OpenMS  3.0.0
SpecArrayFile.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 #pragma once
36 
39 #include <OpenMS/KERNEL/Feature.h>
40 #include <OpenMS/FORMAT/TextFile.h>
41 
42 #include <fstream>
43 #include <vector>
44 
45 namespace OpenMS
46 {
59  class OPENMS_DLLAPI SpecArrayFile
60  {
61 public:
63  SpecArrayFile();
65  virtual ~SpecArrayFile();
66 
75  template <typename FeatureMapType>
76  void load(const String& filename, FeatureMapType& feature_map)
77  {
78  // load input
79  TextFile input(filename, false);
80 
81  // reset map
82  FeatureMapType fmap;
83  feature_map = fmap;
84 
85  TextFile::ConstIterator it = input.begin();
86  if (it == input.end()) return; // no data to load
87 
88  // skip header line
89  ++it;
90  // process content
91  for (; it != input.end(); ++it)
92  {
93  String line = *it;
94 
95  std::vector<String> parts;
96  line.split('\t', parts);
97 
98  if (parts.size() < 5)
99  {
100  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()) + ")");
101  }
102 
103  Feature f;
104  try
105  {
106  f.setMZ(parts[0].toDouble());
107  f.setRT(parts[1].toDouble() * 60.0);
108  f.setMetaValue("s/n", parts[2].toDouble());
109  f.setCharge(parts[3].toInt());
110  f.setIntensity(parts[4].toDouble());
111  }
112  catch ( Exception::BaseException& )
113  {
114  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", String("Failed to convert value into a number (line '") + String((it - input.begin()) + 1) + ")");
115  }
116  feature_map.push_back(f);
117  }
118  }
119 
127  template <typename SpectrumType>
128  void store(const String& filename, const SpectrumType& spectrum) const
129  {
130  std::cerr << "Store() for SpecArrayFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
131  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
132  }
133 
134  };
135 } // namespace OpenMS
136 
OpenMS::SpecArrayFile::load
void load(const String &filename, FeatureMapType &feature_map)
Loads a SpecArray file into a featureXML.
Definition: SpecArrayFile.h:76
OpenMS::StringUtils::toInt
static Int toInt(const String &this_s)
Definition: StringUtils.h:206
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:58
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)
Sets 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:47
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:59
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:428
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
OpenMS::StringUtils::toDouble
static double toDouble(const String &this_s)
Definition: StringUtils.h:216
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:128
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
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.