C++ U2OpStatus::setProgress方法代码示例

void PDBFormat::PDBParser::parseBioStruct3D(BioStruct3D& biostruct, U2OpStatus& ti) {

    QByteArray readBuff(DocumentFormat::READ_BUFF_SIZE + 1, 0);
    char* buf = readBuff.data();
    qint64 len = 0;
    bool firstCompndLine = true;
    while (!ti.isCoR()) {

        bool lineOk = true;

        len = io->readUntil(buf, DocumentFormat::READ_BUFF_SIZE, TextUtils::LINE_BREAKS, IOAdapter::Term_Include, &lineOk);
        if (len == 0) {
            break;
        }

        // there could be no terminator if this is end of file, so we have to check for this
        if (!lineOk && !io->isEof()) {
            ti.setError(U2::PDBFormat::tr("Line is too long"));
            return;
        }
        currentPDBLine = QString(QByteArray(buf, len));

        ti.setProgress(io->getProgress() * 0.8);

        if (currentPDBLine.startsWith("HEADER")) {
            parseHeader(biostruct, ti);
            continue;
        }

        if (currentPDBLine.startsWith("COMPND")) {
            parseMacromolecularContent(firstCompndLine, ti);
            firstCompndLine = false;
            continue;
        }

        if (currentPDBLine.startsWith("SEQRES")) {
            parseSequence(biostruct, ti);
            continue;
        }


        if (currentPDBLine.startsWith("HELIX ") || currentPDBLine.startsWith("SHEET ")
            || currentPDBLine.startsWith("TURN  ")) {
                parseSecondaryStructure(biostruct, ti);
                continue;
        }


        if (currentPDBLine.startsWith("ATOM  ") || currentPDBLine.startsWith("HETATM")) {
            parseAtom(biostruct, ti);
            continue;
        }

        if (currentPDBLine.startsWith("TER")) {
            ++currentChainIndex;
            continue;
        }

        if (currentPDBLine.startsWith("SPLIT ")) {
            parseSplitSection(ti);
            continue;
        }

        if (currentPDBLine.startsWith("MODEL")) {
            currentChainIndex = 1;
            parseModel(biostruct, ti);
            continue;
        }

        if (currentPDBLine.startsWith("ENDMDL")) {
            flagMultipleModels = true;
            ++currentModelIndex;
            continue;
        }
    }

    CHECK_OP(ti,);

    if (!flagAtomRecordPresent) {
        ti.setError(U2::PDBFormat::tr("Some mandatory records are absent"));
    }

    updateSecStructChainIndexes(biostruct);

}

static void load(IOAdapter* io, const U2DbiRef& dbiRef,  QList<GObject*>& objects, const QVariantMap& fs, U2OpStatus& os) {
    DbiOperationsBlock opBlock(dbiRef, os);
    CHECK_OP(os, );
    Q_UNUSED(opBlock);

    U2SequenceImporter seqImporter(fs, true);
    const QString folder = fs.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString();

    QByteArray readBuffer(DocumentFormat::READ_BUFF_SIZE, '\0');
    char* buff  = readBuffer.data();

    QBitArray ALPHAS = TextUtils::ALPHA_NUMS;
    ALPHAS['-'] = true;

    QByteArray seq;
    QString seqName(io->getURL().baseFileName());
    //reading sequence
    QBuffer writer(&seq);
    writer.open(QIODevice::WriteOnly);
    TmpDbiObjects dbiObjects(dbiRef, os);
    bool ok = true;
    int len = 0;
    bool isStarted = false;
    int sequenceCounter = 0;
    bool terminatorFound = false;
    bool isSplit = fs.value((DocumentReadingMode_SequenceAsSeparateHint), false).toBool();


    while (ok && !io->isEof()) {
        len = io->readLine(buff, DocumentFormat::READ_BUFF_SIZE, &terminatorFound);
        if (len <= 0){
            continue;
        }

        seq.clear();
        bool isSeek = writer.seek(0);
                assert(isSeek); Q_UNUSED(isSeek);
        if (os.isCoR()) {
            break;
        }

        for (int i=0; i<len && ok; i++) {
            char c = buff[i];
            if (ALPHAS[(uchar)c]) {
                ok = writer.putChar(c);
            }
        }
        if(seq.size()>0 && isStarted == false ){
            QString name = sequenceCounter == 0 ? seqName : seqName + QString("_%1").arg(sequenceCounter);
            isStarted = true;
            seqImporter.startSequence(dbiRef, folder, name, false, os);
        }
        if(isStarted){
            seqImporter.addBlock(seq.data(),seq.size(),os);
        }
        if (seq.size()>0 && isStarted && terminatorFound && isSplit){
            finishSequence(objects, io, os, dbiRef, fs, dbiObjects, seqImporter);
            sequenceCounter++;
            isStarted = false;
        }
        if (os.isCoR()) {
            break;
        }
        os.setProgress(io->getProgress());
    }
    writer.close();

    CHECK_OP(os, );
    if (sequenceCounter == 0){
        CHECK_EXT(isStarted == true, os.setError(RawDNASequenceFormat::tr("Sequence is empty")), );
    }

//.........这里部分代码省略.........

        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;
    }
}

//.........这里部分代码省略.........
        }
        if (sequenceNumber >= 1 && merge) {
            seqImporter.addDefaultSymbolsBlock(gapSize, os);
            sequenceStart += gapSize;
            CHECK_OP_BREAK(os);
        }
        int sequenceLen = 0;
        while (!os.isCoR()) {
            do {
                len = io->readLine(buff, DocumentFormat::READ_BUFF_SIZE);
                CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );
            } while (len <= 0 && !io->isEof());
            CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );

            if (len <= 0 && io->isEof()) {
                break;
            }
            CHECK_EXT(!io->hasError(), os.setError(io->errorString()), );

            buff[len] = 0;

            if(buff[0] != fastaCommentStartChar && buff[0] != FastaFormat::FASTA_HEADER_START_SYMBOL){
                len = TextUtils::remove(buff, len, TextUtils::WHITES);
                if(len > 0){
                    seqImporter.addBlock(buff, len, os);
                    sequenceLen += len;
                }
            }else if( buff[0] == FastaFormat::FASTA_HEADER_START_SYMBOL){
                headerReaded = true;
                break;
            }

            CHECK_OP_BREAK(os);
            os.setProgress(io->getProgress());
        }

        if (merge) {
            memoryLocker.tryAcquire(headerLine.size());
            CHECK_OP_BREAK(os);
            headers.append(headerLine);
            mergedMapping.append(U2Region(sequenceStart, sequenceLen));
        } else {
            if (objectsCountLimit > 0 && objects.size() >= objectsCountLimit) {
                os.setError(FastaFormat::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;
            }
            memoryLocker.tryAcquire(800);
            CHECK_OP_BREAK(os);
            U2Sequence seq = seqImporter.finalizeSequenceAndValidate(os);
            if (os.hasError() && os.getError() == U2SequenceImporter::EMPTY_SEQUENCE_ERROR) {
                os.setError("");
                emptySeqNames << headerLine;
                continue;
            }
            sequenceRef.entityRef = U2EntityRef(dbiRef, seq.id);

            //TODO parse header
            U2StringAttribute attr(seq.id, DNAInfo::FASTA_HDR, headerLine);
            con.dbi->getAttributeDbi()->createStringAttribute(attr, os);
            CHECK_OP_BREAK(os);

            objects << new U2SequenceObject(seq.visualName, U2EntityRef(dbiRef, seq.id));
            CHECK_OP_BREAK(os);