Example #1
0
void AceImportWidget::initSaveController(const GUrl& url) {
    SaveDocumentControllerConfig config;

    config.defaultFileName = url.getURLString() + EXTENSION;
    config.defaultFormatId = BaseDocumentFormats::UGENEDB;
    config.fileDialogButton = browseButton;
    config.fileNameEdit = fileNameEdit;
    config.parentWidget = this;
    config.saveTitle = tr("Destination UGENEDB file");

    const QList<DocumentFormatId> formats = QList<DocumentFormatId>() << BaseDocumentFormats::UGENEDB;

    saveController = new SaveDocumentController(config, formats, this);
}
Example #2
0
bool VFSAdapter::open(const GUrl& _url, IOAdapterMode m) {
    SAFE_POINT(!isOpen(), "Adapter is already opened!", false);
    SAFE_POINT(buffer == NULL, "Buffers is not null!", false);

    QString vfsPrefix = U2_VFS_URL_PREFIX;
    // assume that all membuf adapters work with files in some vfs
    if( !_url.getURLString().startsWith(vfsPrefix) ) {
        return false; // not a file in vfs
    }
    VirtualFileSystemRegistry * vfsReg = AppContext::getVirtualFileSystemRegistry();
    SAFE_POINT(vfsReg != NULL, "VirtualFileSystemRegistry not found!", false);

    QStringList urlArgs = _url.getURLString().mid(vfsPrefix.size()).split(U2_VFS_FILE_SEPARATOR, QString::SkipEmptyParts);
    if ( 2 != urlArgs.size() ) { // urlArgs - vfsname and filename
        return false;
    }
    VirtualFileSystem * vfs = vfsReg->getFileSystemById( urlArgs[0] );
    if( NULL == vfs ) {
        return false; // no such vfs registered
    }

    if( !vfs->fileExists( urlArgs[1] ) ) {
        if( IOAdapterMode_Read == m ) {
            return false;
        } else {
            vfs->createFile( urlArgs[1], QByteArray() );
        }
    }

    buffer = new QBuffer( &vfs->getFileByName( urlArgs[1] ) );
    QIODevice::OpenMode iomode = m == IOAdapterMode_Read ? QIODevice::ReadOnly : QIODevice::WriteOnly | QIODevice::Truncate;
    if (!buffer->open(iomode)) {
        return false;
    }
    url = _url;
    return true;
}
QString MultipleDocumentsReadingModeDialog::setupNewUrl() {
    QString urlStr = newDocUrl->text();
    if (urlStr.isEmpty()) {
        GUrl url = urls.at(0);
        urlStr = url.getURLString();
    }
    QFileInfo fi(urlStr);
    urlStr = fi.dir().path();

    QString extension4MergedDocument;
    if (mergeMode->isChecked()) {
        extension4MergedDocument = AppContext::getDocumentFormatRegistry()->getFormatById(BaseDocumentFormats::PLAIN_GENBANK)->getSupportedDocumentFileExtensions().first();
    } else if (join2alignmentMode->isChecked()) {
        extension4MergedDocument = AppContext::getDocumentFormatRegistry()->getFormatById(BaseDocumentFormats::CLUSTAL_ALN)->getSupportedDocumentFileExtensions().first();
    }

    return urlStr + "/merged_document." + extension4MergedDocument;
}
Example #4
0
bool LocalFileAdapter::open(const GUrl& url, IOAdapterMode m) {
    SAFE_POINT(!isOpen(), "Adapter is already opened!", false);
    SAFE_POINT(f == NULL, "QFile is not null!", false);

    if (url.isEmpty()) {
        return false;
    }
    f = new QFile(url.getURLString());
    QIODevice::OpenMode iomode;
    switch (m) {
        case IOAdapterMode_Read: iomode = QIODevice::ReadOnly; break;
        case IOAdapterMode_Write: iomode = QIODevice::WriteOnly | QIODevice::Truncate; break;
        case IOAdapterMode_Append: iomode = QIODevice::WriteOnly | QIODevice::Append; break;
    }
    bool res = f->open(iomode);
    if (!res) {
        delete f;
        f = NULL;
        return false;
    }
    fileSize = f->size();
    return true;
}
Example #5
0
bool BgzipTask::checkBgzf(const GUrl &fileUrl) {
    return bgzf_check_bgzf(fileUrl.getURLString().toLatin1().constData());
}
void ConvertAssemblyToSamDialog::buildSamUrl(const GUrl &dbUrl) {
    GUrl url = GUrlUtils::rollFileName(dbUrl.dirPath() + "/" + dbUrl.baseFileName() + ".sam", DocumentUtils::getNewDocFileNameExcludesHint());
    ui->samPathEdit->setText(url.getURLString());
}
Example #7
0
/**
 * 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;
    }
}
Example #8
0
void GTUtilsProject::openFiles(HI::GUITestOpStatus &os, const GUrl &path, const OpenFileSettings& s) {
    openFiles(os, QList<QUrl>() << path.getURLString(), s);
    GTUtilsTaskTreeView::waitTaskFinished(os);
}