74 void updateMembers_()
override;
78 bool compact =
false);
81 void store(std::ostream& os,
const String& filename,
82 const PeakMap& experiment,
bool compact =
false);
91 template <
typename MapType>
101 std::ifstream is(filename.c_str());
103 is.seekg(0, std::ios::end);
104 startProgress(0, is.tellg(),
"loading MGF");
105 is.seekg(0, std::ios::beg);
107 UInt spectrum_number(0);
113 while (getNextSpectrum_(is, spectrum, line_number, spectrum_number))
116 setProgress(is.tellg());
131 std::pair<String, String> getHTTPPeakListEnclosure(
const String& filename)
const;
142 void writeParameterHeader_(
const String& name, std::ostream& os);
145 void writeModifications_(
const std::vector<String>& mods, std::ostream& os,
146 bool variable_mods =
false);
149 void writeHeader_(std::ostream& os);
152 void writeSpectrum_(std::ostream& os,
const PeakSpectrum& spec,
const String& filename,
const String& native_id_type_accession);
155 void writeMSExperiment_(std::ostream& os,
const String& filename,
const PeakMap& experiment);
158 template <
typename SpectrumType>
172 while (getline(is, line,
'\n'))
179 if (line ==
"BEGIN IONS")
181 while (getline(is, line,
'\n'))
186 if (line.empty())
continue;
188 if (isdigit(line[0]))
190 std::vector<String> split;
200 if (line.
split(
' ', split,
false))
209 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 spectrum.push_back(p);
215 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)!",
"");
218 while (getline(is, line,
'\n') && ++line_number && line.
trim() !=
"END IONS");
220 if (line ==
"END IONS")
226 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Reached end of file. Found \"BEGIN IONS\" but not the corresponding \"END IONS\"!",
"");
233 std::vector<String> split;
234 tmp.
split(
' ', split);
235 if (split.size() == 1)
237 spectrum.
getPrecursors()[0].setMZ(split[0].trim().toDouble());
239 else if (split.size() == 2)
241 spectrum.
getPrecursors()[0].setMZ(split[0].trim().toDouble());
242 spectrum.
getPrecursors()[0].setIntensity(split[1].trim().toDouble());
246 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)!",
"");
267 std::vector<String> split;
268 line.
split(
',', split);
271 for (
Size i = 0; i != split.size(); ++i)
273 if (split[i].hasSubstring(
"min"))
275 std::vector<String> split2;
276 split[i].trim().split(
' ', split2);
279 spectrum.
setRT(split2[0].trim().toDouble() * 60.0);
288 std::vector<String> split;
289 if (line.
split(
'=', split))
291 if (split[1] !=
"") spectrum.
setMetaValue(
"TITLE", split[1]);
297 std::vector<String> split;
298 line.
split(
'=', split);
299 if (split.size() == 2)
301 if (split[1] !=
"") spectrum.
setMetaValue(
"TITLE", split[1]);
String & simplify()
merges subsequent whitespaces to one blank character
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:159
A more convenient string class.
Definition: String.h:57
void reset()
Resets all internal values.
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
File not found exception.
Definition: Exception.h:523
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
String & remove(char what)
Remove all occurrences of the character what.
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...
std::map< String, String > mod_group_map_
mapping of modifications with specificity groups, that have to be treated specially (e...
Definition: MascotGenericFile.h:139
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
static bool exists(const String &file)
Method used to test if a file exists.
Int toInt() const
Conversion to int.
double toDouble() const
Conversion to double.
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:149
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void setMSLevel(UInt ms_level)
Sets the MS level.
Exception base class.
Definition: Exception.h:89
Invalid conversion exception.
Definition: Exception.h:362
void setRT(double rt)
Sets the absolute retention time (in seconds)
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
void load(const String &filename, MapType &exp)
loads a Mascot Generic File into a PeakMap
Definition: MascotGenericFile.h:92
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
bool store_compact_
use a compact format for storing (no zero-intensity peaks, limited number of decimal places)...
Definition: MascotGenericFile.h:136
Parse Error exception.
Definition: Exception.h:622