OpenMS  2.6.0
PythonInfo.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 
39 namespace OpenMS
40 {
41  class String;
49  class OPENMS_DLLAPI PythonInfo
50  {
51  public:
63  static bool canRun(String& python_executable, String& error_msg);
64 
65 
76  static bool isPackageInstalled(const String& python_executable, const String& package_name);
77 
87  static String getVersion(const String& python_executable);
88  };
89 
90 }
91 
OpenMS::SVMWrapper::KERNEL_TYPE
the kernel type
Definition: SVMWrapper.h:93
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
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::String
A more convenient string class.
Definition: String.h:59
ParamXMLFile.h
SVMWrapper.h
LibSVMEncoder.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
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
StatisticFunctions.h
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
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:55
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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...
int
OpenMS::SVMWrapper::SIGMA
Definition: SVMWrapper.h:100
ProteinIdentification.h
OpenMS::LibSVMEncoder::destroyProblem
static void destroyProblem(svm_problem *problem)
frees all the memory of the svm_problem instance
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::DataValue::EMPTY
static const DataValue EMPTY
Empty data value for comparisons.
Definition: DataValue.h:62
OpenMS::SVMWrapper::loadModel
void loadModel(std::string modelFilename)
loads the model
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::SVMWrapper
Serves as a wrapper for the libsvm.
Definition: SVMWrapper.h:79
OpenMS::SVMWrapper::BORDER_LENGTH
Definition: SVMWrapper.h:101
OpenMS::PythonInfo
Detect Python and retrieve information.
Definition: PythonInfo.h:49
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::SVMWrapper::setTrainingSample
void setTrainingSample(svm_problem *training_sample)
This is used for being able to perform predictions with non libsvm standard kernels.
OpenMS::ParamXMLFile::load
void load(const String &filename, Param &param)
Read XML file.
OpenMS::SVMWrapper::OLIGO
Definition: SVMWrapper.h:107
TOPPBase.h
OpenMS::SVMWrapper::getSVCProbabilities
void getSVCProbabilities(struct svm_problem *problem, std::vector< double > &probabilities, std::vector< double > &prediction_labels)
This function fills probabilities with the probability estimates for the first class.
OpenMS::LibSVMEncoder::loadLibSVMProblem
svm_problem * loadLibSVMProblem(const String &filename)
loads the LibSVM-encoded data stored in 'filename'
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
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