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OpenMS
2.6.0
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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";
const DRange< 1 > & getIntensityRange() const
returns the intensity range
void reset()
Resets all internal values.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
const DRange< 1 > & getRTRange() const
returns the RT range
A more convenient string class.
Definition: String.h:59
Iterator begin()
Definition: MSExperiment.h:157
void store(const String &filename, const MapType &map) const
Stores a map in a DTA2D file.
Definition: DTA2DFile.h:269
File not found exception.
Definition: Exception.h:523
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
bool encloses(const PositionType &position) const
Checks whether this range contains a certain point.
Definition: DRange.h:174
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool hasMZRange() const
returns true if an MZ range has been set
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
const DRange< 1 > & getMZRange() const
returns the MZ range
DTA2D File adapter.
Definition: DTA2DFile.h:63
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
Size size() const
Definition: MSExperiment.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
void setLoadedFilePath(const String &file_name)
set the file_name_ according to absolute path of the file loaded from preferably done whilst loading
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
void load(const String &filename, MapType &map)
Loads a map from a DTA2D file.
Definition: DTA2DFile.h:95
bool has(Byte byte) const
true if String contains the byte, false otherwise
Unable to create file exception.
Definition: Exception.h:636
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
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
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...
Exception base class.
Definition: Exception.h:89
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
void clear(bool clear_meta_data)
Clears all data and meta data.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Parse Error exception.
Definition: Exception.h:622
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...
bool hasRTRange() const
returns true if an RT range has been set
Iterator end()
Definition: MSExperiment.h:167
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
The representation of a chromatogram.
Definition: MSChromatogram.h:54
bool hasIntensityRange() const
returns true if an intensity range has been set
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
void setLoadedFileType(const String &file_name)
set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably do...
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void setRT(double rt)
Sets the absolute retention time (in seconds)
IntensityType getIntensity() const
Definition: Peak1D.h:110
PeakFileOptions options_
Definition: DTA2DFile.h:67
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
void storeTIC(const String &filename, const MapType &map) const
Stores the TIC of a map in a DTA2D file.
Definition: DTA2DFile.h:308