OpenMS  2.6.0
SpecArrayFile.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
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 SpecArrayFile
61  {
62 public:
64  SpecArrayFile();
66  virtual ~SpecArrayFile();
67 
76  template <typename FeatureMapType>
77  void load(const String& filename, FeatureMapType& feature_map)
78  {
79  // load input
80  TextFile input(filename, false);
81 
82  // reset map
83  FeatureMapType fmap;
84  feature_map = fmap;
85 
86  TextFile::ConstIterator it = input.begin();
87  if (it == input.end()) return; // no data to load
88 
89  // skip header line
90  ++it;
91  // process content
92  for (; it != input.end(); ++it)
93  {
94  String line = *it;
95 
96  std::vector<String> parts;
97  line.split('\t', parts);
98 
99  if (parts.size() < 5)
100  {
101  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert line") + String((it - input.begin()) + 1) + "not enough columns (expected 5 or more, got " + String(parts.size()) + ")");
102  }
103 
104  Feature f;
105  try
106  {
107  f.setMZ(parts[0].toDouble());
108  f.setRT(parts[1].toDouble() * 60.0);
109  f.setMetaValue("s/n", parts[2].toDouble());
110  f.setCharge(parts[3].toInt());
111  f.setIntensity(parts[4].toDouble());
112  }
113  catch ( Exception::BaseException& )
114  {
115  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert value into a number (line '") + String((it - input.begin()) + 1) + ")");
116  }
117  feature_map.push_back(f);
118  }
119  }
120 
128  template <typename SpectrumType>
129  void store(const String& filename, const SpectrumType& spectrum) const
130  {
131  std::cerr << "Store() for SpecArrayFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
132  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
133  }
134 
135  };
136 } // namespace OpenMS
137 
LogStream.h
OpenMS::SpecArrayFile::load
void load(const String &filename, FeatureMapType &feature_map)
Loads a SpecArray file into a featureXML.
Definition: SpecArrayFile.h:77
OpenMS::TextFile::end
ConstIterator end() const
Gives access to the underlying text buffer.
TextFile.h
OpenMS::String
A more convenient string class.
Definition: String.h:59
Feature.h
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Exception.h
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::SpecArrayFile
File adapter for SpecArray (.pepList) files.
Definition: SpecArrayFile.h:60
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
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::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::Exception::NotImplemented
Not implemented exception.
Definition: Exception.h:436
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
String.h
OpenMS::SpecArrayFile::store
void store(const String &filename, const SpectrumType &spectrum) const
Stores a featureXML as a SpecArray file.
Definition: SpecArrayFile.h:129
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
OpenMS::BaseFeature::setCharge
void setCharge(const ChargeType &ch)
Set charge state.