OpenMS  3.0.0
PTMXMLFile.h
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34 
35 #pragma once
36 
37 #include <OpenMS/FORMAT/XMLFile.h>
38 
39 #include <map>
40 #include <vector>
41 
42 namespace OpenMS
43 {
52  class OPENMS_DLLAPI PTMXMLFile :
53  public Internal::XMLFile
54  {
55 public:
57  PTMXMLFile();
58 
68  void load(const String & filename, std::map<String, std::pair<String, String> > & ptm_informations);
69 
77  void store(String filename, std::map<String, std::pair<String, String> > & ptm_informations) const;
78  };
79 
80 } // namespace OpenMS
81 
OpenMS::SVMWrapper::NU
the nu parameter for nu-SVR
Definition: SVMWrapper.h:100
OpenMS::SVMWrapper::KERNEL_TYPE
the kernel type
Definition: SVMWrapper.h:97
OpenMS::LibSVMEncoder::storeLibSVMProblem
bool storeLibSVMProblem(const String &filename, const svm_problem *problem) const
stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale,...
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
XMLFile.h
Size
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::Math::RandomShuffler
Definition: MathFunctions.h:363
OpenMS::SVMWrapper::C
the C parameter of the svm
Definition: SVMWrapper.h:99
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
OpenMS::Math::RandomShuffler::portable_random_shuffle
void portable_random_shuffle(RandomAccessIterator first, RandomAccessIterator last)
Definition: MathFunctions.h:379
OpenMS::String
A more convenient string class.
Definition: String.h:58
ParamXMLFile.h
SVMWrapper.h
Int
LibSVMEncoder.h
IdXMLFile.h
OpenMS::ParamXMLFile
The file pendant of the Param class used to load and store the param datastructure as paramXML.
Definition: ParamXMLFile.h:49
OpenMS::SVMWrapper::saveModel
void saveModel(std::string modelFilename) const
saves the svm model
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
OpenMS::SVMWrapper::getIntParameter
Int getIntParameter(SVM_parameter_type type)
You can get the actual int- parameters of the svm.
OpenMS::LibSVMEncoder
Serves for encoding sequences into feature vectors.
Definition: LibSVMEncoder.h:58
OpenMS::SVMWrapper::setParameter
void setParameter(SVM_parameter_type type, Int value)
You can set the parameters of the svm:
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::PTMXMLFile
Used to load and store PTMXML files.
Definition: PTMXMLFile.h:52
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SVMWrapper::SVM_TYPE
the svm type can be NU_SVR or EPSILON_SVR
Definition: SVMWrapper.h:96
OpenMS::LibSVMEncoder::encodeLibSVMProblemWithCompositionAndLengthVectors
svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector< String > &sequences, std::vector< double > &labels, const String &allowed_characters, UInt maximum_sequence_length)
creates composition vectors with additional length information for 'sequences' and stores them in Lib...
OpenMS::SVMWrapper::SIGMA
Definition: SVMWrapper.h:104
ProteinIdentification.h
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::SVMData
Data structure used in SVMWrapper.
Definition: SVMWrapper.h:58
OpenMS::SVMWrapper::PROBABILITY
Definition: SVMWrapper.h:103
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::SVMWrapper::train
Int train(struct svm_problem *problem)
trains the svm
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::SVMWrapper
Serves as a wrapper for the libsvm.
Definition: SVMWrapper.h:83
OpenMS::SVMWrapper::getDoubleParameter
double getDoubleParameter(SVM_parameter_type type)
You can get the actual double- parameters of the svm.
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::SVMWrapper::BORDER_LENGTH
Definition: SVMWrapper.h:105
OpenMS::SVMWrapper::DEGREE
the degree for the polynomial- kernel
Definition: SVMWrapper.h:98
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::LibSVMEncoder::destroyProblem
static void destroyProblem(svm_problem *&problem, bool free_nodes=true)
frees all the memory of the svm_problem instance
OpenMS::ParamXMLFile::store
void store(const String &filename, const Param &param) const
Write XML file.
OpenMS::SVMWrapper::performCrossValidation
double performCrossValidation(svm_problem *problem_ul, const SVMData &problem_l, const bool is_labeled, const std::map< SVM_parameter_type, double > &start_values_map, const std::map< SVM_parameter_type, double > &step_sizes_map, const std::map< SVM_parameter_type, double > &end_values_map, Size number_of_partitions, Size number_of_runs, std::map< SVM_parameter_type, double > &best_parameters, bool additive_step_sizes=true, bool output=false, String performances_file_name="performances.txt", bool mcc_as_performance_measure=false)
Performs a CV for the data given by 'problem'.
OpenMS::SVMWrapper::OLIGO
Definition: SVMWrapper.h:111
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::LibSVMEncoder::encodeLibSVMProblemWithOligoBorderVectors
svm_problem * encodeLibSVMProblemWithOligoBorderVectors(const std::vector< String > &sequences, std::vector< double > &labels, UInt k_mer_length, const String &allowed_characters, UInt border_length, bool strict=false, bool unpaired=false, bool length_encoding=false)
creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55
StringListUtils.h