OpenMS  2.5.0
QApplicationTOPP.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39 
40 //Qt
41 #include <QtWidgets/QApplication>
42 
43 namespace OpenMS
44 {
50  class OPENMS_GUI_DLLAPI QApplicationTOPP :
51  public QApplication
52  {
53 
54  Q_OBJECT
55 
56 public:
58  QApplicationTOPP(int& argc, char** argv);
59 
61  ~QApplicationTOPP() override;
62 
69  bool notify(QObject* rec, QEvent* ev) override;
70 
74  bool event(QEvent*) override;
75 
82  static void showAboutDialog(QWidget* parent, const QString& toolname);
83 
84 
85 signals:
86  void fileOpen(QString file);
87 
88  };
89 
90 }
91 
LogStream.h
OpenMS::SVMWrapper::KERNEL_TYPE
the kernel type
Definition: SVMWrapper.h:93
QObject
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::Factory::registerProduct
static void registerProduct(const String &name, const FunctionType creator)
register new concrete FactoryProduct
Definition: Factory.h:139
VersionInfo.h
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:58
ParamXMLFile.h
OpenMS::QApplicationTOPP::fileOpen
void fileOpen(QString file)
SVMWrapper.h
LibSVMEncoder.h
OpenMS::QApplicationTOPP
Extension to the QApplication for running TOPPs GUI tools.
Definition: QApplicationTOPP.h:50
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
QDialog
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
QWidget
OpenMS::SVMWrapper::setParameter
void setParameter(SVM_parameter_type type, Int value)
You can set the parameters of the svm:
OpenMS::GUIProgressLoggerImpl::getProductName
static const String getProductName()
name of the model (needed by Factory)
OpenMS::QApplicationTOPP::notify
bool notify(QObject *rec, QEvent *ev) override
: Catch exceptions in Qt GUI applications, preventing ungraceful exit
Definition: QApplicationTOPP.cpp:99
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::File::find
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::QApplicationTOPP::event
bool event(QEvent *) override
Definition: QApplicationTOPP.cpp:118
GUIProgressLoggerImpl.h
Exception.h
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::QApplicationTOPP::showAboutDialog
static void showAboutDialog(QWidget *parent, const QString &toolname)
Show the About-Dialog with License and Citation for all GUI tools.
Definition: QApplicationTOPP.cpp:131
int
OpenMS::SVMWrapper::SIGMA
Definition: SVMWrapper.h:100
ProteinIdentification.h
OpenMS::GUIProgressLoggerImpl::create
static ProgressLogger::ProgressLoggerImpl * create()
create new object (needed by Factory)
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::LibSVMEncoder::destroyProblem
static void destroyProblem(svm_problem *problem)
frees all the memory of the svm_problem instance
OpenMS::Exception::BaseException::getName
const char * getName() const noexcept
Returns the name of the exception.
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::VersionInfo::getRevision
static String getRevision()
Return the revision number from revision control system, e.g. git.
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_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::QApplicationTOPP::QApplicationTOPP
QApplicationTOPP(int &argc, char **argv)
Constructor (no NOT remove the "&" from argc, since Qt will segfault on some platforms otherwise!...
Definition: QApplicationTOPP.cpp:61
OpenMS::SVMWrapper::BORDER_LENGTH
Definition: SVMWrapper.h:101
OpenMS::Exception::BaseException::getMessage
const char * getMessage() const noexcept
Returns the message.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
QApplicationTOPP.h
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.
QApplication
Factory.h
File.h
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::QApplicationTOPP::~QApplicationTOPP
~QApplicationTOPP() override
Destructor.
Definition: QApplicationTOPP.cpp:90
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