| OpenMS 2.5.0

MS2File.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38 #include <OpenMS/CONCEPT/Exception.h>
39 #include <OpenMS/SYSTEM/File.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/METADATA/DocumentIdentifier.h>
42
43 #include <vector>
44 #include <fstream>
45
46 namespace OpenMS
47 {
64 class OPENMS_DLLAPI MS2File :
65 public ProgressLogger
66 {
67 public:
68
70 MS2File();
71
73 virtual ~MS2File();
74
75 template <typename MapType>
76 void load(const String & filename, MapType & exp)
77 {
78 //startProgress(0,0,"loading DTA2D file");
79
80 if (!File::exists(filename))
81 {
82 throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
83 }
84 if (!File::readable(filename))
85 {
86 throw Exception::FileNotReadable(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
87 }
88
89 exp.reset();
90
91 //set DocumentIdentifier
92 exp.setLoadedFileType(filename);
93 exp.setLoadedFilePath(filename);
94
95 std::ifstream in(filename.c_str());
96
97 UInt spectrum_number = 0;
98 typename MapType::SpectrumType spec;
99 typename MapType::SpectrumType::PeakType p;
100
101 String line;
102 bool first_spec(true);
103
104 // line number counter
105 Size line_number = 0;
106
107 while (getline(in, line, '\n'))
108 {
109 ++line_number;
110
111 line.trim();
112 if (line.empty()) continue;
113
114 // header
115 if (line[0] == 'H')
116 {
117 continue;
118 }
119
120 // scan
121 if (line[0] == 'S')
122 {
123 if (!first_spec)
124 {
125 spec.setMSLevel(2);
126 spec.setNativeID(String("index=") + (spectrum_number++));
127 exp.addSpectrum(spec);
128 }
129 else
130 {
131 first_spec = false;
132 }
133 spec.clear(true);
134 line.simplify();
135 std::vector<String> split;
136 line.split(' ', split);
137 if (split.size() != 4)
138 {
139 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "line (" + String(line_number) + ") '" + line + "' should contain four values, got " + String(split.size()) + "!", "");
140 }
141 spec.getPrecursors().resize(1);
142 spec.getPrecursors()[0].setMZ(split[3].toDouble());
143 continue;
144 }
145
146 // charge-independent analysis
147 if (line[0] == 'I')
148 {
149 continue;
150 }
151
152 // charge specification
153 if (line[0] == 'Z')
154 {
155 continue;
156 }
157
158 // charge-dependent analysis
159 if (line[0] == 'D')
160 {
161 continue;
162 }
163
164 // yet another peak, hopefully
165 line.simplify();
166 std::vector<String> split;
167 line.split(' ', split);
168 if (split.size() != 2)
169 {
170 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "line (" + String(line_number) + ") '" + line + "' should contain two values, got " + String(split.size()) + "!", "");
171 }
172
173 try
174 {
175 p.setPosition(split[0].toDouble());
176 p.setIntensity(split[1].toFloat());
177 }
178 catch ( Exception::ConversionError& )
179 {
180 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "ConversionError: line (" + String(line_number) + ") '" + line + "' does not contain two numbers!", "");
181 }
182 spec.push_back(p);
183 }
184
185 if (!first_spec)
186 {
187 spec.setMSLevel(2);
188 spec.setNativeID(String("index=") + (spectrum_number++));
189 exp.addSpectrum(spec);
190 }
191 }
192
193 /*
194 template <typename MapType> void store(const String& filename, MapType& map)
195 {
196
197 }
198 */
199
200 protected:
201
202 };
203
204 } // namespace OpenMS
205
OpenMS::Exception::FileNotReadable
File not readable exception.
Definition: Exception.h:537
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSSpectrum::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
DocumentIdentifier.h
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::DocumentIdentifier::setLoadedFileType
void setLoadedFileType(const String &file_name)
set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably do...
OpenMS::Peak1D::setIntensity
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Exception.h
OpenMS::MS2File
MS2 input file adapter.
Definition: MS2File.h:64
OpenMS::Peak1D::setPosition
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:151
OpenMS::Exception::FileNotFound
File not found exception.
Definition: Exception.h:523
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::DocumentIdentifier::setLoadedFilePath
void setLoadedFilePath(const String &file_name)
set the file_name_ according to absolute path of the file loaded from preferably done whilst loading ...
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::MS2File::load
void load(const String &filename, MapType &exp)
Definition: MS2File.h:76
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
String.h
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MSExperiment::reset
void reset()
Resets all internal values.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:362
OpenMS::MSSpectrum::setMSLevel
void setMSLevel(UInt ms_level)
Sets the MS level.
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.
File.h
OpenMS::SpectrumSettings::setNativeID
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
OpenMS::File::readable
static bool readable(const String &file)
Return true if the file exists and is readable.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::String::simplify
String & simplify()
merges subsequent whitespaces to one blank character
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...