SequenceObject* dnaObj = view->getSequenceInFocus()->getSequenceObject();
assert(dnaObj != NULL);
if (!dnaObj->getAlphabet()->isNucleic()) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("The sequence doesn't have nucleic alphabet, it can not be used in cloning."));
return;
}
QObjectScopedPointer<CreateFragmentDialog> dlg = new CreateFragmentDialog(view->getSequenceInFocus(), QApplication::activeWindow());
dlg->exec();
}
Task::ReportResult GTest_DNAcompareSequencesInTwoObjects::report() {
Document* doc = getContext<Document>(this, docContextName);
if (doc == NULL) {
stateInfo.setError(QString("document not found %1").arg(docContextName));
return ReportResult_Finished;
}
Document* doc2 = getContext<Document>(this, secondDocContextName);
if (doc2 == NULL) {
stateInfo.setError(QString("document not found %1").arg(secondDocContextName));
return ReportResult_Finished;
}
const QList<GObject*>& objs = doc->getObjects();
const QList<GObject*>& objs2 = doc2->getObjects();
GObject*obj=NULL;
GObject*obj2=NULL;
U2SequenceObject * mySequence;
U2SequenceObject * mySequence2;
for(int i=0;(i!=objs.size())&&(i!=objs2.size());i++){
obj = objs.at(i);
obj2 = objs2.at(i);
if((obj->getGObjectType()== GObjectTypes::SEQUENCE)&&(obj2->getGObjectType()== GObjectTypes::SEQUENCE)){
mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj->getGObjectName()).arg(i));
return ReportResult_Finished;
}
mySequence2 = qobject_cast<U2SequenceObject*>(obj2);
if(mySequence2==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj2->getGObjectName()).arg(i));
return ReportResult_Finished;
}
if(mySequence->getWholeSequenceData(stateInfo) != mySequence2->getWholeSequenceData(stateInfo)){
CHECK_OP(stateInfo, ReportResult_Finished);
stateInfo.setError(QString("Sequences of object in position %1 not matched").arg(i));
return ReportResult_Finished;
}
CHECK_OP(stateInfo, ReportResult_Finished);
}
}
if (objs.size() != objs2.size()) {
QString error("Number of objects in doc mismatches: [%1=%2] vs [%3=%4]");
error = error.arg(docContextName).arg(objs.size())
.arg(secondDocContextName).arg(objs2.size());
if (obj) {
error += QString("\nLast good object: %1").arg(obj->getGObjectName());
}
stateInfo.setError(error);
}
return ReportResult_Finished;
}
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"));
}
}
Task::ReportResult GTest_DNASequenceSize::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
int tempLength=mySequence->getSequenceLength();
if (tempLength != seqSize){
stateInfo.setError(QString("sequence size not matched: %1, expected %2 ").arg(tempLength).arg(seqSize));
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNASequenceAlphabetId::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if(obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
const DNAAlphabet *tempAlphabet = mySequence->getAlphabet();
if( tempAlphabet->getId() != alpId){
stateInfo.setError(QString("Alphabet id not matched: %1 expected %2").arg(tempAlphabet->getId()).arg(alpId));
}
return ReportResult_Finished;
}
MAlignment Kalign_Load_Align_Compare_Task::dna_to_ma(QList<GObject*> dnaSeqs) {
int seqCount = dnaSeqs.count();
U2SequenceObject *seq = qobject_cast<U2SequenceObject *>(dnaSeqs[0]);
MAlignment ma("Alignment",seq->getAlphabet());
for(int i=0; i<seqCount; i++) {
seq = qobject_cast<U2SequenceObject *>(dnaSeqs[i]);
if(seq == NULL) {
stateInfo.setError( QString("Can't cast GObject to U2SequenceObject") );
return ma;
}
QByteArray seqData = seq->getWholeSequenceData(stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
ma.addRow(seq->getSequenceName(), seqData, stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
}
return ma;
}
void GTest_SecStructPredictTask::prepare()
{
U2SequenceObject * mySequence = getContext<U2SequenceObject>(this, seqName);
if(mySequence==NULL){
stateInfo.setError( QString("error can't cast to sequence from GObject"));
return;
}
SecStructPredictAlgRegistry* sspr = AppContext::getSecStructPredictAlgRegistry();
if (!sspr->hadRegistered(algName)) {
stateInfo.setError( QString(tr("Algorithm named %1 not found")).arg(algName));
return;
}
SecStructPredictTaskFactory* factory = sspr->getAlgorithm(algName);
QByteArray seqData = mySequence->getWholeSequenceData(stateInfo);
task = factory->createTaskInstance(seqData);
CHECK_OP(stateInfo, );
addSubTask(task);
}
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 ADVClipboard::copySequenceSelection(bool complement, bool amino) {
ADVSequenceObjectContext* seqCtx = getSequenceContext();
if (seqCtx == NULL) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), "No sequence selected!");
return;
}
QString res;
QVector<U2Region> regions = seqCtx->getSequenceSelection()->getSelectedRegions();
#ifdef UGENE_X86
int totalLen = 0;
foreach (const U2Region& r, regions) {
totalLen += r.length;
}
if (totalLen > MAX_COPY_SIZE_FOR_X86) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), COPY_FAILED_MESSAGE);
return;
}
#endif
if (!regions.isEmpty()) {
U2SequenceObject* seqObj = seqCtx->getSequenceObject();
DNATranslation* complTT = complement ? seqCtx->getComplementTT() : NULL;
DNATranslation* aminoTT = amino ? seqCtx->getAminoTT() : NULL;
U2OpStatus2Log os;
QList<QByteArray> seqParts = U2SequenceUtils::extractRegions(seqObj->getSequenceRef(), regions, complTT, aminoTT, false, os);
if (os.hasError()) {
QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), tr("An error occurred during getting sequence data: %1").arg(os.getError()));
return;
}
if (seqParts.size() == 1) {
putIntoClipboard(seqParts.first());
return;
}
res = U1SequenceUtils::joinRegions(seqParts);
}
putIntoClipboard(res);
}
U2SequenceObject *importSequence(DNASequence &sequence,
const QString &objName,
QList<GObject*>& objects,
U2SequenceImporter &seqImporter,
const U2DbiRef& dbiRef,
const QString& folder,
U2OpStatus& os)
{
seqImporter.startSequence(dbiRef, folder, sequence.getName(), sequence.circular, os);
CHECK_OP(os, NULL);
seqImporter.addBlock(sequence.seq.constData(), sequence.seq.length(), os);
CHECK_OP(os, NULL);
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
TmpDbiObjects dbiObjects(dbiRef, os);
dbiObjects.objects << u2seq.id;
CHECK_OP(os, NULL);
U2SequenceObject *seqObj = new U2SequenceObject(objName, U2EntityRef(dbiRef, u2seq.id));
seqObj->setSequenceInfo(sequence.info);
objects << seqObj;
return seqObj;
}
void DotPlotDialog::sl_minLenHeuristics() {
identityBox->setValue(100);
// formula used here: nVariations / lenVariations = wantedResCount (==1000)
// where nVariations == area size
// lenVariations = 4^len where len is result
// so we have len = ln(nVariations/wantedResCount)/ln(4)
int xIdx = xAxisCombo->currentIndex();
int yIdx = yAxisCombo->currentIndex();
U2SequenceObject *objX = sequences.at(xIdx);
U2SequenceObject *objY = sequences.at(yIdx);
qint64 xSeqLen = objX->getSequenceLength();
qint64 ySeqLen = objY->getSequenceLength();
double nVariations = xSeqLen*ySeqLen;
double resCount = 1000;
double len = log(nVariations / resCount) / log(double(4));
minLenBox->setValue((int)len);
}
Task::ReportResult GTest_DNATranslation3to1Test::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if (obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("error can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if(!(mySequence->getAlphabet()->isNucleic())){
stateInfo.setError(QString("error Alphabet is not Nucleic: %1").arg(mySequence->getAlphabet()->getId()));
return ReportResult_Finished;
}
DNATranslation* aminoTransl = 0;
DNATranslationRegistry* tr = AppContext::getDNATranslationRegistry();
QList<DNATranslation*> aminoTs = tr->lookupTranslation(mySequence->getAlphabet(), DNATranslationType_NUCL_2_AMINO);
if (!aminoTs.empty()) {
aminoTransl = tr->getStandardGeneticCodeTranslation(mySequence->getAlphabet());
}
int tempValue;
if(strTo == -1){
tempValue=-1;
} else{
tempValue=(strTo-strFrom+1);
}
QByteArray myByteArray = mySequence->getSequenceData(U2Region(strFrom,tempValue));
QByteArray rezult(myByteArray.length() / 3, 0);
int n = aminoTransl->translate(myByteArray, myByteArray.length(), rezult.data(), rezult.length());
assert(n == rezult.length()); Q_UNUSED(n);
if(rezult != stringValue.toLatin1()){
stateInfo.setError(QString("translated sequence not matched: %1, expected %2 ").arg(rezult.data()).arg(stringValue));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
bool SequenceAccFilterTask::filterAcceptsObject(GObject *obj) {
U2SequenceObject *seqObject = qobject_cast<U2SequenceObject *>(obj);
CHECK(NULL != seqObject, false);
return settings.nameFilterAcceptsString(seqObject->getSequenceInfo()[DNAInfo::ACCESSION].toString());
}
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);
}
/**
* FASTQ format specification: http://maq.sourceforge.net/fastq.shtml
*/
static void load(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& hints, const GUrl& docUrl, QList<GObject*>& objects, U2OpStatus& os,
int gapSize, int predictedSize, QString& writeLockReason) {
DbiOperationsBlock opBlock(dbiRef, os);
CHECK_OP(os, );
Q_UNUSED(opBlock);
writeLockReason.clear();
bool merge = gapSize!=-1;
QByteArray sequence;
QByteArray qualityScores;
QStringList headers;
QSet<QString> uniqueNames;
QVector<U2Region> mergedMapping;
QByteArray gapSequence((merge ? gapSize : 0), 0);
sequence.reserve(predictedSize);
qualityScores.reserve(predictedSize);
// for lower case annotations
GObjectReference sequenceRef;
qint64 sequenceStart = 0;
U2SequenceImporter seqImporter(hints, true);
const QString folder = hints.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();
int seqNumber = 0;
int progressUpNum = 0;
const int objectsCountLimit = hints.contains(DocumentReadingMode_MaxObjectsInDoc) ? hints[DocumentReadingMode_MaxObjectsInDoc].toInt() : -1;
const bool settingsMakeUniqueName = !hints.value(DocumentReadingMode_DontMakeUniqueNames, false).toBool();
while (!os.isCoR()) {
//read header
QString sequenceName = readSequenceName(os, io, '@');
// check for eof while trying to read another FASTQ block
if (io->isEof()) {
break;
}
CHECK_OP_BREAK(os);
if(sequenceName.isEmpty()){
sequenceName = "Sequence";
}
if ((merge == false) || (seqNumber == 0)) {
QString objName = sequenceName;
if (settingsMakeUniqueName) {
objName = (merge) ? "Sequence" : TextUtils::variate(sequenceName, "_", uniqueNames);
objName.squeeze();
uniqueNames.insert(objName);
}
seqImporter.startSequence(dbiRef, folder, objName, false, os);
CHECK_OP_BREAK(os);
}
//read sequence
if (merge && sequence.length() > 0) {
seqImporter.addDefaultSymbolsBlock(gapSize,os);
sequenceStart += sequence.length();
sequenceStart+=gapSize;
CHECK_OP_BREAK(os);
}
sequence.clear();
readSequence(os, io, sequence);
MemoryLocker lSequence(os, qCeil(sequence.size()/(1000*1000)));
CHECK_OP_BREAK(os);
Q_UNUSED(lSequence);
seqImporter.addBlock(sequence.data(),sequence.length(),os);
CHECK_OP_BREAK(os);
QString qualSequenceName = readSequenceName(os, io, '+');
if (!qualSequenceName.isEmpty()) {
static const QString err = U2::FastqFormat::tr("Not a valid FASTQ file: %1, sequence name differs from quality scores name: %2 and %3");
CHECK_EXT_BREAK(sequenceName == qualSequenceName,
os.setError(err.arg(docUrl.getURLString()).arg(sequenceName).arg(qualSequenceName)));
}
// read qualities
qualityScores.clear();
readQuality(os, io, qualityScores, sequence.size());
CHECK_OP_BREAK(os);
static const QString err = U2::FastqFormat::tr("Not a valid FASTQ file: %1. Bad quality scores: inconsistent size.").arg(docUrl.getURLString());
CHECK_EXT_BREAK(sequence.length() == qualityScores.length(), os.setError(err));
seqNumber++;
progressUpNum++;
if (merge) {
headers.append(sequenceName);
mergedMapping.append(U2Region(sequenceStart, sequence.length() ));
}
else {
if (objectsCountLimit > 0 && objects.size() >= objectsCountLimit) {
os.setError(FastqFormat::tr("File \"%1\" contains too many sequences to be displayed. "
"However, you can process these data using instruments from the menu <i>Tools -> NGS data analysis</i> "
"or pipelines built with Workflow Designer.")
.arg(io->getURL().getURLString()));
break;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP_BREAK(os);
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U2SequenceObject* seqObj = new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
CHECK_EXT_BREAK(seqObj != NULL, os.setError("U2SequenceObject is NULL"));
seqObj->setQuality(DNAQuality(qualityScores));
objects << seqObj;
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
}
if (PROGRESS_UPDATE_STEP == progressUpNum) {
progressUpNum = 0;
os.setProgress(io->getProgress());
}
}
CHECK_OP_EXT(os, qDeleteAll(objects); objects.clear(), );
bool emptyObjects = objects.isEmpty();
CHECK_EXT(!emptyObjects || merge, os.setError(Document::tr("Document is empty.")), );
SAFE_POINT(headers.size() == mergedMapping.size(), "headers <-> regions mapping failed!", );
if (!merge) {
return;
}
U2Sequence u2seq = seqImporter.finalizeSequenceAndValidate(os);
CHECK_OP(os,);
sequenceRef = GObjectReference(io->getURL().getURLString(), u2seq.visualName, GObjectTypes::SEQUENCE, U2EntityRef(dbiRef, u2seq.id));
U1AnnotationUtils::addAnnotations(objects, seqImporter.getCaseAnnotations(), sequenceRef, NULL, hints);
objects << new U2SequenceObject(u2seq.visualName, U2EntityRef(dbiRef, u2seq.id));
objects << DocumentFormatUtils::addAnnotationsForMergedU2Sequence(sequenceRef, dbiRef, headers, mergedMapping, hints);
if (headers.size() > 1) {
writeLockReason = DocumentFormat::MERGED_SEQ_LOCK;
}
}
QString AssemblyBrowser::tryAddObject(GObject * obj) {
Document * objDoc = obj->getDocument();
SAFE_POINT(NULL != objDoc, "", tr("Internal error: only object with document can be added to browser"));
if (GObjectTypes::SEQUENCE == obj->getGObjectType()) {
U2SequenceObject * seqObj = qobject_cast<U2SequenceObject*>(obj);
CHECK(NULL != seqObj, tr("Internal error: broken sequence object"));
SAFE_POINT(NULL != objDoc->getDocumentFormat(), "", tr("Internal error: empty document format"));
U2OpStatus2Log os;
qint64 seqLen = seqObj->getSequenceLength();
QStringList errs;
qint64 modelLen = model->getModelLength(os);
if (seqLen != modelLen) {
errs << tr("The lengths of the sequence and assembly are different.");
}
if (seqObj->getGObjectName() != gobject->getGObjectName()) {
errs << tr("The sequence and assembly names are different.");
}
// commented: waiting for fix
//QByteArray refMd5 = model->getReferenceMd5();
//if(!refMd5.isEmpty()) {
// //QByteArray data = QString(seqObj->getSequence()).remove("-").toUpper().toUtf8();
// QByteArray data = QString(seqObj->getSequence()).toUpper().toUtf8();
// QByteArray seqObjMd5 = QCryptographicHash::hash(data, QCryptographicHash::Md5).toHex();
// if(seqObjMd5 != refMd5) {
// errs << tr("- Reference MD5 not match with MD5 written in assembly");
// }
//}
bool setRef = !isAssemblyObjectLocked(true) && !model->isLoadingReference();
setRef &= model->checkPermissions(QFile::WriteUser, setRef);
if(!errs.isEmpty() && setRef) {
const NotificationStack *notificationStack = AppContext::getMainWindow()->getNotificationStack();
const QString message = tr("It seems that sequence \"%1\", set as reference to assembly \"%2\", does not match it.").arg(seqObj->getGObjectName()).arg(gobject->getGObjectName())
+ "\n- " + errs.join("\n- ");
notificationStack->addNotification(message, Warning_Not);
}
if(setRef) {
model->setReference(seqObj);
U2Assembly assembly = model->getAssembly();
U2DataId refId;
QString folder;
const QStringList folders = model->getDbiConnection().dbi->getObjectDbi()->getObjectFolders(assembly.id, os);
if (folders.isEmpty() || os.isCoR()) {
folder = U2ObjectDbi::ROOT_FOLDER;
} else {
folder = folders.first();
}
if (seqObj->getEntityRef().dbiRef == model->getDbiConnection().dbi->getDbiRef()) {
refId = seqObj->getEntityRef().entityId;
} else {
U2CrossDatabaseReferenceDbi * crossDbi = model->getDbiConnection().dbi->getCrossDatabaseReferenceDbi();
U2CrossDatabaseReference crossDbRef;
// Cannot simply use seqObj->getSequenceRef(), since it points to a temporary dbi
// TODO: make similar method seqObj->getPersistentSequenctRef()
crossDbRef.dataRef.dbiRef.dbiId = objDoc->getURLString();
crossDbRef.dataRef.dbiRef.dbiFactoryId = "document";
crossDbRef.dataRef.entityId = seqObj->getGObjectName().toUtf8();
crossDbRef.visualName = "cross_database_reference: " + seqObj->getGObjectName();
crossDbRef.dataRef.version = 1;
crossDbi->createCrossReference(crossDbRef, folder, os);
LOG_OP(os);
refId = crossDbRef.id;
addObjectToView(obj);
}
model->associateWithReference(refId);
}
} else if (GObjectTypes::VARIANT_TRACK == obj->getGObjectType()) {
VariantTrackObject *trackObj = qobject_cast<VariantTrackObject*>(obj);
CHECK(NULL != trackObj, tr("Internal error: broken variant track object"));
model->addTrackObject(trackObj);
addObjectToView(obj);
connect(model.data(), SIGNAL(si_trackRemoved(VariantTrackObject *)), SLOT(sl_trackRemoved(VariantTrackObject *)));
} else {
