A B C D E F G H I L M N O P R S T U V W
All Classes All Packages

A

add(Comment) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

Adds a new Comment to the collection.

addAssay(Assay) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Add assay to assay list

addCharacteristic(Characteristic) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

addComponent(ProtocolComponent) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

addContact(Person) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Add a contact to the Investigation

addContact(Person) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Add new Person to the list

addDesignDescriptor(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Add a new design descriptior to the list

addFactor(Factor) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

addFactorValue(FactorValue) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

addOntology(Ontology) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Add an Ontology to the Investigation

addParameter(ProtocolParameter) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Add a ParameterValue to Protocol

addParameterValue(ParameterValue) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

addProtocol(Protocol) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

addPublication(Publication) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Add a Publication to list

addPublication(Publication) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Add new publication associated with this study

addRole(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

addStudy(Study) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Add a study to this investigation.

Assay - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent an assay in the ISA hierarchy.

Assay(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

Constructor, pass the filename the assay will be written to when using the writeToFile method

ASSAY_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

B

BIOLOGICAL_MATERIAL_ALTITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Altitude of the studied biological material, provided in meters (m).

BIOLOGICAL_MATERIAL_COORDINATES_UNCERTAINTY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Circular uncertainty of the coordinates, preferably provided in meters (m).

BIOLOGICAL_MATERIAL_LATITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Latitude of the studied biological material.

BIOLOGICAL_MATERIAL_LONGITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Latitude of the studied biological material.

BIOLOGICAL_MATERIAL_PREPROCESSING - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Description of any process or treatment applied uniformly to the biological material, prior to the study itself.

C

Characteristic - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Characteristic(WideTableConfigEnum, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

Characteristic(WideTableConfigEnum, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

Characteristic(String, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

Characteristic(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

CHARACTERISTICS - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

closeFile() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

Closes the file and forgets all headers.

Comment - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class representing a Comment that can be assigned to an Investigation, Study, Assay, DataFile, Factor, OntologyAnnotation, Person, Process, Protocol, Publication, Sample, or Source.

Comment(InvestigationConfigEnum, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

Comment(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

COMMENT - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

COMMENT - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

Commentable - Interface in de.ipk_gatersleben.bit.bi.isa4j.components

Interface, which allows to enrich a component with a list of Comments.

CommentCollection - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to wrap the functions to handle the Comments of a component.

CommentCollection() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

comments() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.components.Commentable

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

comments() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

CREATED_WITH_CONFIGURATION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Comment[Created with configuration]
[optional]

D

DataFile - Class in de.ipk_gatersleben.bit.bi.isa4j.components

DataFile(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

Creates a new Data File.

de.ipk_gatersleben.bit.bi.isa4j.components - package de.ipk_gatersleben.bit.bi.isa4j.components

de.ipk_gatersleben.bit.bi.isa4j.configurations - package de.ipk_gatersleben.bit.bi.isa4j.configurations

de.ipk_gatersleben.bit.bi.isa4j.constants - package de.ipk_gatersleben.bit.bi.isa4j.constants

de.ipk_gatersleben.bit.bi.isa4j.exceptions - package de.ipk_gatersleben.bit.bi.isa4j.exceptions

de.ipk_gatersleben.bit.bi.isa4j.util - package de.ipk_gatersleben.bit.bi.isa4j.util

DEFAULT_CHARSET - Static variable in class de.ipk_gatersleben.bit.bi.isa4j.constants.Props

DERIVED_DATA_FILE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

DESCRIPTION_OF_GROWTH_FACILITY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Short description of the facility in which the study was carried out.

E

EMPTY - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

ENTER - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

EXTERNAL_ID - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein.

F

Factor - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class representing a factor to describe an observed sample in the Study or Assay, independent from a Protocol

Factor(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

Factor(String, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

FACTOR_VALUE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

FactorValue - Class in de.ipk_gatersleben.bit.bi.isa4j.components

FactorValue(Factor, double) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

FactorValue(Factor, double, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

FactorValue(Factor, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

FactorValue(Factor, OntologyAnnotation, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

FactorValue(Factor, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

G

GeneralValidation - Class in de.ipk_gatersleben.bit.bi.isa4j.configurations

Class for validating the structure of the general ISA model

GeneralValidation() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.configurations.GeneralValidation

GENUS - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Genus name for the organism under study, according to standard scientific nomenclature.

getAddress() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get address of the Person

getAffiliation() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get affiliation of the Person

getAll() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

Return the list of Comments

getAssays() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get associated assays of this study

getAuthors() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Get the list of authors of this Publication

getByName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

Try to find the Comment in the collection with the given name.

getCategory() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

getCharacteristics() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

getComponents() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

getContacts() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get contact of investigation

getContacts() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get contacts of study

getDate() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getDateTime() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getDescription() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get Description

getDescription() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

get the description of the Ontology

getDescription() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the description of the Protocol

getDescription() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get description of study

getDesignDescriptors() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get descriptor of design for study

getDOI() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Get DOI of the Publication

getEmail() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get email of the Person

getFactors() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

getFactorValues() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

getFax() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get fax number of the Person

getFieldName() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.InvestigationConfigEnum

Provide the name of the field.

getFieldName() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

getFieldName() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

getFieldName() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

getFieldName() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.WideTableConfigEnum

Provide the name of the field.

getFieldsForCharacteristics() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

getFieldsForComments(CommentCollection) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

getFieldsForValues(StudyAssayAttribute, List<T>, Function<T, String>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

getFileName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

Get filename of study

getFirstName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get first name of the Person

getGroupIndex() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

getGroupIndex() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

getGroupIndex() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.WideTableConfigEnum

Provide the position of the field within the Study or Assay File

getHeaders() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

getHeadersForCharacteristics() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

getHeadersForComments(CommentCollection) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

getHeadersForValues(StudyAssayAttribute, List<T>, Function<T, String>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

getIdentifier() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Aet id of invesigation

getIdentifier() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get id of study

getInput() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getInvestigation() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get Investigation, that this study belongs to

getLastName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get last name of the Person

getMeasurementType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

getMidInitials() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get mid initials of the Person

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

Get the name of the Comment

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

get the name of the Ontology

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the name of theProtocol

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolParameter

getName() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

getOntologies() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get all linked Ontology

getOntologyAnnotationExtensionFields(T, Function<T, OntologyAnnotation>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

getOntologyAnnotationExtensionHeaders(T, Function<T, OntologyAnnotation>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

These two methods are meant to simplify getFields and getHeaders for Objects that can have TERM SOURCE REF and TERM ACCESSION NUMBERS but don't have to

getOutput() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getParameters() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get list of ParameterValue of the Protocol

getParameterValues() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getPath() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

getPhone() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get phone number of the Person

getProtocol() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

getProtocols() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

getPublications() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get Publication of investigation

getPublications() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get publications of study

getPublicReleaseDate() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get PublicReleaseDate

getPublicReleaseDate() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get public releaseDate of study

getPubmedID() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Get the ID of the Publication

getRoles() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Get role of the Person

getSection() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.InvestigationConfigEnum

Provide the corresponding block of the field within the Investigation File

getSection() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

getSourceREF() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

get sourceREF

getStatus() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Get the status of the Publication

getStudies() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get studies of investigation

getStudy() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

getSubmissionDate() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get SubmissionDate

getSubmissionDate() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get submissionDate of study

getTechnologyPlatform() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

getTechnologyType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

getTerm() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

get term of ontology term

getTermAccession() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

get accession number of ontology term

getTitle() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Get title

getTitle() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Get title of Publication

getTitle() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Get title of study

getType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

getType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

Get OntologyAnnotation for the type of the Factor

getType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Material

getType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the type of the Protocol

getType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

getURI() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the URI of the Protocol

getURL() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

get the url or path of the Ontology

getValue() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

getValue() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

Get the value of Comment

getVersion() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

get the version of the Ontology

getVersion() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the version of the Protocol

H

hasWrittenHeaders() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

Returns true if headers have already been written to file/stream.

I

IMAGE_FILE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

INFRASPECIFIC_NAME - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Name of any subtaxa level, including variety, crossing name, etc.

Investigation - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent an Investigation in the ISA Context, which contains the overall information about the goals and means of the experiment.

Investigation(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Constructor, every Investigation should have an identifier.

INVESTIGATION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_CONTACTS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_IDENTIFIER - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_LICENSE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

License for the reuse of the data associated with this investigation.

INVESTIGATION_PERSON_ADDRESS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_AFFILIATION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_EMAIL - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_FAX - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_FIRST_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_ID - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

An identifier for the data submitter.

INVESTIGATION_PERSON_LAST_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_MID_INITIALS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_PHONE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PERSON_ROLES - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLIC_RELEASE_DATE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLICATION_AUTHOR_LIST - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLICATION_DOI - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLICATION_STATUS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLICATION_TITLE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBLICATIONS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_PUBMED_ID - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_SUBMISSION_DATE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

INVESTIGATION_TITLE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

InvestigationAttribute - Enum in de.ipk_gatersleben.bit.bi.isa4j.constants

List of constant attributes for the Investigation files.

InvestigationConfigEnum - Interface in de.ipk_gatersleben.bit.bi.isa4j.configurations

Interface for providing functions for the specific investigation fields of an ISA configuration

isRequired() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.InvestigationConfigEnum

Check if the specific field is required in the corresponding configuration

isRequired() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

isRequired() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

isRequired() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

isRequired() - Method in interface de.ipk_gatersleben.bit.bi.isa4j.configurations.WideTableConfigEnum

Check if the specific field is required in the corresponding configuration

L

LAST_OPENED_WITH_CONFIGURATION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Comment[Last Opened With Configuration]
[optional]

M

MAP_OF_EXPERIMENTAL_DESIGN - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Representation of the experimental design.

Material - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Material(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Material

Material(String, String, List<Characteristic>) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Material

MATERIAL_SOURCE_ALTITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Altitude of the material source, provided in metres (m).

MATERIAL_SOURCE_COORDINATES_UNCERTAINTY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Circular uncertainty of the coordinates, provided in meters (m).

MATERIAL_SOURCE_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Description of the material source
e.g.

MATERIAL_SOURCE_DOI - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

of the material source
e.g. doi:10.15454/1.4658436467893904E12
[optional]

MATERIAL_SOURCE_ID - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material.

MATERIAL_SOURCE_LATITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Latitude of the material source.

MATERIAL_SOURCE_LONGITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Longitude of the material source.

measurementType() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

MIAPPE_VERSION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

The version of MIAPPE used.

MIAPPEv1x1 - Class in de.ipk_gatersleben.bit.bi.isa4j.configurations

MIAPPEv1.1 validation class, modeled after https://github.com/MIAPPE/ISA-Tab-for-plant-phenotyping at commit 0e1a29d from October 2019

MIAPPEv1x1() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1

MIAPPEv1x1.AssayFile - Enum in de.ipk_gatersleben.bit.bi.isa4j.configurations

MIAPPEv1x1.InvestigationFile - Enum in de.ipk_gatersleben.bit.bi.isa4j.configurations

MIAPPEv1x1.StudyFile - Enum in de.ipk_gatersleben.bit.bi.isa4j.configurations

MissingFieldException - Exception in de.ipk_gatersleben.bit.bi.isa4j.exceptions

MissingFieldException(String) - Constructor for exception de.ipk_gatersleben.bit.bi.isa4j.exceptions.MissingFieldException

N

name - Variable in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

O

OBSERVATION_UNIT_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

General description of the observation units in the study.

OBSERVATION_UNIT_LEVEL_HIERARCHY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Hierarchy of the different levels of repetitions between each others
[optional]

OBSERVATION_UNIT_TYPE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant
placeholder
[optional]

OBSERVATION_UNIT_TYPE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant
plant
[required]

Ontology - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent an ontology

Ontology(String, URL, String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

Full constructor for an Ontology.

ONTOLOGY_SOURCE_REFERENCE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

OntologyAnnotation - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class representing a Ontology based term.

OntologyAnnotation(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

OntologyAnnotation(String, String, Ontology) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

openFile() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

ORGANISM - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

An identifier for the organism at the species level.

P

PARAMETER_VALUE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

ParameterValue - Class in de.ipk_gatersleben.bit.bi.isa4j.components

ParameterValue(ProtocolParameter, double) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

ParameterValue(ProtocolParameter, double, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

ParameterValue(ProtocolParameter, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

ParameterValue(ProtocolParameter, OntologyAnnotation, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

ParameterValue(ProtocolParameter, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

Person - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent a person as Person for the described Investigation or Study

Person(String, String, String, String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Process - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Process(Protocol) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Process

Props - Class in de.ipk_gatersleben.bit.bi.isa4j.constants

Class to collect static general properties for the isa4J API

Props() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.constants.Props

Protocol - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent a protocol/process for a Study, which contains several ParameterValue

Protocol(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Constructor the name of the Protocol

Protocol(String, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

PROTOCOL - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

PROTOCOL_DATE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

ProtocolComponent - Class in de.ipk_gatersleben.bit.bi.isa4j.components

ProtocolComponent(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

ProtocolComponent(String, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

ProtocolParameter - Class in de.ipk_gatersleben.bit.bi.isa4j.components

ProtocolParameter(OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolParameter

ProtocolParameter(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolParameter

Publication - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class representing a Publication connected to a Investigation or Study

Publication(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Publication(String, String, String, String, OntologyAnnotation) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

putNameInAttribute(T, String) - Static method in class de.ipk_gatersleben.bit.bi.isa4j.util.StringUtil

In constants, the position of ?

R

RAW_DATA_FILE - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

RedundantItemException - Exception in de.ipk_gatersleben.bit.bi.isa4j.exceptions

Exception to handling non-unique parameter or attribute names

RedundantItemException(String) - Constructor for exception de.ipk_gatersleben.bit.bi.isa4j.exceptions.RedundantItemException

releaseStream() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

S

Sample - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Sample(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

Sample(String, List<Characteristic>) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

SAMPLE_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

sanitize(String) - Static method in class de.ipk_gatersleben.bit.bi.isa4j.util.StringUtil

Removes Symbol.TABs and Symbol.ENTERs from an input String and replaces them with Symbol.EMPTY.

SEMICOLON - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

set(List<Comment>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

Deletes all saved comments and adds the ones from the passed list.

setAddress(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set address of the Person

setAffiliation(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set affiliation of the Person

setAssays(List<Assay>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set assays of study

setAuthors(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Set the list of authors of this Publication

setCategory(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

Sets the category of this characteristic, i.e. the part that will be printed in the header of the ISA file: Characteristic[category]

setCharacteristics(List<Characteristic>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

setComponents(List<ProtocolComponent>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

setContacts(List<Person>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set contact of investigation

setContacts(List<Person>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set contacts of study

setDate(LocalDate) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

Sets a Date for this Process (without time of day).

setDateTime(LocalDateTime) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

Sets a DateTime for this Process.

setDescription(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set Description

setDescription(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

set the description of the Ontology

setDescription(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Set the description of the Protocol

setDescription(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set description of study

setDesignDescriptors(List<OntologyAnnotation>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set descriptor of design for study

setDOI(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Set DOI of the Publication

setEmail(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set email of the Person

setFactors(List<Factor>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

setFactorValues(List<FactorValue>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

setFax(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set fax number of the Person

setFileName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

setFirstName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set first name of the Person

setIdentifier(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set id of investigation

setIdentifier(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

setInput(StudyOrAssayTableObject) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

Declares the input to this Process.

setInvestigation(Investigation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set Investigation, that this study belongs to But this function can't be used by user

setLastName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set last name of the Person

setMeasurementType(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

setMidInitials(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set mid initials of the Person

setName(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolParameter

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

Set the name of the Comment

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

set the name of the Ontology

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Set the name of the Protocol

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

setName(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

setNextStudyOrAssayTableObject(StudyOrAssayTableObject) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

setOntologies(List<Ontology>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set linked Ontology

setOutput(StudyOrAssayTableObject) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

Declares the output of this Process.

setOutputStream(OutputStream) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

setParameters(List<ProtocolParameter>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Set the URI of the Protocol

setParameterValues(List<ParameterValue>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

setPath(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

setPhone(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set phone number of the Person

setProtocol(Protocol) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

setProtocols(List<Protocol>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

setPublications(ArrayList<Publication>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set publications of study

setPublications(List<Publication>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set Publication of investigation

setPublications(List<Publication>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

setPublicReleaseDate(LocalDate) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set PublicReleaseDate

setPublicReleaseDate(Date) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set public releaseDate of study

setPubmedID(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Set the pubmedID of the Publication

setRoles(List<OntologyAnnotation>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

Set role of the Person

setSourceREF(Ontology) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

set source REF

setStatus(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Set status of the Publication

setStudies(List<Study>) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set studies of investigation

setStudy(Study) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

setSubmissionDate(LocalDate) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set SubmissionDate

setSubmissionDate(Date) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set submissionDate of study

setTechnologyPlatform(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

setTechnologyType(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

setTerm(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

set term of ontology term

setTermAccession(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

set accession number of ontology term

setTitle(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

Set title

setTitle(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

Set title of the Publication

setTitle(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Set title of study

setType(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

Set OntologyAnnotation of the Factor type

setType(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Set the type of the Ontology

setType(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

setType(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

setType(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Material

setURI(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the URI of the Protocol

setURL(URL) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

set the url or path of the Ontology

setValue(OntologyAnnotation) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

Sets the value of this characteristic.

setValue(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

Set the value of the Comment

setVersion(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

set the version of the Ontology

setVersion(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

Get the version of the Protocol

Source - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Source(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Source

Source(String, List<Characteristic>) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Source

SOURCE_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

SPACE - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

SPATIAL_DISTRIBUTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

provided as a key-value pair of the form type:value.

SPECIES - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

for the organism under study, according to standard scientific nomenclature.

StringUtil - Class in de.ipk_gatersleben.bit.bi.isa4j.util

Utility class with functions to handle several String tasks

StringUtil() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.util.StringUtil

Study - Class in de.ipk_gatersleben.bit.bi.isa4j.components

Class to represent a study in context of the ISA hierarchy.

Study(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Constructor, give the identifier of study, filename is same with identifier

Study(String, String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.Study

Constructor, give the identifier and filename

STUDY - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_ALTITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Altitude of the experimental site, provided in metres (m).

STUDY_ASSAY_FILE_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_ASSAY_MEASUREMENT_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_ASSAY_TECHNOLOGY_PLATFORM - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_ASSAY_TECHNOLOGY_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_ASSAYS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_CONTACT_INSTITUTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Name and address of the institution responsible for the study.

STUDY_CONTACTS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_COUNTRY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

The country where the experiment took place, either as a full name or preferably as a 2-letter code.

STUDY_DATA_FILE_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Description of the format of the data file.

STUDY_DATA_FILE_LINK - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

in a public database or in a persistant institutional repository; or identifier of the data file when submitted together with the MIAPPE submission.

STUDY_DATA_FILE_VERSION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

The version of the dataset (the actual data).

STUDY_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_DESIGN_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Short description of the experimental design, possibly including statistical design.

STUDY_DESIGN_DESCRIPTORS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_DESIGN_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_END_DATE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Date and, if relevant, time when the experiment ende
e.g. 2002-11-27
[optional]

STUDY_EXPERIMENTAL_SITE_NAME - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place.

STUDY_FACTOR_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Free text description of the experimental factor.

STUDY_FACTOR_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_FACTOR_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_FACTOR_VALUES - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

List of possible values for the factor.

STUDY_FACTORS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_FILE_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_IDENTIFIER - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_LATITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Latitude of the experimental site in degrees, in decimal format.

STUDY_LONGITUDE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Longititute of the experimental site in degrees, in decimal format.

STUDY_PERSON_ADDRESS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_AFFILIATION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_EMAIL - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_FAX - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_FIRST_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_ID - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

An identifier for the data submitter.

STUDY_PERSON_LAST_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_MID_INITIALS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_PHONE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PERSON_ROLES - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_COMPONENTS_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_COMPONENTS_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_PARAMETERS_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_TYPE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_URI - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOL_VERSION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PROTOCOLS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLIC_RELEASE_DATE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLICATION_AUTHOR_LIST - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLICATION_DOI - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLICATION_STATUS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLICATION_TITLE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBLICATIONS - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_PUBMED_ID - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_START_DATE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Date and, if relevant, time when the experiment started
e.g. 2002-04-04
[required]

STUDY_SUBMISSION_DATE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

STUDY_TITLE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

StudyAssayAttribute - Enum in de.ipk_gatersleben.bit.bi.isa4j.constants

Constants for fixed attribute names for Study and Assay file creation

StudyOrAssayTableObject - Class in de.ipk_gatersleben.bit.bi.isa4j.components

StudyOrAssayTableObject() - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.StudyOrAssayTableObject

Symbol - Enum in de.ipk_gatersleben.bit.bi.isa4j.constants

Constants for frequently used symbols String symbols and literals

T

TAB - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

TERM_ACCESSION_NUMBER - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

TERM_ACCESSION_NUMBER - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

TERM_SOURCE_DESCRIPTION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

TERM_SOURCE_FILE - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

TERM_SOURCE_NAME - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

TERM_SOURCE_REF - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

TERM_SOURCE_REF - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

TERM_SOURCE_VERSION - de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Assay

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Characteristic

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Comment

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.CommentCollection

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.DataFile

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Factor

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.FactorValue

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Material

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Ontology

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.OntologyAnnotation

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ParameterValue

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Person

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Process

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Protocol

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolComponent

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.ProtocolParameter

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Publication

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Sample

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Source

toString() - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Study

toString() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

toString() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

toString() - Method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

TRAIT_DEFINITION_FILE - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

(MIAPPE: name and url to Trait definition file.

TYPE_OF_GROWTH_FACILITY - de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology (subclass of CO_715:0000005).

U

UNIT - de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

V

validate(Assay) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

validate(Investigation) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

validate(Study) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

validateAssayFile(Assay) - Static method in class de.ipk_gatersleben.bit.bi.isa4j.configurations.GeneralValidation

Test if the given Assay is linked to a Study

validateInvestigationFile(Investigation) - Static method in class de.ipk_gatersleben.bit.bi.isa4j.configurations.GeneralValidation

Test if the given Investigation is associated with Study and Assay

validateStudyFile(Study) - Static method in class de.ipk_gatersleben.bit.bi.isa4j.configurations.GeneralValidation

Test if the given Study is linked to an Investigation

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.AssayFile

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.InvestigationFile

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.configurations.MIAPPEv1x1.StudyFile

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.InvestigationAttribute

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.StudyAssayAttribute

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

Returns an array containing the constants of this enum type, in the order they are declared.

W

WideTableConfigEnum - Interface in de.ipk_gatersleben.bit.bi.isa4j.configurations

Interface for providing functions for the specific Study and Assay fields of an ISA configuration

WideTableFile - Class in de.ipk_gatersleben.bit.bi.isa4j.components

WideTableFile(String) - Constructor for class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

Constructor, give the filename

WILDCARD - de.ipk_gatersleben.bit.bi.isa4j.constants.Symbol

writeHeadersFromExample(StudyOrAssayTableObject) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

writeLine(StudyOrAssayTableObject) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.WideTableFile

Write a single line for a Study or Assay into the corresponding OutputStream or File.

writeToFile(String) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

writeToStream(OutputStream) - Method in class de.ipk_gatersleben.bit.bi.isa4j.components.Investigation

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