A C D E G H I M R S T U W

A

addDeprecatedURI(URI) - Method in class uk.ac.ebi.miriam.data.DataType
Adds a URI to the list of deprecated URIs.
addDoc(URI) - Method in class uk.ac.ebi.miriam.data.DataType
Adds another reference to a piece of documentation
addResource(Resource) - Method in class uk.ac.ebi.miriam.data.DataType
Adds another resource to the data type
addSynonym(String) - Method in class uk.ac.ebi.miriam.data.DataType
Adds a synonym to the list of synonyms.
addTag(String, String) - Method in class uk.ac.ebi.miriam.data.DataType
Adds one tag to the list.

C

checkRegExp(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Checks if the identifier given follows the regular expression of its data collection (also provided).
compareTo(Object) - Method in class uk.ac.ebi.miriam.data.DataType
Compares to objects and determine whether they are equivalent or not.
compareTo(Object) - Method in class uk.ac.ebi.miriam.data.Resource
Compares to objects and determine whether they are equivalent or not.
compareTo(Object) - Method in class uk.ac.ebi.miriam.data.URI
Compares to objects and determine whether they are equivalent or not.
convertURL(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Converts an Identifiers.org URL into its equivalent MIRIAM URN.
convertURLs(String[]) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Converts a list of Identifiers.org URLs into their equivalent MIRIAM URNs.
convertURN(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Converts a MIRIAM URN into its equivalent Identifiers.org URL.
convertURNs(String[]) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Converts a list of MIRIAM URNs into their equivalent Identifiers.org URLs.

D

DataType - Class in uk.ac.ebi.miriam.data
Contains all the information about a MIRIAM data type.
DataType() - Constructor for class uk.ac.ebi.miriam.data.DataType
Default constructor
destroy() - Method in class uk.ac.ebi.miriam.data.DataType
Destroys the object (free the memory)

E

equals(Resource) - Method in class uk.ac.ebi.miriam.data.Resource
Tests if two Resource objects are the same (only checks the ID).
equals(Object) - Method in class uk.ac.ebi.miriam.data.URI
Indicates whether some other object is "equal to" this one.

G

getAddress() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Getter of the address of the web services (endPoint).
getDataEntries(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getLocations(String, String) instead.
getDataEntries(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getLocations(String) instead.
getDataEntriesPrefix() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the prefix of the physical location of all the data entries (one precise element)
getDataEntriesSuffix() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the suffix of the physical location of all the data entries (one precise element)
getDataEntry(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getLocation(String, String) instead.
getDataEntryPrefix(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the prefix of the physical location of one data entry (one precise element) WARNING: no check of the validity of the parameter ('out of range' possible...)
getDataEntrySuffix(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the suffix of the physical location of one data entry (one precise element)
getDataResource(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the physical location of one precise resource (information page)
getDataResources() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the physical locations of all the resources (information page)
getDataResources(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves all the physical locations (URLs) of the services providing the data collection (web page).
getDataTypeAllURIs(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getDataTypeURIs(String) instead.
getDataTypeDef(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the definition of a data collection.
getDataTypePattern(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the pattern (regular expression) used by the identifiers within a data collection.
getDataTypesId() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the internal identifier (stable and perennial) of all the data collections (for example: "MIR:00000005").
getDataTypesName() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the list of names of all the data collections available.
getDataTypeSynonyms(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves all the synonym names of a data collection (this list includes the original name).
getDataTypeURI(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. URLs are not used any more as identifiers in MIRIAM. A new scheme as been released based on URNs. Use MiriamLink.getDataTypeURI(String) instead.
getDataTypeURI(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the unique (official) URI of a data collection (example: "urn:miriam:uniprot").
getDataTypeURIs(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. URLs are not used any more as identifiers in MIRIAM. A new scheme as been released based on URNs. Use MiriamLink.getDataTypeURIs(String) instead.
getDataTypeURIs(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves all the URIs of a data collection, including all the deprecated ones (examples: "urn:miriam:uniprot", "http://www.uniprot.org/", "urn:lsid:uniprot.org:uniprot", ...).
getDataTypeURL(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. URLs are not used any more as identifiers in MIRIAM. A new scheme as been released based on URNs. Use MiriamLink.getDataTypeURI(String) instead.
getDataTypeURLs(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. URLs are not used any more as identifiers in MIRIAM. A new scheme as been released based on URNs. You can use MiriamLink.getDataTypeURIs(String) instead.
getDataTypeURN(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getDataTypeURI(String) instead.
getDataTypeURNs(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getDataTypeURIs(String) instead.
getDateCreation() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the date (Date) of creation of the data type
getDateModification() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the date (Date) of last modification of the data type
getDefinition() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the definition of the data type
getDeprecatedURI(int) - Method in class uk.ac.ebi.miriam.data.DataType
Returns one precise deprecated URI of the data type
getDeprecatedURIs() - Method in class uk.ac.ebi.miriam.data.DataType
Returns all the deprecated URIs of the data type
getDoc(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of a specific reference to a piece of documentation
getDocs() - Method in class uk.ac.ebi.miriam.data.DataType
Getter
getExample() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the example
getHtmlUrl() - Method in class uk.ac.ebi.miriam.data.Resource
Returns the URL to access an example of data stored by this resource, specially formated for HTML usage in javascript functions.
getId() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the stable ID (in the database) of the data type
getId() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the stable identifier of the resource
getInfo() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of some general information about the resource
getInstitution() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the institution managing the resource
getLibraryVersion() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the current version of MIRIAM Web Services Library.
getLocation() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the country of the institution
getLocation(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the physical location (URL) of a web page providing knowledge about a specific entity, using a specific resource.
getLocations(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the physical locationS (URLs) of web pageS providing knowledge about a specific entity.
getLocations(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the physical locationS (URLs) of web pageS providing knowledge about an entity.
getLocationsWithToken(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the list of (non obsolete) generic physical locations (URLs) of web pageS providing the dataset of a given data collection.
getMiriamURI(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Transforms a MIRIAM URI into its official equivalent (to transform obsolete URIs into current valid ones).
getName() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the official name (not a synonym) of the data type
getName(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the common name of a data collection.
getNames(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves all the names (with synonyms) of a data collection.
getObsoleteComment() - Method in class uk.ac.ebi.miriam.data.DataType
Getter
getOfficialDataTypeURI(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the official URI (it will always be URN) of a data collection corresponding to the deprecated one.
getOfficialURI(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getOfficialDataTypeURI(String) instead.
getRegexp() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the regular expression of the data type
getReplacedBy() - Method in class uk.ac.ebi.miriam.data.DataType
Getter
getResource(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of a specific resource (physical location) of the data type
getResourceInfo(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the information about a resource.
getResourceInstitution(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the institution which manages a resource (example: "European Bioinformatics Institute").
getResourceLocation(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the location (or country) of a resource (example: "United Kingdom").
getResources() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the resources (physical locations) of the data type
getServicesInfo() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves some information about these Web Services.
getServicesVersion() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the current version of MIRIAM Web Services.
getSynonym(int) - Method in class uk.ac.ebi.miriam.data.DataType
Getter of one of the synonyms of the name of the data type
getSynonyms() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the synonyms of the name of the data type
getTags() - Method in class uk.ac.ebi.miriam.data.DataType
Getter
getType() - Method in class uk.ac.ebi.miriam.data.URI
Getter
getTypeURL() - Static method in class uk.ac.ebi.miriam.data.URI
Getter of the URL type of URI
getTypeURN() - Static method in class uk.ac.ebi.miriam.data.URI
Getter of the URN type of URI
getURI() - Method in class uk.ac.ebi.miriam.data.URI
Getter
getURI(String, String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getURI(String, String) instead.
getURI(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the unique MIRIAM URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202").
getURIs(String[], String[]) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Retrieves the unique URIs for a list of specific entities (example: "urn:miriam:obo.go:GO%3A0045202").
getURL(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getURI(String, String) instead.
getUrl_prefix() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the prefix part of the address (link to an element)
getUrl_root() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the resource address (front page)
getUrl_suffix() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the suffix part of the address (link to an element)
getURN() - Method in class uk.ac.ebi.miriam.data.DataType
Getter of the official URN of the data type
getURN(String, String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Deprecated. Use MiriamLink.getURI(String, String) instead.

H

hasOfficialResource() - Method in class uk.ac.ebi.miriam.data.DataType
Checks if the data type has (at least) one resource is official (there is at least one resource and the resources are not all deprecated)

I

isDeprecated(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
To know if a URI of a data collection is deprecated.
isLibraryUpdated() - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Tests if the Java library used is the latest available.
isObsolete() - Method in class uk.ac.ebi.miriam.data.DataType
Getter
isObsolete() - Method in class uk.ac.ebi.miriam.data.Resource
Getter of the obsolete parameter

M

main(String[]) - Static method in class uk.ac.ebi.miriam.test.WebServicesTesting
Sample testing program
MiriamLink - Class in uk.ac.ebi.miriam.lib
Library for using MIRIAM Registry Web Services easily (via a Java program).
MiriamLink() - Constructor for class uk.ac.ebi.miriam.lib.MiriamLink
Default constructor: initialisation of some parameters

R

Resource - Class in uk.ac.ebi.miriam.data
Contains all the information about a MIRIAM resource.
Resource() - Constructor for class uk.ac.ebi.miriam.data.Resource
Default constructor (empty object).

S

setAddress(String) - Method in class uk.ac.ebi.miriam.lib.MiriamLink
Setter of the address of the web services (endPoint).
setDateCreation(Date) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the date (Date) of creation of the data type
setDateModification(Date) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the date (Date) of last modification of the data type
setDefinition(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the definition of the data type
setDeprecatedURIs(List<URI>) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the deprecated forms of the URI (URN or URL) of the data type
setDocs(List<URI>) - Method in class uk.ac.ebi.miriam.data.DataType
Setter
setExample(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the example.
setId(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the internal ID (in the database) of the data type
setId(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the stable identifier of the resource
setInfo(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of some general information about the resource
setInstitution(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the institution managing the resource
setLocation(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the country of the institution
setName(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the official name of the data type
setObsolete(boolean) - Method in class uk.ac.ebi.miriam.data.DataType
Setter
setObsolete(int) - Method in class uk.ac.ebi.miriam.data.DataType
Setter (from int)
setObsolete(boolean) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the obsolete parameter
setObsoleteComment(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter
setRegexp(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the regular expression of the data type
setReplacedBy(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter
setResources(List<Resource>) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the resources (physical locations) of the data type
setSynonyms(List<String>) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the synonyms of the data type
setTags(Map<String, String>) - Method in class uk.ac.ebi.miriam.data.DataType
Setter
setURI(String) - Method in class uk.ac.ebi.miriam.data.URI
Setter (also updates the type of URI)
setUrl_prefix(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the prefix part of the address (link to an element)
setUrl_root(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the resource address (front page)
setUrl_suffix(String) - Method in class uk.ac.ebi.miriam.data.Resource
Setter of the suffix part of the address (link to an element)
setURN(URI) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the official URN of the data type
setURN(String) - Method in class uk.ac.ebi.miriam.data.DataType
Setter of the official URN of the data type Warning: if the URI is actually a URL, its type will be 'URL'!

T

toString() - Method in class uk.ac.ebi.miriam.data.DataType
Overrides the 'toString()' method for the 'DataType' object
toString() - Method in class uk.ac.ebi.miriam.data.Resource
Overrides the 'toString()' method for the 'Resource' object
toString() - Method in class uk.ac.ebi.miriam.data.URI
Overrides the 'toString()' method for the 'Reference' object

U

uk.ac.ebi.miriam.data - package uk.ac.ebi.miriam.data
 
uk.ac.ebi.miriam.lib - package uk.ac.ebi.miriam.lib
 
uk.ac.ebi.miriam.test - package uk.ac.ebi.miriam.test
 
URI - Class in uk.ac.ebi.miriam.data
Contains all the information about a URI (which can be a URN or a URL).
URI() - Constructor for class uk.ac.ebi.miriam.data.URI
Default constructor.
URI(String) - Constructor for class uk.ac.ebi.miriam.data.URI
Constructor allowing to set a type of URI.
URI(URI.typeURI) - Constructor for class uk.ac.ebi.miriam.data.URI
Constructor allowing to set a type of URI.

W

WebServicesTesting - Class in uk.ac.ebi.miriam.test
Sample program in order to show the use of MiriamLib for accessing MIRIAM Registry Web Services
WebServicesTesting() - Constructor for class uk.ac.ebi.miriam.test.WebServicesTesting
 

A C D E G H I M R S T U W

BioModels.net, EMBL-EBI - Feb 2012