OpenMS: MsInspectFile.h Source File

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MsInspectFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38 #include <OpenMS/CONCEPT/Exception.h>
39 #include <OpenMS/CONCEPT/LogStream.h>
40 #include <OpenMS/KERNEL/Feature.h>
41 #include <OpenMS/FORMAT/TextFile.h>
42
43 #include <fstream>
44 #include <vector>
45
46 namespace OpenMS
47 {
60 class OPENMS_DLLAPI MsInspectFile
61 {
62 public:
64 MsInspectFile();
66 virtual ~MsInspectFile();
67
76 template <typename FeatureMapType>
77 void load(const String& filename, FeatureMapType& feature_map)
78 {
79 // load input
80 TextFile input(filename);
81
82 // reset map
83 FeatureMapType fmap;
84 feature_map = fmap;
85
86 bool first_line = true;
87 for (TextFile::ConstIterator it = input.begin(); it != input.end(); ++it)
88 {
89 String line = *it;
90
91 //ignore comment lines
92 if (line.empty() || line[0] == '#') continue;
93
94 //skip leader line
95 if (first_line)
96 {
97 first_line = false;
98 continue;
99 }
100
101 //split lines: scan\ttime\tmz\taccurateMZ\tmass\tintensity\tcharge\tchargeStates\tkl\tbackground\tmedian\tpeaks\tscanFirst\tscanLast\tscanCount\ttotalIntensity\tsumSquaresDist\tdescription
102 std::vector<String> parts;
103 line.split('\t', parts);
104
105 if (parts.size() < 18)
106 {
107 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert line ") + String((it - input.begin()) + 1) + ". Not enough columns (expected 18 or more, got " + String(parts.size()) + ")");
108 }
109
110 //create feature
111 Feature f;
112 Size column_to_convert = 0;
113 try
114 {
115 column_to_convert = 1;
116 f.setRT(parts[1].toDouble());
117 column_to_convert = 2;
118 f.setMZ(parts[2].toDouble());
119 column_to_convert = 5;
120 f.setIntensity(parts[5].toDouble());
121 column_to_convert = 6;
122 f.setCharge(parts[6].toInt());
123 column_to_convert = 8;
124 f.setOverallQuality(parts[8].toDouble());
125
126 column_to_convert = 3;
127 f.setMetaValue("accurateMZ", parts[3]);
128 column_to_convert = 4;
129 f.setMetaValue("mass", parts[4].toDouble());
130 column_to_convert = 7;
131 f.setMetaValue("chargeStates", parts[7].toInt());
132 column_to_convert = 9;
133 f.setMetaValue("background", parts[9].toDouble());
134 column_to_convert = 10;
135 f.setMetaValue("median", parts[10].toDouble());
136 column_to_convert = 11;
137 f.setMetaValue("peaks", parts[11].toInt());
138 column_to_convert = 12;
139 f.setMetaValue("scanFirst", parts[12].toInt());
140 column_to_convert = 13;
141 f.setMetaValue("scanLast", parts[13].toInt());
142 column_to_convert = 14;
143 f.setMetaValue("scanCount", parts[14].toInt());
144 column_to_convert = 15;
145 f.setMetaValue("totalIntensity", parts[15].toDouble());
146 column_to_convert = 16;
147 f.setMetaValue("sumSquaresDist", parts[16].toDouble());
148 }
149 catch ( Exception::BaseException& )
150 {
151 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert value in column ") + String(column_to_convert + 1) + " into a number (line '" + String((it - input.begin()) + 1) + ")");
152 }
153 f.setMetaValue("description", parts[17]);
154 feature_map.push_back(f);
155 }
156
157 }
158
166 template <typename SpectrumType>
167 void store(const String& filename, const SpectrumType& spectrum) const
168 {
169 std::cerr << "Store() for MsInspectFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
170 throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
171 }
172
173 };
174 } // namespace OpenMS
175
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::Exception::NotImplemented
Not implemented exception.
Definition: Exception.h:436
OpenMS::BaseFeature::setCharge
void setCharge(const ChargeType &ch)
Set charge state.
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
LogStream.h
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MsInspectFile::load
void load(const String &filename, FeatureMapType &feature_map)
Loads a MsInspect file into a featureXML.
Definition: MsInspectFile.h:77
Exception.h
OpenMS::TextFile::end
ConstIterator end() const
Gives access to the underlying text buffer.
Feature.h
String.h
OpenMS::Feature::setOverallQuality
void setOverallQuality(QualityType q)
Set the overall quality.
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::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
TextFile.h
OpenMS::MsInspectFile::store
void store(const String &filename, const SpectrumType &spectrum) const
Stores a featureXML as a MsInspect file.
Definition: MsInspectFile.h:167
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MsInspectFile
File adapter for MsInspect files.
Definition: MsInspectFile.h:60
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46