Uses of Interface
uk.ac.ebi.pride.jmztab2.model.IMZTabColumn

Packages that use IMZTabColumn

Package	Description
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.io.validators	This package contains implementations for validation of mzTab-M parts during parsing.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of IMZTabColumn in de.isas.mztab2.io.serialization

Methods in de.isas.mztab2.io.serialization with parameters of type IMZTabColumn

Modifier and Type	Method	Description
static void	Serializers.writeAsNumberArray(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, List<? extends Number> elements)	writeAsNumberArray.
static void	Serializers.writeAsStringArray(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, List<String> elements)	writeAsStringArray.
static void	Serializers.writeNumber(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, Double value)	writeNumber.
static void	Serializers.writeNumber(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, Integer value)	writeNumber.
static void	Serializers.writeObject(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, Object value)	writeObject.
static void	Serializers.writeString(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, String value)	writeString.

Uses of IMZTabColumn in de.isas.mztab2.io.validators

Methods in de.isas.mztab2.io.validators with parameters of type IMZTabColumn

Modifier and Type	Method	Description
default List<MZTabError>	FieldValidator.validateLine(int lineNumber, MZTabParserContext parserContext, IMZTabColumn column, String field, T t)	Validate the given object of type T, using the provided parser context and column to check the state of not yet completely parsed and constructed mzTab hierarchy.
List<MZTabError>	SpectraRefValidator.validateLine(int lineNumber, MZTabParserContext parserContext, IMZTabColumn column, String field, List<SpectraRef> refList)
protected Optional<MZTabError>	SpectraRefValidator.validatePattern(Pattern pattern, String reference, int lineNumber, IMZTabColumn column, String field, MsRun run)

Uses of IMZTabColumn in uk.ac.ebi.pride.jmztab2.model

Subinterfaces of IMZTabColumn in uk.ac.ebi.pride.jmztab2.model

Modifier and Type	Interface	Description
interface	ISmallMoleculeColumn	ISmallMoleculeColumn interface.
interface	ISmallMoleculeEvidenceColumn	ISmallMoleculeEvidenceColumn interface.
interface	ISmallMoleculeFeatureColumn	ISmallMoleculeFeatureColumn interface.

Classes in uk.ac.ebi.pride.jmztab2.model that implement IMZTabColumn

Modifier and Type	Class	Description
class	AbundanceColumn	If the data exporter wishes to report only final results for 'Summary' files (i.e. following averaging over replicates), then these MUST be reported as quantitative values in the columns associated with the study_variable[1-n] (e.g.
class	MZTabColumn	Define a column header which used in Section.Protein_Header, Section.Peptide_Header, Section.PSM_Header, or Section.Small_Molecule_Header.
class	OptionColumn	Additional columns can be added to the end of the protein table.
class	ParameterOptionColumn	An kind of OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.
class	SmallMoleculeColumn	Define the stable columns which have stable order in the small molecule header line
class	SmallMoleculeEvidenceColumn	Define the stable columns which have stable order in the small molecule evidence header line.
class	SmallMoleculeFeatureColumn	Define the stable columns which have stable order in the small molecule feature header line.

Methods in uk.ac.ebi.pride.jmztab2.model that return IMZTabColumn

Modifier and Type	Method	Description
IMZTabColumn	MZTabColumnFactory.findColumnByHeader(String header)	Query the MZTabColumn in factory, based on column header with case-insensitive.

Methods in uk.ac.ebi.pride.jmztab2.model that return types with arguments of type IMZTabColumn

Modifier and Type	Method	Description
SortedMap<String,IMZTabColumn>	MZTabColumnFactory.getColumnMapping()	Get all columns in the factory.
SortedMap<Integer,IMZTabColumn>	MZTabColumnFactory.getOffsetColumnsMap()	The offset record the position of MZTabColumn in header line.
SortedMap<String,IMZTabColumn>	MZTabColumnFactory.getOptionalColumnMapping()	Get all optional columns, including option column with stable order and name, abundance columns, optional columns and cv param optional columns.
SortedMap<String,IMZTabColumn>	MZTabColumnFactory.getStableColumnMapping()	Get stable columns mapping.

Uses of IMZTabColumn in uk.ac.ebi.pride.jmztab2.utils.parser

Fields in uk.ac.ebi.pride.jmztab2.utils.parser with type parameters of type IMZTabColumn

Modifier and Type	Field	Description
protected SortedMap<Integer,IMZTabColumn>	MZTabDataLineParser.mapping

Methods in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type IMZTabColumn

Modifier and Type	Method	Description
protected List<String>	MZTabDataLineParser.checkAmbiguityMembers(IMZTabColumn column, String ambiguityMembers)	Check and translate target string into parameter list which split by ',' character..
protected Double	MZTabDataLineParser.checkBestSearchEngineScore(IMZTabColumn column, String bestSearchEngineScore)	The best search engine score (for this type of score) for the given peptide across all replicates reported.
protected Double	MZTabDataLineParser.checkCalcMassToCharge(IMZTabColumn column, String calc_mass_to_charge)	Check and translate calc_mass_to_charge string into Double.
protected Integer	MZTabDataLineParser.checkCharge(IMZTabColumn column, String charge)	Check and translate charge string into Integer.
protected String	MZTabDataLineParser.checkChemicalFormula(IMZTabColumn column, String chemical_formula)	Check chemical_formula string.
protected String	MZTabDataLineParser.checkData(IMZTabColumn column, String target, boolean allowNull)	In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
protected String	MZTabDataLineParser.checkDatabase(IMZTabColumn column, String database)	Check target string.
protected String	MZTabDataLineParser.checkDatabaseVersion(IMZTabColumn column, String databaseVersion)	Check target string.
protected String	MZTabDataLineParser.checkDescription(IMZTabColumn column, String description)	Check target string.
protected Double	MZTabDataLineParser.checkDouble(IMZTabColumn column, String target)	Check and translate target string into Double.
protected Double	MZTabDataLineParser.checkDouble(IMZTabColumn column, String target, boolean allowNull)	Check and translate target string into Double.
protected List<Double>	MZTabDataLineParser.checkDoubleList(IMZTabColumn column, String target)	Check and translate target string into parameter list which split by splitChar character..
protected String	MZTabDataLineParser.checkEnd(IMZTabColumn column, String end)	Check target string.
protected Double	MZTabDataLineParser.checkExpMassToCharge(IMZTabColumn column, String exp_mass_to_charge)	Check and translate exp_mass_to_charge string into Double.
protected List<String>	MZTabDataLineParser.checkGOTerms(IMZTabColumn column, String go_terms)	Check and translate target string into string list which split by ',' character..
protected List<String>	MZTabDataLineParser.checkIdentifier(IMZTabColumn column, String identifier)	Check and translate identifier string into string list which split by '|' character..
protected List<String>	MZTabDataLineParser.checkInchiKey(IMZTabColumn column, String inchi_key)	Check and translate inchi_key string into parameter list which split by '|' character..
protected Integer	MZTabDataLineParser.checkInteger(IMZTabColumn column, String target)	Check and translate target string into Integer.
protected Integer	MZTabDataLineParser.checkInteger(IMZTabColumn column, String target, boolean allowNull)	Check and translate target string into Integer.
protected List<Integer>	MZTabDataLineParser.checkIntegerList(IMZTabColumn column, String target, char splitChar)	Check and translate target string into integer list which split by splitChar character..
protected List<Integer>	MZTabDataLineParser.checkIntegerList(IMZTabColumn column, String target, char splitChar, boolean allowNull)	Check and translate target string into integer list which split by splitChar character..
protected Double	MZTabDataLineParser.checkMassToCharge(IMZTabColumn column, String mass_to_charge)	Check and translate mass_to_charge string into Double.
protected MZBoolean	MZTabDataLineParser.checkMZBoolean(IMZTabColumn column, String target)	Check and translate target to MZBoolean.
protected Integer	MZTabDataLineParser.checkNumPeptidesDistinct(IMZTabColumn column, String numPeptidesDistinct)	Check and translate numPeptidesDistinct string into Integer.
protected Integer	MZTabDataLineParser.checkNumPeptidesUnique(IMZTabColumn column, String numPeptidesUnique)	Check and translate numPeptidesUnique string into Integer.
protected Integer	MZTabDataLineParser.checkNumPSMs(IMZTabColumn column, String numPSMs)	Check and translate numPSMs string into Integer.
protected Parameter	MZTabDataLineParser.checkParameter(IMZTabColumn column, String target, boolean allowNull)	checkParameter.
protected List<Parameter>	MZTabDataLineParser.checkParamList(IMZTabColumn column, String target)	Check and translate target string into parameter list which split by '|' character..
protected String	MZTabDataLineParser.checkPost(IMZTabColumn column, String post)	Check target string.
protected String	MZTabDataLineParser.checkPre(IMZTabColumn column, String pre)	Check target string.
protected Double	MZTabDataLineParser.checkProteinCoverage(IMZTabColumn column, String protein_coverage)	Check and translate protein_coverage string into Double.
protected Integer	MZTabDataLineParser.checkPSMID(IMZTabColumn column, String psm_id)	Check and translate psm_id string into Integer.
protected List<Double>	MZTabDataLineParser.checkRetentionTime(IMZTabColumn column, String retention_time)	Check and translate retention_time string into Double list which split by '|' character..
protected List<Double>	MZTabDataLineParser.checkRetentionTimeWindow(IMZTabColumn column, String retention_time_window)	Check and translate retention_time_window string into Double list which split by '|' character..
protected List<Parameter>	MZTabDataLineParser.checkSearchEngine(IMZTabColumn column, String searchEngine)	Check and translate searchEngine string into parameter list which split by '|' character..
protected Double	MZTabDataLineParser.checkSearchEngineScore(IMZTabColumn column, String searchEngineScore)	The search engine score for the given peptide in the defined ms run.
protected String	MZTabDataLineParser.checkSequence(IMZTabColumn column, String sequence)	Check and translate peptide sequence.
protected List<String>	MZTabDataLineParser.checkSmiles(IMZTabColumn column, String smiles)	Check and translate smiles string into parameter list which split by '|' character..
protected String	MZTabDataLineParser.checkSpecies(IMZTabColumn column, String species)	Check target string.
protected List<SpectraRef>	MZTabDataLineParser.checkSpectraRef(MZTabParserContext context, IMZTabColumn column, String spectraRef, boolean allowNull)	Check and translate spectraRef string into SpectraRef list.
protected String	MZTabDataLineParser.checkStart(IMZTabColumn column, String start)	Check target string.
protected String	MZTabDataLineParser.checkString(IMZTabColumn column, String target)	In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
protected String	MZTabDataLineParser.checkString(IMZTabColumn column, String target, boolean allowNull)	In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
protected List<String>	MZTabDataLineParser.checkStringList(IMZTabColumn column, String target, char splitChar)	Check and translate target string into parameter list which split by splitChar character..
protected Integer	MZTabDataLineParser.checkTaxid(IMZTabColumn column, String taxid)	Check and translate taxid string into Integer.
protected MZBoolean	MZTabDataLineParser.checkUnique(IMZTabColumn column, String unique)	Check and translate unique to MZBoolean.
protected String	MZTabDataLineParser.checkURI(IMZTabColumn column, String uri)	Checks the provided URI string.