libpappsomspp
Library for mass spectrometry
pappso::XyMsFileReader Class Reference

#include <xymsfilereader.h>

Inheritance diagram for pappso::XyMsFileReader:
pappso::MsFileReader

Public Member Functions

 XyMsFileReader (const QString &file_name)
 
virtual ~XyMsFileReader ()
 
virtual MzFormat getFileFormat () override
 
virtual std::vector< MsRunIdCstSPtrgetMsRunIds (const QString &run_prefix) override
 
MsRunReaderselectMsRunReader (const QString &file_name) const
 

Private Member Functions

virtual std::size_t initialize ()
 
- Private Member Functions inherited from pappso::MsFileReader
 MsFileReader (const QString &file_name)
 
virtual ~MsFileReader ()
 

Additional Inherited Members

- Private Attributes inherited from pappso::MsFileReader
QString m_fileName
 
MzFormat m_fileFormat = MzFormat::unknown
 

Detailed Description

Definition at line 16 of file xymsfilereader.h.

Constructor & Destructor Documentation

◆ XyMsFileReader()

pappso::XyMsFileReader::XyMsFileReader ( const QString &  file_name)

Definition at line 28 of file xymsfilereader.cpp.

29  : MsFileReader{file_name}
30 {
31  initialize();
32 }

◆ ~XyMsFileReader()

pappso::XyMsFileReader::~XyMsFileReader ( )
virtual

Definition at line 35 of file xymsfilereader.cpp.

36 {
37 }

Member Function Documentation

◆ getFileFormat()

MzFormat pappso::XyMsFileReader::getFileFormat ( )
overridevirtual

Implements pappso::MsFileReader.

Definition at line 99 of file xymsfilereader.cpp.

100 {
101  return m_fileFormat;
102 }

References pappso::MsFileReader::m_fileFormat.

Referenced by pappso::MsFileAccessor::getMsRunIds().

◆ getMsRunIds()

std::vector< MsRunIdCstSPtr > pappso::XyMsFileReader::getMsRunIds ( const QString &  run_prefix)
overridevirtual

Implements pappso::MsFileReader.

Definition at line 106 of file xymsfilereader.cpp.

107 {
108  std::vector<MsRunIdCstSPtr> ms_run_ids;
109 
110  if(!initialize())
111  return ms_run_ids;
112 
113  // Finally create the MsRunId with the file name.
114  MsRunId ms_run_id(m_fileName);
115  ms_run_id.setMzFormat(m_fileFormat);
116 
117  // We need to set the unambiguous xmlId string.
118  ms_run_id.setXmlId(
119  QString("%1%2").arg(run_prefix).arg(Utils::getLexicalOrderedString(0)));
120 
121  // Craft a meaningful sample name because otherwise all the files loaded from
122  // text files will have the same sample name and it will be difficult to
123  // differentiate them.
124  // Orig version:
125  // ms_run_id.setRunId("Single spectrum");
126  // Now the sample name is nothing but the file name without the path.
127 
128  QFileInfo file_info(m_fileName);
129 
130  // qDebug() << "file name:" << m_fileName;
131 
132  QString sample_name = file_info.fileName();
133 
134  // qDebug() << "sample name:" << sample_name;
135 
136  ms_run_id.setRunId(sample_name);
137 
138  // Now set the sample name to the run id:
139 
140  ms_run_id.setSampleName(ms_run_id.getRunId());
141 
142  // Now set the sample name to the run id:
143 
144  ms_run_id.setSampleName(ms_run_id.getRunId());
145 
146  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
147  //<< "Current ms_run_id:" << ms_run_id.toString();
148 
149  // Finally make a shared pointer out of it and append it to the vector.
150  ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
151 
152  return ms_run_ids;
153 }

References pappso::Utils::getLexicalOrderedString(), pappso::MsRunId::getRunId(), initialize(), pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, pappso::MsRunId::setMzFormat(), pappso::MsRunId::setRunId(), pappso::MsRunId::setSampleName(), and pappso::MsRunId::setXmlId().

Referenced by pappso::MsFileAccessor::getMsRunIds().

◆ initialize()

std::size_t pappso::XyMsFileReader::initialize ( )
privatevirtual

Definition at line 41 of file xymsfilereader.cpp.

42 {
43  // Here we just test all the lines of the file to check that they comply with
44  // the xy format.
45 
46  std::size_t line_count = 0;
47 
48  QFile file(m_fileName);
49 
50  if(!file.open(QFile::ReadOnly | QFile::Text))
51  {
52  qDebug() << "Failed to open file" << m_fileName;
53 
54  return 0;
55  }
56 
57  QRegularExpressionMatch regExpMatch;
58 
59  QString line;
60  bool file_reading_failed = false;
61 
62  while(!file.atEnd())
63  {
64  line = file.readLine();
65  ++line_count;
66 
67  // We only read a given number of lines from the file, that would be
68  // enough to check if that file has the right syntax or not.
69  // if(linesRead >= 2000)
70  // return true;
71 
72  if(line.startsWith('#') || line.isEmpty() ||
73  Utils::endOfLineRegExp.match(line).hasMatch())
74  continue;
75 
76  // qDebug() << __FILE__ << __LINE__ << "Current xy format line:" << line;
77 
78  if(Utils::xyMassDataFormatRegExp.match(line).hasMatch())
79  continue;
80  else
81  {
82  file_reading_failed = true;
83  break;
84  }
85  }
86 
87  if(!file_reading_failed && line_count >= 1)
88  m_fileFormat = MzFormat::xy;
89  else
90  m_fileFormat = MzFormat::unknown;
91 
92  qDebug() << "m_fileFormat: " << static_cast<int>(m_fileFormat);
93 
94  return line_count;
95 }

References pappso::Utils::endOfLineRegExp, pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, and pappso::Utils::xyMassDataFormatRegExp.

Referenced by getMsRunIds().

◆ selectMsRunReader()

MsRunReader* pappso::XyMsFileReader::selectMsRunReader ( const QString &  file_name) const

The documentation for this class was generated from the following files:
pappso::Utils::endOfLineRegExp
static QRegularExpression endOfLineRegExp
Regular expression that tracks the end of line in text files.
Definition: utils.h:62
pappso::MsFileReader::m_fileFormat
MzFormat m_fileFormat
Definition: msfilereader.h:18
pappso::MsFileReader::m_fileName
QString m_fileName
Definition: msfilereader.h:17
pappso::MsFileReader::MsFileReader
MsFileReader(const QString &file_name)
Definition: msfilereader.cpp:19
pappso::XyMsFileReader::initialize
virtual std::size_t initialize()
Definition: xymsfilereader.cpp:41
pappso::Utils::xyMassDataFormatRegExp
static QRegularExpression xyMassDataFormatRegExp
Definition: utils.h:53
pappso::Utils::getLexicalOrderedString
static const QString getLexicalOrderedString(unsigned int num)
Definition: utils.cpp:52