xymsfilereader.cpp
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/////////////////////// StdLib includes
#include <iostream>
#include <iomanip>
/////////////////////// Qt includes
#include <QDebug>
#include <QFile>
#include <QFileInfo>
/////////////////////// libpwiz includes
#include <pwiz/data/msdata/DefaultReaderList.hpp>
/////////////////////// Local includes
#include "xymsfilereader.h"
#include "../exception/exceptionnotfound.h"
#include "../utils.h"
#include "../types.h"
#include "../msrun/msrunid.h"
namespace pappso
{
XyMsFileReader::XyMsFileReader(const QString &file_name)
: MsFileReader{file_name}
{
initialize();
}
XyMsFileReader::~XyMsFileReader()
{
}
std::size_t
XyMsFileReader::initialize()
{
// Here we just test all the lines of the file to check that they comply with
// the xy format.
std::size_t line_count = 0;
QFile file(m_fileName);
if(!file.open(QFile::ReadOnly | QFile::Text))
{
qDebug() << "Failed to open file" << m_fileName;
return 0;
}
QRegularExpressionMatch regExpMatch;
QString line;
bool file_reading_failed = false;
while(!file.atEnd())
{
line = file.readLine();
++line_count;
// We only read a given number of lines from the file, that would be
// enough to check if that file has the right syntax or not.
// if(linesRead >= 2000)
// return true;
if(line.startsWith('#') || line.isEmpty() ||
Utils::endOfLineRegExp.match(line).hasMatch())
continue;
// qDebug() << __FILE__ << __LINE__ << "Current xy format line:" << line;
if(Utils::xyMassDataFormatRegExp.match(line).hasMatch())
continue;
else
{
file_reading_failed = true;
break;
}
}
if(!file_reading_failed && line_count >= 1)
m_fileFormat = MzFormat::xy;
else
m_fileFormat = MzFormat::unknown;
qDebug() << "m_fileFormat: " << static_cast<int>(m_fileFormat);
return line_count;
}
MzFormat
XyMsFileReader::getFileFormat()
{
return m_fileFormat;
}
std::vector<MsRunIdCstSPtr>
XyMsFileReader::getMsRunIds(const QString &run_prefix)
{
std::vector<MsRunIdCstSPtr> ms_run_ids;
if(!initialize())
return ms_run_ids;
// Finally create the MsRunId with the file name.
MsRunId ms_run_id(m_fileName);
ms_run_id.setMzFormat(m_fileFormat);
// We need to set the unambiguous xmlId string.
ms_run_id.setXmlId(
QString("%1%2").arg(run_prefix).arg(Utils::getLexicalOrderedString(0)));
// Craft a meaningful sample name because otherwise all the files loaded from
// text files will have the same sample name and it will be difficult to
// differentiate them.
// Orig version:
// ms_run_id.setRunId("Single spectrum");
// Now the sample name is nothing but the file name without the path.
QFileInfo file_info(m_fileName);
// qDebug() << "file name:" << m_fileName;
QString sample_name = file_info.fileName();
// qDebug() << "sample name:" << sample_name;
ms_run_id.setRunId(sample_name);
// Now set the sample name to the run id:
ms_run_id.setSampleName(ms_run_id.getRunId());
// Now set the sample name to the run id:
ms_run_id.setSampleName(ms_run_id.getRunId());
// qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
//<< "Current ms_run_id:" << ms_run_id.toString();
// Finally make a shared pointer out of it and append it to the vector.
ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
return ms_run_ids;
}
} // namespace pappso
pappso::MsFileReader
Definition: msfilereader.h:15
pappso::MsFileReader::m_fileFormat
MzFormat m_fileFormat
Definition: msfilereader.h:18
pappso::MsFileReader::m_fileName
QString m_fileName
Definition: msfilereader.h:17
pappso::MsRunId
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
Definition: msrunid.h:53
pappso::MsRunId::getRunId
const QString & getRunId() const
Definition: msrunid.cpp:130
pappso::MsRunId::setRunId
void setRunId(const QString &run_id)
Definition: msrunid.cpp:123
pappso::MsRunId::setMzFormat
void setMzFormat(MzFormat format)
Definition: msrunid.cpp:158
pappso::MsRunId::setXmlId
void setXmlId(const QString &xml_id)
set an XML unique identifier for this MsRunId
Definition: msrunid.cpp:137
pappso::MsRunId::setSampleName
void setSampleName(const QString &name)
set a sample name for this MsRunId
Definition: msrunid.cpp:79
pappso::Utils::xyMassDataFormatRegExp
static QRegularExpression xyMassDataFormatRegExp
Definition: utils.h:53
pappso::Utils::getLexicalOrderedString
static const QString getLexicalOrderedString(unsigned int num)
Definition: utils.cpp:52
pappso::Utils::endOfLineRegExp
static QRegularExpression endOfLineRegExp
Regular expression that tracks the end of line in text files.
Definition: utils.h:62
pappso::XyMsFileReader::initialize
virtual std::size_t initialize()
Definition: xymsfilereader.cpp:41
pappso::XyMsFileReader::getMsRunIds
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
Definition: xymsfilereader.cpp:106
pappso::XyMsFileReader::getFileFormat
virtual MzFormat getFileFormat() override
Definition: xymsfilereader.cpp:99
pappso::XyMsFileReader::XyMsFileReader
XyMsFileReader(const QString &file_name)
Definition: xymsfilereader.cpp:28
pappso::XyMsFileReader::~XyMsFileReader
virtual ~XyMsFileReader()
Definition: xymsfilereader.cpp:35
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::MzFormat
MzFormat
Definition: types.h:107
pappso::MzFormat::xy
@ xy
(x,y) format
pappso::MzFormat::unknown
@ unknown
unknown format
xymsfilereader.h