|
OpenMS
2.6.0
|
Go to the documentation of this file.
68 void load(
const String & filename, std::map<
String, std::pair<String, String> > & ptm_informations);
77 void store(
String filename, std::map<
String, std::pair<String, String> > & ptm_informations)
const;
the nu parameter for nu-SVR
Definition: SVMWrapper.h:96
the kernel type
Definition: SVMWrapper.h:93
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,...
Base class for TOPP applications.
Definition: TOPPBase.h:144
the C parameter of the svm
Definition: SVMWrapper.h:95
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
A more convenient string class.
Definition: String.h:59
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
The file pendant of the Param class used to load and store the param datastructure as paramXML.
Definition: ParamXMLFile.h:49
void saveModel(std::string modelFilename) const
saves the svm model
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
Int getIntParameter(SVM_parameter_type type)
You can get the actual int- parameters of the svm.
Serves for encoding sequences into feature vectors.
Definition: LibSVMEncoder.h:55
void setParameter(SVM_parameter_type type, Int value)
You can set the parameters of the svm:
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Used to load and store PTMXML files.
Definition: PTMXMLFile.h:52
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
the svm type cab be NU_SVR or EPSILON_SVR
Definition: SVMWrapper.h:92
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...
Definition: SVMWrapper.h:100
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
Data structure used in SVMWrapper.
Definition: SVMWrapper.h:54
Definition: SVMWrapper.h:99
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Int train(struct svm_problem *problem)
trains the svm
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Serves as a wrapper for the libsvm.
Definition: SVMWrapper.h:79
double getDoubleParameter(SVM_parameter_type type)
You can get the actual double- parameters of the svm.
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
Definition: SVMWrapper.h:101
the degree for the polynomial- kernel
Definition: SVMWrapper.h:94
Management and storage of parameters / INI files.
Definition: Param.h:73
void store(const String &filename, const Param ¶m) const
Write XML file.
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'.
Definition: SVMWrapper.h:107
Used to load and store idXML files.
Definition: IdXMLFile.h:63
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
Representation of a peptide hit.
Definition: PeptideHit.h:55