OpenMS  3.0.0
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:97
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::StringUtils::toInt
static Int toInt(const String &this_s)
Definition: StringUtils.h:206
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::StringUtils::toFloat
static float toFloat(const String &this_s)
Definition: StringUtils.h:211
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
StatisticFunctions.h
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::SVMWrapper::loadModel
void loadModel(std::string modelFilename)
loads the model
OpenMS::ParamValue::toString
std::string toString(bool full_precision=true) const
Convert ParamValue to string.
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::BORDER_LENGTH
Definition: SVMWrapper.h:105
OpenMS::PythonInfo
Detect Python and retrieve information.
Definition: PythonInfo.h:49
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::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::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::SVMWrapper::OLIGO
Definition: SVMWrapper.h:111
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:68
OpenMS::ParamValue::EMPTY
static const ParamValue EMPTY
Empty data value for comparisons.
Definition: ParamValue.h:60
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