256 unsigned fraction_group = 1;
257 unsigned fraction = 1;
258 std::string path =
"UNKNOWN_FILE";
270 const std::vector< std::vector < String > >& content,
271 const std::map< unsigned, Size >& sample_to_rowindex,
272 const std::map< String, Size >& columnname_to_columnindex
279 void addSample(
unsigned sample,
const std::vector<String>& content = {});
391 unsigned getSample(
unsigned fraction_group,
unsigned label = 1);
A container for consensus elements.
Definition: ConsensusMap.h:90
Definition: ExperimentalDesign.h:253
MSFileSectionEntry()=default
Definition: ExperimentalDesign.h:264
SampleSection(const std::vector< std::vector< String > > &content, const std::map< unsigned, Size > &sample_to_rowindex, const std::map< String, Size > &columnname_to_columnindex)
std::vector< std::vector< String > > content_
Definition: ExperimentalDesign.h:301
std::map< String, Size > columnname_to_columnindex_
Definition: ExperimentalDesign.h:309
String getFactorValue(unsigned sample, const String &factor) const
bool hasSample(unsigned sample) const
std::set< String > getFactors() const
Size getFactorColIdx(const String &factor) const
bool hasFactor(const String &factor) const
std::set< unsigned > getSamples() const
std::map< unsigned, Size > sample_to_rowindex_
Definition: ExperimentalDesign.h:305
void addSample(unsigned sample, const std::vector< String > &content={})
Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesi...
Definition: ExperimentalDesign.h:243
unsigned getNumberOfLabels() const
static void errorIfAlreadyExists(std::set< T > &container, T &item, const String &message)
unsigned getNumberOfFractions() const
static ExperimentalDesign fromConsensusMap(const ConsensusMap &c)
Extract experimental design from consensus map.
std::map< std::vector< String >, std::set< unsigned > > getUniqueSampleRowToSampleMapping() const
unsigned getSample(unsigned fraction_group, unsigned label=1)
unsigned getNumberOfSamples() const
void setSampleSection(const SampleSection &sample_section)
std::vector< unsigned > getLabels_() const
bool sameNrOfMSFilesPerFraction() const
Size filterByBasenames(const std::set< String > &bns)
unsigned getNumberOfFractionGroups() const
std::map< unsigned int, std::vector< String > > getFractionToMSFilesMapping() const
return fraction index to file paths (ordered by fraction_group)
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToFractionMapping(bool use_basename_only) const
return <file_path, label> to fraction mapping
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToPrefractionationMapping(bool use_basename_only) const
std::map< std::vector< String >, std::set< unsigned > > getConditionToSampleMapping() const
return a condition (unique combination of sample section values except replicate) to Sample index map...
void setMSFileSection(const MSFileSection &msfile_section)
std::vector< MSFileSectionEntry > MSFileSection
Definition: ExperimentalDesign.h:312
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToConditionMapping(bool use_basename_only) const
MSFileSection msfile_section_
Definition: ExperimentalDesign.h:439
static ExperimentalDesign fromIdentifications(const std::vector< ProteinIdentification > &proteins)
Extract experimental design from identifications.
std::map< std::pair< String, unsigned >, unsigned > pathLabelMapper_(bool, unsigned(*f)(const ExperimentalDesign::MSFileSectionEntry &)) const
Generic Mapper (Path, Label) -> f(row)
ExperimentalDesign(const MSFileSection &msfile_section, const SampleSection &sample_section)
bool isFractionated() const
std::vector< unsigned > getFractions_() const
const MSFileSection & getMSFileSection() const
std::vector< String > getFileNames_(bool basename) const
const ExperimentalDesign::SampleSection & getSampleSection() const
std::map< unsigned, unsigned > getSampleToConditionMapping() const
static ExperimentalDesign fromFeatureMap(const FeatureMap &f)
Extract experimental design from feature map.
std::vector< std::vector< std::pair< String, unsigned > > > getConditionToPathLabelVector() const
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToSampleMapping(bool use_basename_only) const
return <file_path, label> to sample mapping
SampleSection sample_section_
Definition: ExperimentalDesign.h:440
ExperimentalDesign()=default
unsigned getNumberOfMSFiles() const
std::map< std::pair< String, unsigned >, unsigned > getPathLabelToFractionGroupMapping(bool use_basename_only) const
return <file_path, label> to fraction_group mapping
std::map< unsigned, unsigned > getSampleToPrefractionationMapping() const
A container for features.
Definition: FeatureMap.h:106
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
const double c
Definition: Constants.h:209
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47