bool CodingWidget::loadFile(QString xmlFilename) {
qDebug() << "CodingWidget::loadFile(QString xmlFilename)";
QFile xmlFile(xmlFilename);
if (!xmlFile.open(QFile::ReadOnly | QFile::Text)) {
QMessageBox::warning(this, tr("MDI"),
tr("Cannot read file %1:\n%2.")
.arg(xmlFilename)
.arg(xmlFile.errorString()));
return false;
}
xmlFile.setObjectName(xmlFilename);
codingElementCount = 0;
codingElementSize = 0;
QApplication::setOverrideCursor(Qt::WaitCursor);
reader = new CodingReader();
reader->read(&xmlFile, this);
xmlFile.reset();
// XML
QTextStream inXml(&xmlFile);
setXml(inXml.readAll());
// XSD
QFile xsdFile(getXsdFilename());
qDebug() << "getXsdFilename()): " << getXsdFilename();
if (!xsdFile.open(QFile::ReadOnly | QFile::Text)) {
QMessageBox::warning(this, tr("MDI"),
tr("Cannot read file %1:\n%2.")
.arg(getXsdFilename())
.arg(xsdFile.errorString()));
return false;
}
QTextStream inXsd(&xsdFile);
setXsd(inXsd.readAll());
QApplication::restoreOverrideCursor();
return true;
}
void ContigsPrinter::run()
{
SortedReferenceMetadata::Contigs originalContigs;
if (!originalSortedReferenceXml_.empty())
{
SortedReferenceMetadata inXml(reference::loadSortedReferenceXml(originalSortedReferenceXml_));
originalContigs = inXml.getContigs();
}
SortedReferenceMetadata::Contigs outputContigs;
std::ifstream is(genomeFile_.string().c_str());
if (!is) {
BOOST_THROW_EXCEPTION(isaac::common::IoException(errno, "Failed to open reference file " + genomeFile_.string()));
}
int64_t lastAcgtCount(0), lastBasesCount(0), lastContigByteStart(0), lineNumber(0), lastContigGenomicStart(0), streamPos(0);
unsigned index = 0;
std::string lastHeader, line;
SortedReferenceMetadata outXml;
isaac::common::MD5Sum md5Sum;
// TODO: use the MultiFastaReader component to ensure consistency (particularly for the index)
while (std::getline(is, line))
{
streamPos = is.tellg();
++lineNumber;
if ('>' == line[0])
{
std::cerr << "header at:" << streamPos << "\n";
if (!lastHeader.empty())
{
const std::string contigName = lastHeader.substr(1, lastHeader.find_first_of(" \t\r") - 1);
SortedReferenceMetadata::Contigs::const_iterator originalContigIt =
std::find_if(originalContigs.begin(), originalContigs.end(), boost::bind(&SortedReferenceMetadata::Contig::name_, _1) == contigName);
outXml.putContig(lastContigGenomicStart,
contigName,
genomeFile_,
lastContigByteStart,
streamPos - lastContigByteStart - (1 + line.length()), //byte length (assuming newline is one byte long)
lastBasesCount, lastAcgtCount, index, index,
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqAs_),
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqUr_),
isaac::common::MD5Sum::toHexString( md5Sum.getDigest().data, 16 ));
++index;
}
// Reset counters
lastAcgtCount = 0;
lastHeader = line;
lastContigByteStart = streamPos;
lastContigGenomicStart += lastBasesCount;
lastBasesCount = 0;
md5Sum.clear();
}
else
{
lastAcgtCount += std::count_if(line.begin(), line.end(), boost::bind(&oligo::getValue, _1) != oligo::INVALID_OLIGO);
// ignore untranslated '\r'
lastBasesCount += std::count_if(line.begin(), line.end(),
[](char c){return c != '\r';});
// boost::bind(&boost::ref<char>, _1) != '\r');
// MD5 with format characters stripped out
std::string lineStd = line;
boost::to_upper(lineStd);
lineStd.erase(std::remove_if(lineStd.begin(), lineStd.end(), &isspace), lineStd.end()); // isspace should remove ' ', '\n', '\r', '\t'
md5Sum.update( lineStd.c_str(), lineStd.size() );
}
}
if (!is.eof()) {
BOOST_THROW_EXCEPTION(
isaac::common::IoException(errno, "Failed while reading sequence."
" Line:" + boost::lexical_cast<std::string>(lineNumber)
+ " Position:" + boost::lexical_cast<std::string>(is.tellg())
+ " Buffer:" + line + "\n"));
}
std::cerr << "end of stream at:" << streamPos << "\n";
if (!lastHeader.empty())
{
const std::string contigName = lastHeader.substr(1, lastHeader.find_first_of(" \t\r") - 1);
SortedReferenceMetadata::Contigs::const_iterator originalContigIt =
std::find_if(originalContigs.begin(), originalContigs.end(), boost::bind(&SortedReferenceMetadata::Contig::name_, _1) == contigName);
outXml.putContig(lastContigGenomicStart,
contigName,
genomeFile_,
lastContigByteStart,
streamPos - lastContigByteStart, //byte length
lastBasesCount, lastAcgtCount, index, index,
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqAs_),
(originalContigs.end() == originalContigIt ? "" : originalContigIt->bamSqUr_),
isaac::common::MD5Sum::toHexString( md5Sum.getDigest().data, 16 ));
++index;
}
saveSortedReferenceXml(std::cout, outXml);
}
