Package uk.ac.ebi.pride.jmztab2.utils.parser

Class MZTabParserContext

java.lang.Object

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext

public class MZTabParserContext
extends Object

MZTabParserContext is used to keep track of indexed elements and interrelations during parsing.

Since:

11/09/17

Author:

nilshoffmann

Constructor Summary

Constructors

Constructor	Description
MZTabParserContext()

Method Summary

Modifier and Type	Method	Description
de.isas.mztab2.model.Assay	addAssay(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Assay assay)	Add a assay into metadata.
de.isas.mztab2.model.Assay	addAssayCustom(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter param)	Add a assay[id]-custom[i] into metadata.
de.isas.mztab2.model.Assay	addAssayExternalUri(de.isas.mztab2.model.Metadata metadata, Integer id, URI location)	Add a assay[id]-external_uri into metadata.
de.isas.mztab2.model.Assay	addAssayMsRun(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.MsRun msRun)	Add assay[id]-ms_run_ref into metadata.
de.isas.mztab2.model.Assay	addAssaySample(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Sample sample)	Add assay[id]-sample_ref into metadata.
de.isas.mztab2.model.Contact	addContact(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Contact contact)	Add a contact into metadata.
de.isas.mztab2.model.Contact	addContactAffiliation(de.isas.mztab2.model.Metadata metadata, Integer id, String affiliation)	Add contact[id]-affiliation.
de.isas.mztab2.model.Contact	addContactEmail(de.isas.mztab2.model.Metadata metadata, Integer id, String email)	Add contact[id]-email
de.isas.mztab2.model.Contact	addContactName(de.isas.mztab2.model.Metadata metadata, Integer id, String name)	Add contact[id]-name.
de.isas.mztab2.model.CV	addCV(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.CV cv)	Add a controlled vocabularies/ontologies into metadata.
de.isas.mztab2.model.CV	addCVFullName(de.isas.mztab2.model.Metadata metadata, Integer id, String fullName)	Add a cv[id]-full_name.
de.isas.mztab2.model.CV	addCVLabel(de.isas.mztab2.model.Metadata metadata, Integer id, String label)	Add a cv[id]-label.
de.isas.mztab2.model.CV	addCVURI(de.isas.mztab2.model.Metadata metadata, Integer id, String uri)	Add a cv[id]-uri.
de.isas.mztab2.model.CV	addCVVersion(de.isas.mztab2.model.Metadata metadata, Integer id, String version)	Add a cv[id]-version.
de.isas.mztab2.model.Database	addDatabase(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Database database)	addDatabase.
de.isas.mztab2.model.Database	addDatabasePrefix(de.isas.mztab2.model.Metadata metadata, Integer id, String valueLabel)	addDatabasePrefix.
de.isas.mztab2.model.Database	addDatabaseUri(de.isas.mztab2.model.Metadata metadata, Integer id, URI checkURI)	addDatabaseUri.
de.isas.mztab2.model.Database	addDatabaseVersion(de.isas.mztab2.model.Metadata metadata, Integer id, String version)	addDatabaseVersion.
de.isas.mztab2.model.Instrument	addInstrument(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Instrument instrument)	Add a instrument[id] to metadata.
de.isas.mztab2.model.Instrument	addInstrumentAnalyzer(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter analyzer)	Add a parameter for instrument[id]-analyzer[i]
de.isas.mztab2.model.Instrument	addInstrumentDetector(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter detector)	Add a parameter for instrument[id]-detector
de.isas.mztab2.model.Instrument	addInstrumentName(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter name)	Add a parameter for instrument[id]-name
de.isas.mztab2.model.Instrument	addInstrumentSource(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter source)	Add a parameter for instrument[id]-source
de.isas.mztab2.model.MsRun	addMsRun(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.MsRun msRun)	Add a ms_run[id] into metadata.
de.isas.mztab2.model.MsRun	addMsRunFormat(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter format)	Add ms_run[id]-format into metadata.
de.isas.mztab2.model.MsRun	addMsRunFragmentationMethod(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter fragmentationMethod)	Add ms_run[id]-fragmentation_method into metadata.
de.isas.mztab2.model.MsRun	addMsRunHash(de.isas.mztab2.model.Metadata metadata, Integer id, String hash)	addMsRunHash.
de.isas.mztab2.model.MsRun	addMsRunHashMethod(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter hashMethod)	addMsRunHashMethod.
de.isas.mztab2.model.MsRun	addMsRunIdFormat(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter idFormat)	Add ms_run[id]-id_format into metadata.
de.isas.mztab2.model.MsRun	addMsRunInstrumentRef(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Instrument instrument)	Add ms_run[id]-instrument_ref into metadata.
de.isas.mztab2.model.MsRun	addMsRunLocation(de.isas.mztab2.model.Metadata metadata, Integer id, URI location)	Add ms_run[id]-location into metadata.
de.isas.mztab2.model.MsRun	addMsRunScanPolarity(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter scanPolarity)	addMsRunScanPolarity.
de.isas.mztab2.model.Publication	addPublication(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Publication publication)	Add a publiction to metadata.
de.isas.mztab2.model.Publication	addPublicationItem(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.PublicationItem.TypeEnum type, String accession)	Add a publication item to metadata.
de.isas.mztab2.model.Publication	addPublicationItems(de.isas.mztab2.model.Metadata metadata, Integer id, Collection<de.isas.mztab2.model.PublicationItem> items)	Add a couple of publication items into publication[id].
de.isas.mztab2.model.Sample	addSample(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Sample sample)	Add a sample to metadata.
de.isas.mztab2.model.Sample	addSampleCellType(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter cellType)	Add a sample[id]-cell_type into sample.
de.isas.mztab2.model.Sample	addSampleCustom(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter custom)	Add a sample[id]-custom into sample.
de.isas.mztab2.model.Sample	addSampleDescription(de.isas.mztab2.model.Metadata metadata, Integer id, String description)	Add a sample[id]-description into sample.
de.isas.mztab2.model.Sample	addSampleDisease(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter disease)	Add a sample[id]-disease into sample.
de.isas.mztab2.model.SampleProcessing	addSampleProcessing(de.isas.mztab2.model.Metadata metadata, Integer id, List<de.isas.mztab2.model.Parameter> sampleProcessing)	Add a sample_processing[id].
de.isas.mztab2.model.SampleProcessing	addSampleProcessingParameter(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter param)	Add a processing parameter to sample_processing[id]
de.isas.mztab2.model.Sample	addSampleSpecies(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter species)	Add a sample[id]-species into sample.
de.isas.mztab2.model.Sample	addSampleTissue(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter tissue)	Add a sample[id]-tissue into sample.
void	addSmallMoleculeColUnit(de.isas.mztab2.model.Metadata metadata, String columnName, de.isas.mztab2.model.Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	addSmallMoleculeEvidenceColUnit(de.isas.mztab2.model.Metadata metadata, String columnName, de.isas.mztab2.model.Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
void	addSmallMoleculeFeatureColUnit(de.isas.mztab2.model.Metadata metadata, String columnName, de.isas.mztab2.model.Parameter param)	Defines the unit for the data reported in a column of the small molecule section.
de.isas.mztab2.model.Software	addSoftware(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.Software software)	Add a software to metadata, which used to analyze the data and obtain the reported results.
de.isas.mztab2.model.Software	addSoftwareParameter(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter param)	Add a software[id] parameter.
de.isas.mztab2.model.Software	addSoftwareSetting(de.isas.mztab2.model.Metadata metadata, Integer id, String setting)	Add a software[id]-setting.
de.isas.mztab2.model.StudyVariable	addStudyVariable(de.isas.mztab2.model.Metadata metadata, de.isas.mztab2.model.StudyVariable studyVariable)	Add a study variable into metadata.
de.isas.mztab2.model.StudyVariable	addStudyVariableAssay(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Assay assay)	Add a study_variable[id]-assay_refs.
de.isas.mztab2.model.StudyVariable	addStudyVariableAverageFunction(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter checkParameter)	Add a study_variable[id]-average_function.
de.isas.mztab2.model.StudyVariable	addStudyVariableDescription(de.isas.mztab2.model.Metadata metadata, Integer id, String description)	Add a study_variable[id]-description.
de.isas.mztab2.model.StudyVariable	addStudyVariableFactors(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter checkParameter)	Add a study_variable[id]-factor.
de.isas.mztab2.model.StudyVariable	addStudyVariableVariationFunction(de.isas.mztab2.model.Metadata metadata, Integer id, de.isas.mztab2.model.Parameter checkParameter)	Add a study_variable[id]-variation_function.
Map<String,String>	getColUnitMap()	Defines a method to access the colUnit to help in the transformation from columnName String -> to columnName MZTabColumn

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MZTabParserContext

public MZTabParserContext()

Method Detail

addSample

public de.isas.mztab2.model.Sample addSample(de.isas.mztab2.model.Metadata metadata,
                                             de.isas.mztab2.model.Sample sample)

Add a sample to metadata. Samples are NOT MANDATORY in mzTab, since many software packages cannot determine what type of sample was analysed (e.g. whether biological or technical replication was performed).

Parameters:

sample - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleSpecies

public de.isas.mztab2.model.Sample addSampleSpecies(de.isas.mztab2.model.Metadata metadata,
                                                    Integer id,
                                                    de.isas.mztab2.model.Parameter species)

Add a sample[id]-species into sample.

Parameters:

id - SHOULD be positive integer.

species - if null ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleTissue

public de.isas.mztab2.model.Sample addSampleTissue(de.isas.mztab2.model.Metadata metadata,
                                                   Integer id,
                                                   de.isas.mztab2.model.Parameter tissue)

Add a sample[id]-tissue into sample.

Parameters:

id - SHOULD be positive integer.

tissue - if null ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleCellType

public de.isas.mztab2.model.Sample addSampleCellType(de.isas.mztab2.model.Metadata metadata,
                                                     Integer id,
                                                     de.isas.mztab2.model.Parameter cellType)

Add a sample[id]-cell_type into sample.

Parameters:

id - SHOULD be positive integer.

cellType - if null ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleDisease

public de.isas.mztab2.model.Sample addSampleDisease(de.isas.mztab2.model.Metadata metadata,
                                                    Integer id,
                                                    de.isas.mztab2.model.Parameter disease)

Add a sample[id]-disease into sample.

Parameters:

id - SHOULD be positive integer.

disease - if null ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleDescription

public de.isas.mztab2.model.Sample addSampleDescription(de.isas.mztab2.model.Metadata metadata,
                                                        Integer id,
                                                        String description)

Add a sample[id]-description into sample.

Parameters:

id - SHOULD be positive integer.

description - if empty ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleCustom

public de.isas.mztab2.model.Sample addSampleCustom(de.isas.mztab2.model.Metadata metadata,
                                                   Integer id,
                                                   de.isas.mztab2.model.Parameter custom)

Add a sample[id]-custom into sample. Add a custom parameter for sample.

Parameters:

id - SHOULD be positive integer.

custom - if null ignore operation.

metadata - a Metadata object.

Returns:

a Sample object.

addSampleProcessing

public de.isas.mztab2.model.SampleProcessing addSampleProcessing(de.isas.mztab2.model.Metadata metadata,
                                                                 Integer id,
                                                                 List<de.isas.mztab2.model.Parameter> sampleProcessing)

Add a sample_processing[id]. A list of parameters describing a sample processing step. The order of the data_processing items should reflect the order these processing steps were performed in. If multiple parameters are given for a step these MUST be separated by a "|".

Parameters:

id - SHOULD be positive integer.

sampleProcessing - if null ignore operation.

metadata - a Metadata object.

Returns:

a SampleProcessing object.

addSampleProcessingParameter

public de.isas.mztab2.model.SampleProcessing addSampleProcessingParameter(de.isas.mztab2.model.Metadata metadata,
                                                                          Integer id,
                                                                          de.isas.mztab2.model.Parameter param)

Add a processing parameter to sample_processing[id]

Parameters:

id - SHOULD be positive integer.

param - if null ignore operation.

metadata - a Metadata object.

Returns:

a SampleProcessing object.

addInstrument

public de.isas.mztab2.model.Instrument addInstrument(de.isas.mztab2.model.Metadata metadata,
                                                     de.isas.mztab2.model.Instrument instrument)

Add a instrument[id] to metadata.

Parameters:

instrument - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Instrument object.

addInstrumentName

public de.isas.mztab2.model.Instrument addInstrumentName(de.isas.mztab2.model.Metadata metadata,
                                                         Integer id,
                                                         de.isas.mztab2.model.Parameter name)

Add a parameter for instrument[id]-name

Parameters:

id - SHOULD be positive integer.

name - if null ignore operation.

metadata - a Metadata object.

Returns:

a Instrument object.

addInstrumentSource

public de.isas.mztab2.model.Instrument addInstrumentSource(de.isas.mztab2.model.Metadata metadata,
                                                           Integer id,
                                                           de.isas.mztab2.model.Parameter source)

Add a parameter for instrument[id]-source

Parameters:

id - SHOULD be positive integer.

source - if null ignore operation.

metadata - a Metadata object.

Returns:

a Instrument object.

addInstrumentAnalyzer

public de.isas.mztab2.model.Instrument addInstrumentAnalyzer(de.isas.mztab2.model.Metadata metadata,
                                                             Integer id,
                                                             de.isas.mztab2.model.Parameter analyzer)

Add a parameter for instrument[id]-analyzer[i]

Parameters:

id - SHOULD be positive integer.

analyzer - if null ignore operation.

metadata - a Metadata object.

Returns:

a Instrument object.

addInstrumentDetector

public de.isas.mztab2.model.Instrument addInstrumentDetector(de.isas.mztab2.model.Metadata metadata,
                                                             Integer id,
                                                             de.isas.mztab2.model.Parameter detector)

Add a parameter for instrument[id]-detector

Parameters:

id - SHOULD be positive integer.

detector - if null ignore operation.

metadata - a Metadata object.

Returns:

a Instrument object.

addSoftware

public de.isas.mztab2.model.Software addSoftware(de.isas.mztab2.model.Metadata metadata,
                                                 de.isas.mztab2.model.Software software)

Add a software to metadata, which used to analyze the data and obtain the reported results.

Parameters:

software - SHOULD NOT be null

metadata - a Metadata object.

Returns:

a Software object.

addSoftwareParameter

public de.isas.mztab2.model.Software addSoftwareParameter(de.isas.mztab2.model.Metadata metadata,
                                                          Integer id,
                                                          de.isas.mztab2.model.Parameter param)

Add a software[id] parameter. The parameter's value SHOULD contain the software's version. The order (numbering) should reflect the order in which the tools were used.

Parameters:

id - SHOULD be positive integer.

param - if null ignore operation.

metadata - a Metadata object.

Returns:

a Software object.

addSoftwareSetting

public de.isas.mztab2.model.Software addSoftwareSetting(de.isas.mztab2.model.Metadata metadata,
                                                        Integer id,
                                                        String setting)

Add a software[id]-setting. This field MAY occur multiple times for a single software. The value of this field is deliberately set as a String, since there currently do not exist cvParameters for every possible setting.

Parameters:

id - SHOULD be positive integer.

setting - if empty ignore operation.

metadata - a Metadata object.

Returns:

a Software object.

addPublication

public de.isas.mztab2.model.Publication addPublication(de.isas.mztab2.model.Metadata metadata,
                                                       de.isas.mztab2.model.Publication publication)

Add a publiction to metadata. A publication associated with this file. Several publications can be given by indicating the number in the square brackets after "publication". PubMed ids must be prefixed by "pubmed:", DOIs by "doi:". Multiple identifiers MUST be separated by "|".

Parameters:

publication - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Publication object.

addPublicationItem

public de.isas.mztab2.model.Publication addPublicationItem(de.isas.mztab2.model.Metadata metadata,
                                                           Integer id,
                                                           de.isas.mztab2.model.PublicationItem.TypeEnum type,
                                                           String accession)

Add a publication item to metadata. PubMed ids must be prefixed by "pubmed:", DOIs by "doi:". Multiple identifiers MUST be separated by "|".

Parameters:

id - SHOULD be positive integer.

type - SHOULD NOT be null.

accession - SHOULD NOT set empty.

metadata - a Metadata object.

Returns:

a Publication object.

addPublicationItems

public de.isas.mztab2.model.Publication addPublicationItems(de.isas.mztab2.model.Metadata metadata,
                                                            Integer id,
                                                            Collection<de.isas.mztab2.model.PublicationItem> items)

Add a couple of publication items into publication[id]. Several publications can be given by indicating the number in the square brackets after "publication". PubMed ids must be prefixed by "pubmed:", DOIs by "doi:". Multiple identifiers MUST be separated by "|".

Parameters:

id - SHOULD be positive integer.

items - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Publication object.

addContact

public de.isas.mztab2.model.Contact addContact(de.isas.mztab2.model.Metadata metadata,
                                               de.isas.mztab2.model.Contact contact)

Add a contact into metadata.

Parameters:

contact - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Contact object.

addContactName

public de.isas.mztab2.model.Contact addContactName(de.isas.mztab2.model.Metadata metadata,
                                                   Integer id,
                                                   String name)

Add contact[id]-name. Several contacts can be given by indicating the number in the square brackets after "contact". A contact has to be supplied in the format [first name] [initials] [last name] (see example).

Parameters:

id - SHOULD be positive integer.

name - SHOULD NOT set empty.

metadata - a Metadata object.

Returns:

a Contact object.

addContactAffiliation

public de.isas.mztab2.model.Contact addContactAffiliation(de.isas.mztab2.model.Metadata metadata,
                                                          Integer id,
                                                          String affiliation)

Add contact[id]-affiliation.

Parameters:

id - SHOULD be positive integer.

affiliation - SHOULD NOT set empty.

metadata - a Metadata object.

Returns:

a Contact object.

addContactEmail

public de.isas.mztab2.model.Contact addContactEmail(de.isas.mztab2.model.Metadata metadata,
                                                    Integer id,
                                                    String email)

Add contact[id]-email

Parameters:

id - SHOULD be positive integer.

email - SHOULD NOT set empty.

metadata - a Metadata object.

Returns:

a Contact object.

addMsRun

public de.isas.mztab2.model.MsRun addMsRun(de.isas.mztab2.model.Metadata metadata,
                                           de.isas.mztab2.model.MsRun msRun)

Add a ms_run[id] into metadata. An MS run is effectively one run (or set of runs on pre-fractionated samples) on an MS instrument, and is referenced from assay in different contexts.

Parameters:

msRun - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a MsRun object.

addMsRunFormat

public de.isas.mztab2.model.MsRun addMsRunFormat(de.isas.mztab2.model.Metadata metadata,
                                                 Integer id,
                                                 de.isas.mztab2.model.Parameter format)

Add ms_run[id]-format into metadata. A parameter specifying the data format of the external MS data file.

Parameters:

id - SHOULD be positive integer.

format - if null ignore operation.

metadata - a Metadata object.

Returns:

a MsRun object.

addMsRunLocation

public de.isas.mztab2.model.MsRun addMsRunLocation(de.isas.mztab2.model.Metadata metadata,
                                                   Integer id,
                                                   URI location)

Add ms_run[id]-location into metadata. Location of the external data file. If the actual location of the MS run is unknown, a "null" MUST be used as a place holder value.

Parameters:

id - SHOULD be positive integer.

location - if null ignore operation.

metadata - a Metadata object.

Returns:

a MsRun object.

addMsRunInstrumentRef

public de.isas.mztab2.model.MsRun addMsRunInstrumentRef(de.isas.mztab2.model.Metadata metadata,
                                                        Integer id,
                                                        de.isas.mztab2.model.Instrument instrument)

Add ms_run[id]-instrument_ref into metadata. Reference to a commonly used instrument.

Parameters:

metadata - a Metadata object.

id - SHOULD be positive integer.

instrument - if null ignore operation.

Returns:

a MsRun object.

addMsRunIdFormat

public de.isas.mztab2.model.MsRun addMsRunIdFormat(de.isas.mztab2.model.Metadata metadata,
                                                   Integer id,
                                                   de.isas.mztab2.model.Parameter idFormat)

Add ms_run[id]-id_format into metadata. Parameter specifying the id format used in the external data file.

Parameters:

id - SHOULD be positive integer.

idFormat - if null ignore operation.

metadata - a Metadata object.

Returns:

a MsRun object.

addMsRunFragmentationMethod

public de.isas.mztab2.model.MsRun addMsRunFragmentationMethod(de.isas.mztab2.model.Metadata metadata,
                                                              Integer id,
                                                              de.isas.mztab2.model.Parameter fragmentationMethod)

Add ms_run[id]-fragmentation_method into metadata. A list of "|" separated parameters describing all the types of fragmentation used in a given ms run.

Parameters:

id - SHOULD be positive integer.

fragmentationMethod - if null ignore operation.

metadata - a Metadata object.

Returns:

a MsRun object.

addMsRunHash

public de.isas.mztab2.model.MsRun addMsRunHash(de.isas.mztab2.model.Metadata metadata,
                                               Integer id,
                                               String hash)

addMsRunHash.

Parameters:

metadata - a Metadata object.

id - a Integer object.

hash - a String object.

Returns:

a MsRun object.

addMsRunHashMethod

public de.isas.mztab2.model.MsRun addMsRunHashMethod(de.isas.mztab2.model.Metadata metadata,
                                                     Integer id,
                                                     de.isas.mztab2.model.Parameter hashMethod)

addMsRunHashMethod.

Parameters:

metadata - a Metadata object.

id - a Integer object.

hashMethod - a Parameter object.

Returns:

a MsRun object.

addMsRunScanPolarity

public de.isas.mztab2.model.MsRun addMsRunScanPolarity(de.isas.mztab2.model.Metadata metadata,
                                                       Integer id,
                                                       de.isas.mztab2.model.Parameter scanPolarity)

addMsRunScanPolarity.

Parameters:

metadata - a Metadata object.

id - a Integer object.

scanPolarity - a Parameter object.

Returns:

a MsRun object.

addAssay

public de.isas.mztab2.model.Assay addAssay(de.isas.mztab2.model.Metadata metadata,
                                           de.isas.mztab2.model.Assay assay)

Add a assay into metadata. The application of a measurement about the sample (in this case through MS) - producing values about small molecules, peptides or proteins. One assay is typically mapped to one MS run in the case of label-free MS analysis or multiple assays are mapped to one MS run for multiplexed techniques, along with a description of the label or tag applied.

Parameters:

assay - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a Assay object.

addAssayCustom

public de.isas.mztab2.model.Assay addAssayCustom(de.isas.mztab2.model.Metadata metadata,
                                                 Integer id,
                                                 de.isas.mztab2.model.Parameter param)

Add a assay[id]-custom[i] into metadata. The application of a measurement about the sample (in this case through MS) - producing values about small molecules, peptides or proteins. One assay is typically mapped to one MS run in the case of label-free MS analysis or multiple assays are mapped to one MS run for multiplexed techniques, along with a description of the label or tag applied.

Parameters:

metadata - a Metadata object.

id - SHOULD NOT be null.

param - the parameter.

Returns:

a Assay object.

addAssayExternalUri

public de.isas.mztab2.model.Assay addAssayExternalUri(de.isas.mztab2.model.Metadata metadata,
                                                      Integer id,
                                                      URI location)

Add a assay[id]-external_uri into metadata. The application of a measurement about the sample (in this case through MS) - producing values about small molecules, peptides or proteins. One assay is typically mapped to one MS run in the case of label-free MS analysis or multiple assays are mapped to one MS run for multiplexed techniques, along with a description of the label or tag applied.

Parameters:

metadata - a Metadata object.

id - the id of the assay element.

location - SHOULD NOT be null.

Returns:

a Assay object.

addAssaySample

public de.isas.mztab2.model.Assay addAssaySample(de.isas.mztab2.model.Metadata metadata,
                                                 Integer id,
                                                 de.isas.mztab2.model.Sample sample)

Add assay[id]-sample_ref into metadata. An association from a given assay to the sample analysed.

Parameters:

id - SHOULD be positive integer.

sample - SHOULD NOT be null, and SHOULD be defined in metadata first.

metadata - a Metadata object.

Returns:

a Assay object.

addAssayMsRun

public de.isas.mztab2.model.Assay addAssayMsRun(de.isas.mztab2.model.Metadata metadata,
                                                Integer id,
                                                de.isas.mztab2.model.MsRun msRun)

Add assay[id]-ms_run_ref into metadata. An association from a given assay to the source MS run.

Parameters:

id - SHOULD be positive integer.

msRun - SHOULD NOT be null, and SHOULD be defined in metadata first.

metadata - a Metadata object.

Returns:

a Assay object.

addStudyVariable

public de.isas.mztab2.model.StudyVariable addStudyVariable(de.isas.mztab2.model.Metadata metadata,
                                                           de.isas.mztab2.model.StudyVariable studyVariable)

Add a study variable into metadata. The variables about which the final results of a study are reported, which may have been derived following averaging across a group of replicate measurements (assays). In files where assays are reported, study variables have references to assays. The same concept has been defined by others as "experimental factor".

Parameters:

studyVariable - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a StudyVariable object.

addStudyVariableAssay

public de.isas.mztab2.model.StudyVariable addStudyVariableAssay(de.isas.mztab2.model.Metadata metadata,
                                                                Integer id,
                                                                de.isas.mztab2.model.Assay assay)

Add a study_variable[id]-assay_refs. Comma-separated references to the IDs of assays grouped in the study variable.

Parameters:

id - SHOULD be positive integer.

assay - SHOULD NOT be null, and should be defined in metadata first.

metadata - a Metadata object.

Returns:

a StudyVariable object.

addStudyVariableDescription

public de.isas.mztab2.model.StudyVariable addStudyVariableDescription(de.isas.mztab2.model.Metadata metadata,
                                                                      Integer id,
                                                                      String description)

Add a study_variable[id]-description. A textual description of the study variable.

Parameters:

metadata - a Metadata object.

id - SHOULD be positive integer.

description - if empty ignore operation.

Returns:

a StudyVariable object.

addStudyVariableFactors

public de.isas.mztab2.model.StudyVariable addStudyVariableFactors(de.isas.mztab2.model.Metadata metadata,
                                                                  Integer id,
                                                                  de.isas.mztab2.model.Parameter checkParameter)

Add a study_variable[id]-factor. A Parameter further refining what is known about the study design.

Parameters:

metadata - a Metadata object.

id - id SHOULD be positive integer.

checkParameter - the study variable factor Parameter to add.

Returns:

a StudyVariable object.

addStudyVariableVariationFunction

public de.isas.mztab2.model.StudyVariable addStudyVariableVariationFunction(de.isas.mztab2.model.Metadata metadata,
                                                                            Integer id,
                                                                            de.isas.mztab2.model.Parameter checkParameter)

Add a study_variable[id]-variation_function. This is a Parameter detailing how the reported study variable abundances have been calculated.

Parameters:

metadata - a Metadata object.

id - SHOULD be positive integer.

checkParameter - the parameter.

Returns:

a StudyVariable object.

addStudyVariableAverageFunction

public de.isas.mztab2.model.StudyVariable addStudyVariableAverageFunction(de.isas.mztab2.model.Metadata metadata,
                                                                          Integer id,
                                                                          de.isas.mztab2.model.Parameter checkParameter)

Add a study_variable[id]-average_function. This is a Parameter detailing how the reported study variable abundances have been calculated.

Parameters:

metadata - a Metadata object.

id - SHOULD be positive integer.

checkParameter - the parameter.

Returns:

a StudyVariable object.

addCV

public de.isas.mztab2.model.CV addCV(de.isas.mztab2.model.Metadata metadata,
                                     de.isas.mztab2.model.CV cv)

Add a controlled vocabularies/ontologies into metadata. Define the controlled vocabularies/ontologies used in the mzTab file.

Parameters:

cv - SHOULD NOT be null.

metadata - a Metadata object.

Returns:

a CV object.

addCVLabel

public de.isas.mztab2.model.CV addCVLabel(de.isas.mztab2.model.Metadata metadata,
                                          Integer id,
                                          String label)

Add a cv[id]-label. A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file

Parameters:

id - SHOULD be positive integer.

metadata - a Metadata object.

label - a String object.

Returns:

a CV object.

addCVFullName

public de.isas.mztab2.model.CV addCVFullName(de.isas.mztab2.model.Metadata metadata,
                                             Integer id,
                                             String fullName)

Add a cv[id]-full_name. A string describing the full names of the controlled vocabularies/ontologies used in the mzTab file

Parameters:

id - SHOULD be positive integer.

metadata - a Metadata object.

fullName - a String object.

Returns:

a CV object.

addCVVersion

public de.isas.mztab2.model.CV addCVVersion(de.isas.mztab2.model.Metadata metadata,
                                            Integer id,
                                            String version)

Add a cv[id]-version. A string describing the version of the controlled vocabularies/ontologies used in the mzTab file

Parameters:

id - SHOULD be positive integer.

metadata - a Metadata object.

version - a String object.

Returns:

a CV object.

addCVURI

public de.isas.mztab2.model.CV addCVURI(de.isas.mztab2.model.Metadata metadata,
                                        Integer id,
                                        String uri)

Add a cv[id]-uri. A string containing the URIs of the controlled vocabularies/ontologies used in the mzTab file

Parameters:

id - SHOULD be positive integer.

metadata - a Metadata object.

uri - a String object.

Returns:

a CV object.

addSmallMoleculeColUnit

public void addSmallMoleculeColUnit(de.isas.mztab2.model.Metadata metadata,
                                    String columnName,
                                    de.isas.mztab2.model.Parameter param)

Defines the unit for the data reported in a column of the small molecule section. Defines the used unit for a column in the small molecule section. The format of the value has to be {column name}={Parameter defining the unit} This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule-quantification_unit.

Parameters:

metadata - a Metadata object.

columnName - SHOULD NOT be null

param - SHOULD NOT be null

addSmallMoleculeFeatureColUnit

public void addSmallMoleculeFeatureColUnit(de.isas.mztab2.model.Metadata metadata,
                                           String columnName,
                                           de.isas.mztab2.model.Parameter param)

Defines the unit for the data reported in a column of the small molecule section. Defines the used unit for a column in the small molecule section. The format of the value has to be {column name}={Parameter defining the unit} This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule-quantification_unit.

Parameters:

metadata - a Metadata object.

columnName - SHOULD NOT be null

param - SHOULD NOT be null

addSmallMoleculeEvidenceColUnit

public void addSmallMoleculeEvidenceColUnit(de.isas.mztab2.model.Metadata metadata,
                                            String columnName,
                                            de.isas.mztab2.model.Parameter param)

Defines the unit for the data reported in a column of the small molecule section. Defines the used unit for a column in the small molecule section. The format of the value has to be {column name}={Parameter defining the unit} This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule-quantification_unit.

Parameters:

metadata - a Metadata object.

columnName - SHOULD NOT be null

param - SHOULD NOT be null

getColUnitMap

public Map<String,String> getColUnitMap()

Defines a method to access the colUnit to help in the transformation from columnName String -> to columnName MZTabColumn

Returns:

a Map object.

addDatabase

public de.isas.mztab2.model.Database addDatabase(de.isas.mztab2.model.Metadata metadata,
                                                 de.isas.mztab2.model.Database database)

addDatabase.

Parameters:

metadata - a Metadata object.

database - a Database object.

Returns:

a Database object.

addDatabasePrefix

public de.isas.mztab2.model.Database addDatabasePrefix(de.isas.mztab2.model.Metadata metadata,
                                                       Integer id,
                                                       String valueLabel)

addDatabasePrefix.

Parameters:

metadata - a Metadata object.

id - a Integer object.

valueLabel - a String object.

Returns:

a Database object.

addDatabaseVersion

public de.isas.mztab2.model.Database addDatabaseVersion(de.isas.mztab2.model.Metadata metadata,
                                                        Integer id,
                                                        String version)

addDatabaseVersion.

Parameters:

metadata - a Metadata object.

id - a Integer object.

version - a String object.

Returns:

a Database object.

addDatabaseUri

public de.isas.mztab2.model.Database addDatabaseUri(de.isas.mztab2.model.Metadata metadata,
                                                    Integer id,
                                                    URI checkURI)

addDatabaseUri.

Parameters:

metadata - a Metadata object.

id - a Integer object.

checkURI - a URI object.

Returns:

a Database object.