OpenMS  3.0.0
MarkerMower.h
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31 // $Maintainer: Mathias Walzer $
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34 //
35 #pragma once
36 
40 
43 
44 #include <vector>
45 #include <map>
46 
47 namespace OpenMS
48 {
54  class OPENMS_DLLAPI MarkerMower :
55  public DefaultParamHandler
56  {
57 public:
58 
59  // @name Constructors and Destructors
60  // @{
62  MarkerMower();
64  ~MarkerMower() override;
65 
67  MarkerMower(const MarkerMower & source);
69  MarkerMower & operator=(const MarkerMower & source);
70  // @}
71 
72  // @name Accessors
73  // @{
75  template <typename SpectrumType>
76  void filterSpectrum(SpectrumType & spectrum)
77  {
78  typedef typename SpectrumType::Iterator Iterator;
79 
80  std::map<double, int> marks;
81  for (std::vector<PeakMarker *>::const_iterator cvit = markers_.begin(); cvit != markers_.end(); ++cvit)
82  {
83  std::map<double, bool> marked;
84  (*cvit)->apply(marked, spectrum);
85  for (std::map<double, bool>::const_iterator cmit = marked.begin(); cmit != marked.end(); ++cmit)
86  {
87  if (cmit->second)
88  {
89  marks[cmit->first]++;
90  }
91  }
92  }
93 
94  for (Iterator it = spectrum.begin(); it != spectrum.end(); )
95  {
96  if (marks[it->getMZ()] > 0)
97  {
98  ++it;
99  }
100  else
101  {
102  it = spectrum.erase(it);
103  }
104  }
105  }
106 
107  void filterPeakSpectrum(PeakSpectrum & spectrum);
108 
109  void filterPeakMap(PeakMap & exp);
110 
111  static const String getProductName()
112  {
113  return "MarkerMower";
114  }
115 
117  void insertmarker(PeakMarker * peak_marker);
118 
119  //TODO reimplement DefaultParamHandler::updateMembers_()
120 
121  // @}
122 
123 private:
125  std::vector<PeakMarker *> markers_;
126 
127  };
128 }
LogStream.h
DefaultParamHandler.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
FileTypes.h
Size
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::PeptideIdentification::insertHit
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
PeakMarker.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
Int
OpenMS::String::removeWhitespaces
String & removeWhitespaces()
removes whitespaces (space, tab, line feed, carriage return)
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
IdXMLFile.h
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
Constants.h
OpenMS::MarkerMower::getProductName
static const String getProductName()
Definition: MarkerMower.h:111
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
ProgressLogger.h
OpenMS::File::copyDirRecursively
static bool copyDirRecursively(const QString &from_dir, const QString &to_dir, File::CopyOptions option=CopyOptions::OVERWRITE)
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::FileHandler::loadExperiment
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::MarkerMower
MarkerMower uses PeakMarker to find peaks, those that are not marked get removed.
Definition: MarkerMower.h:54
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
CsvFile.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Iterator
OpenMS::CsvFile
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::File::TempDir
Class representing a temporary directory.
Definition: File.h:64
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::MarkerMower::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: MarkerMower.h:76
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:152
OpenMS::MarkerMower::markers_
std::vector< PeakMarker * > markers_
used peak markers
Definition: MarkerMower.h:125
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:128
OpenMS::FileHandler::storeExperiment
void storeExperiment(const String &filename, const MSExperiment &exp, ProgressLogger::LogType log=ProgressLogger::NONE)
Stores an MSExperiment to a file.
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
StandardTypes.h
File.h
TOPPBase.h
MSSpectrum.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55
StringListUtils.h