OpenMS  3.0.0
MascotGenericFile.h
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34 
35 #pragma once
36 
42 #include <OpenMS/SYSTEM/File.h>
43 
44 #include <vector>
45 #include <fstream>
46 
47 #ifdef _OPENMP
48 #include <omp.h>
49 #endif
50 
51 namespace OpenMS
52 {
62  class OPENMS_DLLAPI MascotGenericFile :
63  public ProgressLogger,
64  public DefaultParamHandler
65  {
66 public:
67 
70 
72  ~MascotGenericFile() override;
73 
75  void updateMembers_() override;
76 
78  void store(const String& filename, const PeakMap& experiment,
79  bool compact = false);
80 
82  void store(std::ostream& os, const String& filename,
83  const PeakMap& experiment, bool compact = false);
84 
92  template <typename MapType>
93  void load(const String& filename, MapType& exp)
94  {
95  if (!File::exists(filename))
96  {
97  throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
98  }
99 
100  exp.reset();
101 
102  std::ifstream is(filename.c_str());
103  // get size of file
104  is.seekg(0, std::ios::end);
105  startProgress(0, is.tellg(), "loading MGF");
106  is.seekg(0, std::ios::beg);
107 
108  UInt spectrum_number(0);
109  Size line_number(0); // carry line number for error messages within getNextSpectrum()
110 
111  typename MapType::SpectrumType spectrum;
112  spectrum.setMSLevel(2);
113  spectrum.getPrecursors().resize(1);
114  spectrum.setType(SpectrumSettings::SpectrumType::CENTROID); // MGF is always centroided, by definition
115  while (getNextSpectrum_(is, spectrum, line_number, spectrum_number))
116  {
117  exp.addSpectrum(spectrum);
118  setProgress(is.tellg());
119  ++spectrum_number;
120  } // next spectrum
121 
122  endProgress();
123  }
124 
132  std::pair<String, String> getHTTPPeakListEnclosure(const String& filename) const;
133 
135  void writeSpectrum(std::ostream& os, const PeakSpectrum& spec, const String& filename, const String& native_id_type_accession);
136 
137 protected:
138 
141 
143  std::map<String, String> mod_group_map_;
144 
146  void writeParameterHeader_(const String& name, std::ostream& os);
147 
149  void writeModifications_(const std::vector<String>& mods, std::ostream& os,
150  bool variable_mods = false);
151 
153  void writeHeader_(std::ostream& os);
154 
156  void writeMSExperiment_(std::ostream& os, const String& filename, const PeakMap& experiment);
157 
159  template <typename SpectrumType>
160  bool getNextSpectrum_(std::ifstream& is, SpectrumType& spectrum, Size& line_number, const Size& spectrum_number)
161  {
162  spectrum.resize(0);
163  spectrum.setNativeID(String("index=") + (spectrum_number));
164 
165  if (spectrum.metaValueExists("TITLE"))
166  {
167  spectrum.removeMetaValue("TITLE");
168  }
169  typename SpectrumType::PeakType p;
170 
171  String line;
172  // seek to next peak list block
173  while (getline(is, line, '\n'))
174  {
175  ++line_number;
176 
177  line.trim(); // remove whitespaces, line-endings etc
178 
179  // found peak list block?
180  if (line == "BEGIN IONS")
181  {
182  while (getline(is, line, '\n'))
183  {
184  ++line_number;
185  line.trim(); // remove whitespaces, line-endings etc
186 
187  if (line.empty()) continue;
188 
189  if (isdigit(line[0])) // actual data .. this comes first, since its the most common case
190  {
191  std::vector<String> split;
192  do
193  {
194  if (line.empty())
195  {
196  continue;
197  }
198 
199  line.simplify(); // merge double spaces (explicitly allowed by MGF), to prevent empty split() chunks and subsequent parse error
200  line.substitute('\t', ' '); // also accept Tab (strictly, only space(s) are allowed)
201  if (line.split(' ', split, false))
202  {
203  try
204  {
205  p.setPosition(split[0].toDouble());
206  p.setIntensity(split[1].toDouble());
207  }
208  catch (Exception::ConversionError& /*e*/)
209  {
210  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The content '" + line + "' at line #" + String(line_number) + " could not be converted to a number! Expected two (m/z int) or three (m/z int charge) numbers separated by whitespace (space or tab).", "");
211  }
212  spectrum.push_back(p);
213  }
214  else
215  {
216  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The content '" + line + "' at line #" + String(line_number) + " does not contain m/z and intensity values separated by whitespace (space or tab)!", "");
217  }
218  }
219  while (getline(is, line, '\n') && ++line_number && line.trim() != "END IONS"); // line.trim() is important here!
220 
221  if (line == "END IONS")
222  {
223  return true; // found end of spectrum
224  }
225  else
226  {
227  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, R"(Reached end of file. Found "BEGIN IONS" but not the corresponding "END IONS"!)", "");
228  }
229  }
230  else if (line.hasPrefix("PEPMASS")) // parse precursor position
231  {
232  String tmp = line.substr(8); // copy since we might need the original line for error reporting later
233  tmp.substitute('\t', ' ');
234  std::vector<String> split;
235  tmp.split(' ', split);
236  if (split.size() == 1)
237  {
238  spectrum.getPrecursors()[0].setMZ(split[0].trim().toDouble());
239  }
240  else if (split.size() == 2)
241  {
242  spectrum.getPrecursors()[0].setMZ(split[0].trim().toDouble());
243  spectrum.getPrecursors()[0].setIntensity(split[1].trim().toDouble());
244  }
245  else
246  {
247  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Cannot parse PEPMASS in '" + line + "' at line #" + String(line_number) + " (expected 1 or 2 entries, but " + String(split.size()) + " were present)!", "");
248  }
249  }
250  else if (line.hasPrefix("CHARGE"))
251  {
252  String tmp = line.substr(7);
253  tmp.remove('+');
254  spectrum.getPrecursors()[0].setCharge(tmp.toInt());
255  }
256  else if (line.hasPrefix("RTINSECONDS"))
257  {
258  String tmp = line.substr(12);
259  spectrum.setRT(tmp.toDouble());
260  }
261  else if (line.hasPrefix("TITLE"))
262  {
263  // test if we have a line like "TITLE= Cmpd 1, +MSn(595.3), 10.9 min"
264  if (line.hasSubstring("min"))
265  {
266  try
267  {
268  std::vector<String> split;
269  line.split(',', split);
270  if (!split.empty())
271  {
272  for (Size i = 0; i != split.size(); ++i)
273  {
274  if (split[i].hasSubstring("min"))
275  {
276  std::vector<String> split2;
277  split[i].trim().split(' ', split2);
278  if (!split2.empty())
279  {
280  spectrum.setRT(split2[0].trim().toDouble() * 60.0);
281  }
282  }
283  }
284  }
285  }
286  catch (Exception::BaseException& /*e*/)
287  {
288  // just do nothing and write the whole title to spec
289  std::vector<String> split;
290  if (line.split('=', split))
291  {
292  if (!split[1].empty()) spectrum.setMetaValue("TITLE", split[1]);
293  }
294  }
295  }
296  else // just write the title as metainfo to the spectrum and add native ID to make the titles unique
297  {
298  Size firstEqual = line.find('=', 4);
299  if (firstEqual != std::string::npos)
300  {
301  if (String(spectrum.getMetaValue("TITLE")).hasSubstring(spectrum.getNativeID()))
302  {
303  spectrum.setMetaValue("TITLE", line.substr(firstEqual + 1));
304  }
305  else
306  {
307  spectrum.setMetaValue("TITLE", line.substr(firstEqual + 1) + "_" + spectrum.getNativeID());
308  }
309  }
310  }
311  }
312  }
313  }
314  }
315 
316  return false; // found end of file
317  }
318 
319  };
320 
321 } // namespace OpenMS
OpenMS::SpectrumLookup::findByRT
Size findByRT(double rt) const
Look up spectrum by retention time (RT).
DefaultParamHandler.h
OpenMS::StringUtils::split
static bool split(const String &this_s, const char splitter, std::vector< String > &substrings, bool quote_protect)
Definition: StringUtilsSimple.h:360
OpenMS::MascotRemoteQuery
Class which handles the communication between OpenMS and the Mascot server.
Definition: MascotRemoteQuery.h:56
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::StringUtils::hasSubstring
static bool hasSubstring(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:137
FileHandler.h
OpenMS::MascotXMLFile
Used to load Mascot XML files.
Definition: MascotXMLFile.h:57
FileTypes.h
OpenMS::MzDataFile
File adapter for MzData files.
Definition: MzDataFile.h:53
Size
MascotRemoteQuery.h
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::MascotRemoteQuery::setQuerySpectra
void setQuerySpectra(const String &exp)
sets the query spectra, given in MGF file format
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::MSExperiment::reset
void reset()
Clear all internal data (spectra, ranges, metadata)
MascotXMLFile.h
OpenMS::File::basename
static String basename(const String &file)
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::String::toDouble
double toDouble() const
Conversion to double.
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::PepXMLFileMascot::load
void load(const String &filename, std::map< String, std::vector< AASequence > > &peptides)
Loads peptide sequences with modifications out of a PepXML file.
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::MascotInfile
Mascot input file adapter.
Definition: MascotInfile.h:58
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
OpenMS::Exception::FileNotFound
File not found exception.
Definition: Exception.h:509
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
Int
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
SearchEngineBase.h
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:354
OpenMS::MascotInfile::setInstrument
void setInstrument(const String &instrument)
sets the instrument type (Default: Default). Possible instruments: ESI-QUAD-TOF, MALDI-TOF-PSD,...
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::MascotInfile::setTaxonomy
void setTaxonomy(const String &taxonomy)
sets the taxonomy (default: All entries). See <mascot path>/config/taxonomy for possible settings.
OpenMS::PepXMLFileMascot
Used to load Mascot PepXML files.
Definition: PepXMLFileMascot.h:54
OpenMS::SpectrumSettings::setType
void setType(SpectrumType type)
sets the spectrum type
OpenMS::MzDataFile::load
void load(const String &filename, MapType &map)
Loads a map from a MzData file.
OpenMS::Peak1D::setIntensity
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OpenMS::FileHandler::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
SpectrumSettings.h
OpenMS::MascotGenericFile::mod_group_map_
std::map< String, String > mod_group_map_
mapping of modifications with specificity groups, that have to be treated specially (e....
Definition: MascotGenericFile.h:143
OpenMS::MascotInfile::setModifications
void setModifications(const std::vector< String > &mods)
sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible setting...
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::ParamValue::toBool
bool toBool() const
Conversion to bool.
OpenMS::String::hasPrefix
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::MascotRemoteQuery::getSearchIdentifier
String getSearchIdentifier() const
returns the search number
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::String::simplify
String & simplify()
merges subsequent whitespaces to one blank character
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::File::writable
static bool writable(const String &file)
Return true if the file is writable.
OpenMS::MascotInfile::setMassType
void setMassType(const String &mass_type)
sets the used mass type "Monoisotopic" or "Average" (default: Monoisotopic)
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::DateTime::get
void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the date and the time.
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::MetaInfoInterface::removeMetaValue
void removeMetaValue(const String &name)
Removes the DataValue corresponding to name if it exists.
OpenMS::StringUtils::remove
static String & remove(String &this_s, char what)
Definition: StringUtilsSimple.h:595
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::MascotXMLFile::load
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, const SpectrumMetaDataLookup &lookup)
Loads data from a Mascot XML file.
OpenMS::ProteinIdentification::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
ProgressLogger.h
OpenMS::ProteinIdentification::getHits
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::SpectrumLookup
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
OpenMS::MascotInfile::setVariableModifications
void setVariableModifications(const std::vector< String > &mods)
sets the fixed modifications (default: none). See <mascot path>/config/mod_file for possible setting...
QProcess
OpenMS::MascotInfile::setDB
void setDB(const String &db)
sets the DB to use (default: MSDB). See <mascot path>/config/mascot.dat in "Databases" section for po...
OpenMS::FileHandler::loadExperiment
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
OpenMS::MascotRemoteQuery::getErrorMessage
const String & getErrorMessage() const
returns the error message, if hasError can be used to check whether an error has occurred
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::SpectrumLookup::readSpectra
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
OpenMS::MascotRemoteQuery::setExportDecoys
void setExportDecoys(const bool b)
request export of decoy summary and decoys (note: internal decoy search must be enabled in the MGF fi...
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::MascotInfile::setCharges
void setCharges(std::vector< Int > &charges)
sets the charges (default: 1+, 2+ and 3+)
MascotInfile.h
OpenMS::MascotRemoteQuery::hasError
bool hasError() const
predicate which returns true if an error occurred during the query
OpenMS::MascotInfile::setHits
void setHits(const String &hits)
sets the number of hits to report back (default: 20)
OpenMS::MascotInfile::setPeakMassTolerance
void setPeakMassTolerance(float ion_mass_tolerance)
sets the peak mass tolerance in Da (default: 1.0)
OpenMS::Peak1D::setPosition
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:149
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::Param::exists
bool exists(const std::string &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::MSSpectrum::setMSLevel
void setMSLevel(UInt ms_level)
Sets the MS level.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::FileTypes::MASCOTXML
Mascot XML file format for peptide identifications (.xml)
Definition: FileTypes.h:83
MascotGenericFile.h
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:62
OpenMS::MascotInfile::setCleavage
void setCleavage(const String &cleavage)
sets the enzyme used for cleavage (default: Trypsin). See <mascot path>/config/enzymes for possible ...
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::MSExperiment::resize
void resize(Size s)
Definition: MSExperiment.h:125
OpenMS::MascotInfile::setMissedCleavages
void setMissedCleavages(UInt missed_cleavages)
sets the number of allowed missed cleavages (default: 1)
OpenMS::SearchEngineBase
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:54
OpenMS::SpectrumSettings::getNativeID
const String & getNativeID() const
returns the native identifier for the spectrum, used by the acquisition software.
OpenMS::ProteinIdentification::insertHit
void insertHit(const ProteinHit &input)
Appends a protein hit.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::Constants::h
const double h
Definition: Constants.h:162
OpenMS::MascotXMLFile::initializeLookup
static void initializeLookup(SpectrumMetaDataLookup &lookup, const PeakMap &experiment, const String &scan_regex="")
Initializes a helper object for looking up spectrum meta data (RT, m/z)
OpenMS::MascotInfile::setPrecursorMassTolerance
void setPrecursorMassTolerance(float precursor_mass_tolerance)
sets the precursor mass tolerance in Da (default: 2.0)
MSExperiment.h
OpenMS::SpectrumMetaDataLookup
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
OpenMS::StringUtils::toDouble
static double toDouble(const String &this_s)
Definition: StringUtils.h:216
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::File::absolutePath
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::FileTypes::MGF
Mascot Generic Format (.mgf)
Definition: FileTypes.h:66
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::MascotGenericFile::getNextSpectrum_
bool getNextSpectrum_(std::ifstream &is, SpectrumType &spectrum, Size &line_number, const Size &spectrum_number)
reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a MGF file
Definition: MascotGenericFile.h:160
OpenMS::MSExperiment::getSpectra
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
PepXMLFileMascot.h
OpenMS::MascotRemoteQuery::getMascotXMLResponse
const QByteArray & getMascotXMLResponse() const
returns the Mascot XML response which contains the identifications
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
String.h
OpenMS::FileHandler::stripExtension
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
MzDataFile.h
OpenMS::StringUtils::trim
static String & trim(String &this_s)
Definition: StringUtilsSimple.h:229
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::String::remove
String & remove(char what)
Remove all occurrences of the character what.
OpenMS::MascotInfile::store
void store(const String &filename, const PeakSpectrum &spec, double mz, double retention_time, String search_title)
stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
IDFilter.h
OpenMS::MascotGenericFile::store_compact_
bool store_compact_
use a compact format for storing (no zero-intensity peaks, limited number of decimal places)?
Definition: MascotGenericFile.h:140
OpenMS::MascotRemoteQuery::getMascotXMLDecoyResponse
const QByteArray & getMascotXMLDecoyResponse() const
returns the Mascot XML response which contains the decoy identifications (note: setExportDecoys must ...
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::ProteinIdentification::setIdentifier
void setIdentifier(const String &id)
Sets the identifier.
OpenMS::Exception::ElementNotFound
Element could not be found exception.
Definition: Exception.h:674
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::MSSpectrum::setRT
void setRT(double rt)
Sets the absolute retention time (in seconds)
OpenMS::Param::remove
void remove(const std::string &key)
Remove the entry key or a section key (when suffix is ':')
OpenMS::DefaultParamHandler::writeParametersToMetaValues
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
Writes all parameters to meta values.
StandardTypes.h
OpenMS::String::toInt
Int toInt() const
Conversion to int.
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:58
File.h
OpenMS::MascotInfile::setBoundary
void setBoundary(const String &boundary)
sets the boundary used for the MIME format. By default a 22 character random string is used
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::MascotGenericFile::load
void load(const String &filename, MapType &exp)
loads a Mascot Generic File into a PeakMap
Definition: MascotGenericFile.h:93
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::SpectrumSettings::setNativeID
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55
StringListUtils.h