A C G I S T U

A

addSynonym(String) - Method in class uk.ac.ebi.sbo.common.Term
Adds a synonym to the list of synonyms.

C

convertId(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Converts an unofficial SBO identifier (Integer) into an official one (String).

G

getChildren(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of direct children of the given SBO term.
getComment() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getDateCreation() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getDateUpdate() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getDefinition() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getFramework(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the value of the framework (its identifier) given an SBO expression identifier.
getIdentifier() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getIdentifierInt() - Method in class uk.ac.ebi.sbo.common.Term
Getter of the numerical part of the identifier, without the "SBO:" but with the front '0's.
getJavaLibraryVersion() - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the latest version of the Java library available.
getMathml() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getName() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getObsolete() - Method in class uk.ac.ebi.sbo.common.Term
Getter (for usage in JSTL, cf. http://stackoverflow.com/questions/1118261/what-is-the-correct-syntax-for-is-variable-getter-setters-in-a-pojo-class)
getOWLTerm(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the OWL of a term, given its identifier.
getOWLTerms(List<String>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the OWL version of a list of terms, given their identifiers.
getOWLTree(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves in the OWL format, the subtree starting from the term which identifier is given in parameter.
getParents(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of direct parents of the given SBO term.
getRoot() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getServicesInfo() - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves some information about these Web Services.
getServicesVersion() - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the current version of these Web Services.
getStringTermById(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getXMLTerm(String) instead, as an official SBO identifier looks like SBO:0000192.
getStringTermsByIds(List<Integer>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getXMLTerms(List) instead, as an official SBO identifier looks like SBO:0000192.
getStringTree(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getXMLTree(String) instead, as an official SBO identifier looks like SBO:0000192.
getSynonym(int) - Method in class uk.ac.ebi.sbo.common.Term
Retrieves a specific synonym from the list of synonyms.
getSynonyms() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getTerm(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the Term corresponding to the given identifier.
getTermById(int) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getTerm(String) instead, as an official SBO identifier looks like SBO:0000192.
getTermByIdOWL(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getOWLTerm(String) instead, as an official SBO identifier looks like SBO:0000192.
getTerms(List<String>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of Term corresponding to the given identifiers.
getTermsByIds(List<Integer>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getTerms(List) instead, as official SBO identifiers look like SBO:0000192.
getTermsByIdsOWL(List<Integer>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getOWLTerms(List) instead, as an official SBO identifier looks like SBO:0000192.
getTree(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of Term which composed the subtree starting with the term corresponding to the given identifier.
getTree(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getTree(String) instead, as an official SBO identifier looks like SBO:0000192.
getTreeOWL(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use getOWLTree(String) instead, as an official SBO identifier looks like SBO:0000192.
getType() - Method in class uk.ac.ebi.sbo.common.Term
Getter
getXMLTerm(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the XML version of a term, given its identifier.
getXMLTerms(List<String>) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the XML version of a list of terms, given their identifiers.
getXMLTree(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the subtree starting from the given term.

I

isChildOf(String, String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Checks if one term is a child (even indirect) of a second term.
isChildOf(Integer, Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use isChildOf(String, String) instead, as an official SBO identifier looks like SBO:0000192.
isDirectChildOf(String, String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Checks if one term is a direct child of a second term.
isDirectChildOf(Integer, Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use isDirectChildOf(String, String) instead, as an official SBO identifier looks like SBO:0000192.
isLibraryUpdated() - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Tests if the Java library used is the latest available.
isObsolete() - Method in class uk.ac.ebi.sbo.common.Term
Getter
isObsolete(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
checks if a term is obsolete or not.
isObsolete(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use isObsolete(String) instead, as an official SBO identifier looks like SBO:0000192.
isRoot(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Checks if a term is root or not.
isRoot(Integer) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Deprecated. Use isRoot(String) instead, as an official SBO identifier looks like SBO:0000192.

S

sayHi(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Returns to the user the sentence he sent.
SBOLink - Class in uk.ac.ebi.sbo.ws.client
SBO JAX-WS library (interface between the end user and the Web Services).
SBOLink() - Constructor for class uk.ac.ebi.sbo.ws.client.SBOLink
Default constructor.
search(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Global search on the whole content of the ontology.
searchOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which related information (name, synonym, definition, comment, mathML) contain the given parameter.
searchPossibleCompletions(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of Term which name contains the word(s) given in parameter.
searchPossibleCompletionsOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the OWL version of the list of terms which name contains the word(s) given in parameter.
searchString(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which related information (name, synonym, definition, comment, mathML) contain the given parameter.
searchStringPossibleCompletions(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which name contains the given parameter.
searchStringTermDetails(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which details contain the given parameter.
searchStringTermMath(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which MathML contain the given parameter.
searchStringTermName(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which name contain the given parameter.
searchStringTermSynonyms(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which synonym(s) contain the given parameter.
searchTermDetails(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Searches for the occurrence of the given parameter in the details (comment and definition) of terms from the ontology.
searchTermDetailsOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which details contain the given parameter.
searchTermMath(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Searches for the occurrence of the word given in parameter in the MathML of terms in the ontology.
searchTermMathOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which MathML contain the given parameter.
searchTermName(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Searches for the occurrence of the word given in parameter in the name of terms of the ontology.
searchTermNameOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which name contain the given parameter.
searchTermSynonyms(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of Term with a synonym containing the word(s) given in parameter.
searchTermSynonymsOWL(String) - Method in class uk.ac.ebi.sbo.ws.client.SBOLink
Retrieves the list of terms which synonym contains the given parameter.
setComment(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setDateCreation(Date) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setDateUpdate(Date) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setDefinition(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setIdentifier(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setIdentifier(Integer) - Method in class uk.ac.ebi.sbo.common.Term
Setter for data coming from database, the accession does not include the 'SBO:'
setMathml(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setName(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setObsolete(Boolean) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setObsolete(Integer) - Method in class uk.ac.ebi.sbo.common.Term
Setter for with data coming from database (1 or 0).
setRoot(Boolean) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setRoot(Integer) - Method in class uk.ac.ebi.sbo.common.Term
Setter for with data coming from database (1 or 0).
setSynonyms(List<String>) - Method in class uk.ac.ebi.sbo.common.Term
Setter
setType(String) - Method in class uk.ac.ebi.sbo.common.Term
Setter

T

Term - Class in uk.ac.ebi.sbo.common
Simpler and easy object which stores everything about a term.
Term() - Constructor for class uk.ac.ebi.sbo.common.Term
Constructor
toString() - Method in class uk.ac.ebi.sbo.common.Term
Returns a string representation of the object.

U

uk.ac.ebi.sbo.common - package uk.ac.ebi.sbo.common
 
uk.ac.ebi.sbo.ws.client - package uk.ac.ebi.sbo.ws.client
 

A C G I S T U

BioModels.net, EMBL-EBI - 12 Mar 2013