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OpenMS
2.5.0
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38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
41 #include <QtWidgets/QApplication>
69 bool notify(
QObject* rec, QEvent* ev)
override;
74 bool event(QEvent*)
override;
82 static void showAboutDialog(
QWidget* parent,
const QString& toolname);
86 void fileOpen(QString file);
the kernel type
Definition: SVMWrapper.h:93
Base class for TOPP applications.
Definition: TOPPBase.h:144
static void registerProduct(const String &name, const FunctionType creator)
register new concrete FactoryProduct
Definition: Factory.h:139
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.
A more convenient string class.
Definition: String.h:58
void fileOpen(QString file)
Extension to the QApplication for running TOPPs GUI tools.
Definition: QApplicationTOPP.h:50
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
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
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:
static const String getProductName()
name of the model (needed by Factory)
bool notify(QObject *rec, QEvent *ev) override
: Catch exceptions in Qt GUI applications, preventing ungraceful exit
Definition: QApplicationTOPP.cpp:99
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool event(QEvent *) override
Definition: QApplicationTOPP.cpp:118
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...
static void showAboutDialog(QWidget *parent, const QString &toolname)
Show the About-Dialog with License and Citation for all GUI tools.
Definition: QApplicationTOPP.cpp:131
Definition: SVMWrapper.h:100
static ProgressLogger::ProgressLoggerImpl * create()
create new object (needed by Factory)
Exception base class.
Definition: Exception.h:89
QString toQString() const
Conversion to Qt QString.
static String getVersion()
Return the version number of OpenMS.
static void destroyProblem(svm_problem *problem)
frees all the memory of the svm_problem instance
const char * getName() const noexcept
Returns the name of the exception.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
static const DataValue EMPTY
Empty data value for comparisons.
Definition: DataValue.h:62
static String getRevision()
Return the revision number from revision control system, e.g. git.
void loadModel(std::string modelFilename)
loads the model
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Serves as a wrapper for the libsvm.
Definition: SVMWrapper.h:79
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
QApplicationTOPP(int &argc, char **argv)
Constructor (no NOT remove the "&" from argc, since Qt will segfault on some platforms otherwise!...
Definition: QApplicationTOPP.cpp:61
Definition: SVMWrapper.h:101
const char * getMessage() const noexcept
Returns the message.
Management and storage of parameters / INI files.
Definition: Param.h:73
void setTrainingSample(svm_problem *training_sample)
This is used for being able to perform predictions with non libsvm standard kernels.
void load(const String &filename, Param ¶m)
Read XML file.
Definition: SVMWrapper.h:107
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.
svm_problem * loadLibSVMProblem(const String &filename)
loads the LibSVM-encoded data stored in 'filename'
Used to load and store idXML files.
Definition: IdXMLFile.h:63
~QApplicationTOPP() override
Destructor.
Definition: QApplicationTOPP.cpp:90
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