94 template <
typename MapType>
97 startProgress(0, 0,
"loading DTA2D file");
100 std::ifstream is(filename.c_str());
113 std::vector<String> strings(3);
126 bool time_in_minutes =
false;
135 Size line_number = 0;
137 while (getline(is, line,
'\n'))
142 if (line.empty())
continue;
158 line.
split(delimiter, strings);
163 bool int_set =
false;
166 for (
Size i = 0; i < 3; ++i)
168 if (strings[i] ==
"RT" || strings[i] ==
"RETENTION_TIME" || strings[i] ==
"MASS-TO-CHARGE" || strings[i] ==
"IT" || strings[i] ==
"INTENSITY")
170 std::cerr <<
"Warning: This file contains the deprecated keyword '" << strings[i] <<
"'." <<
"\n";
171 std::cerr <<
" Please use only the new keywords SEC/MIN, MZ, INT." <<
"\n";
173 if ((strings[i] ==
"SEC" || strings[i] ==
"RT" || strings[i] ==
"RETENTION_TIME") && rt_set ==
false)
178 else if ((strings[i] ==
"MIN") && rt_set ==
false)
182 time_in_minutes =
true;
184 else if ((strings[i] ==
"MZ" || strings[i] ==
"MASS-TO-CHARGE") && mz_set ==
false)
189 else if ((strings[i] ==
"INT" || strings[i] ==
"IT" || strings[i] ==
"INTENSITY") && int_set ==
false)
196 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Misformatted header line!", filename);
204 line.
split(delimiter, strings);
205 if (strings.size() != 3)
207 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, std::string(
"Bad data line (" +
String(line_number) +
"): \"") + line +
"\" (got " +
String(strings.size()) +
", expected 3 entries)", filename);
210 p.
setMZ(strings[mz_dim].toDouble());
211 rt = (strings[rt_dim].toDouble()) * (time_in_minutes ? 60.0 : 1.0);
216 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, std::string(
"Bad data line (" +
String(line_number) +
"): \"") + line +
"\"", filename);
220 if (fabs(rt - spec.
getRT()) > 0.0001)
268 template <
typename MapType>
271 startProgress(0, map.
size(),
"storing DTA2D file");
273 std::ofstream os(filename.c_str());
280 os <<
"#SEC\tMZ\tINT\n";
287 setProgress(count++);
307 template <
typename MapType>
310 startProgress(0, map.
size(),
"storing DTA2D file");
312 std::ofstream os(filename.c_str());
319 os <<
"#SEC\tMZ\tINT\n";
bool encloses(const PositionType &position) const
Checks whether this range contains a certain point.
Definition: DRange.h:174
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
bool hasRTRange() const
returns true if an RT range has been set
The representation of a chromatogram.
Definition: MSChromatogram.h:54
PeakFileOptions options_
Definition: DTA2DFile.h:67
Size size() const
Definition: MSExperiment.h:127
DTA2D File adapter.
Definition: DTA2DFile.h:63
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
const MSChromatogram getTIC(float rt_bin_size=0) const
Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT se...
bool hasMZRange() const
returns true if an MZ range has been set
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Iterator end()
Definition: MSExperiment.h:167
Iterator begin()
Definition: MSExperiment.h:157
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool hasIntensityRange() const
returns true if an intensity range has been set
void load(const String &filename, MapType &map)
Loads a map from a DTA2D file.
Definition: DTA2DFile.h:95
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
File not found exception.
Definition: Exception.h:523
void storeTIC(const String &filename, const MapType &map) const
Stores the TIC of a map in a DTA2D file.
Definition: DTA2DFile.h:308
const DRange< 1 > & getMZRange() const
returns the MZ range
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
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...
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
Unable to create file exception.
Definition: Exception.h:636
void store(const String &filename, const MapType &map) const
Stores a map in a DTA2D file.
Definition: DTA2DFile.h:269
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void clear(bool clear_meta_data)
Clears all data and meta data.
IntensityType getIntensity() const
Definition: Peak1D.h:110
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void setLoadedFilePath(const String &file_name)
set the file_name_ according to absolute path of the file loaded from preferably done whilst loading ...
void reset()
Resets all internal values.
bool has(Byte byte) const
true if String contains the byte, false otherwise
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
const DRange< 1 > & getRTRange() const
returns the RT range
Parse Error exception.
Definition: Exception.h:622
const PrecisionWrapper< FloatingPointType > precisionWrapper(const FloatingPointType rhs)
Wrapper function that sets the appropriate precision for output temporarily. The original precision i...
Definition: PrecisionWrapper.h:95
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Exception base class.
Definition: Exception.h:89
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
A more convenient string class.
Definition: String.h:58
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
void setLoadedFileType(const String &file_name)
set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably do...
const DRange< 1 > & getIntensityRange() const
returns the intensity range
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46