A B C D E F G H I M O P R S T U V W X

A

accessions - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

B

between(MmDatabase, MmDatabase) - Static method in enum uk.ac.ebi.ep.mm.Relationship
Gets the usual relationship between two databases.

C

characters(char[], int, int) - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
characters(char[], int, int) - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
ChebiCompounds - Class in uk.ac.ebi.ep.mm.app
 
ChebiCompounds() - Constructor for class uk.ac.ebi.ep.mm.app.ChebiCompounds
 
CliOptionsParser - Class in uk.ac.ebi.ep.mm.app
A parser of the command line options for the mega-mapper parsers.
CliOptionsParser() - Constructor for class uk.ac.ebi.ep.mm.app.CliOptionsParser
 
closeMap() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
closeMap() - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
Closes the mega-map.
closeMap() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
closeMap() - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Closes the mega-map.
commit() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
commit() - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
commit() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
commit() - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Commits any pending changes to the underlying mega-map.
Compounds - Class in uk.ac.ebi.ep.mm.app
 
Compounds() - Constructor for class uk.ac.ebi.ep.mm.app.Compounds
 
Compounds(Long) - Constructor for class uk.ac.ebi.ep.mm.app.Compounds
 
Compounds(String, String) - Constructor for class uk.ac.ebi.ep.mm.app.Compounds
 
Compounds(Long, String, String, Date, String, String) - Constructor for class uk.ac.ebi.ep.mm.app.Compounds
 
CompoundsDAOImpl - Class in uk.ac.ebi.ep.mm.app
This class is to retrieve compounds from chebi database and write them to the mega mapper
CompoundsDAOImpl(String) - Constructor for class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
computeChebiEntry(String, String) - Method in class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
computeUniprotEntry(String, String) - Method in class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
computeXref(Entry, Entry, String) - Method in class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
currentChars - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
The text value of the current element being parsed.
CustomEntity - Class in uk.ac.ebi.ep.mm.app
the aim of this class if to provide a transfer object ( place holder) for the entities that will be returned from the hibernate query
CustomEntity() - Constructor for class uk.ac.ebi.ep.mm.app.CustomEntity
 
CustomEntity(Compounds) - Constructor for class uk.ac.ebi.ep.mm.app.CustomEntity
 
CustomEntity(Reference) - Constructor for class uk.ac.ebi.ep.mm.app.CustomEntity
 
CustomEntity(Compounds, Reference) - Constructor for class uk.ac.ebi.ep.mm.app.CustomEntity
 
CustomEntity(String, String, String, String, String) - Constructor for class uk.ac.ebi.ep.mm.app.CustomEntity
 

D

DatabaseResources - Class in uk.ac.ebi.ep.mm.app
 
DatabaseResources(String) - Constructor for class uk.ac.ebi.ep.mm.app.DatabaseResources
 
deleteEntry(Entry) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
Deletes one entry and all the associated accessions and xrefs.

E

EbeyeParser - Class in uk.ac.ebi.ep.mm.app
Deprecated. use EbeyeSaxParser instead, this one requires lots of memory for big files.
EbeyeParser() - Constructor for class uk.ac.ebi.ep.mm.app.EbeyeParser
Deprecated.  
EbeyeSaxParser - Class in uk.ac.ebi.ep.mm.app
Parser for EB-Eye XML files to populate a mega-map.
EbeyeSaxParser() - Constructor for class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
ecs - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
endDocument() - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
endElement(String, String, String) - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
endElement(String, String, String) - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
Stores interesting data into the index.
Entry - Class in uk.ac.ebi.ep.mm
 
Entry() - Constructor for class uk.ac.ebi.ep.mm.Entry
 
entryNames - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
equals(Object) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
equals(Object) - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
equals(Object) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
equals(Object) - Method in class uk.ac.ebi.ep.mm.Entry
 
equals(Object) - Method in class uk.ac.ebi.ep.mm.XRef
 

F

finalize() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
finalize() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 

G

getAccession_number() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getAccessionField() - Method in enum uk.ac.ebi.ep.mm.MmDatabase
 
getAllUniProtAccessions(MmDatabase) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getAllUniProtAccessions(MmDatabase) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
to retrieve all accessions for the given database
getAllUniProtAccessions(MmDatabase) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getAllUniProtAccessions(MmDatabase) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
 
getAsciiName() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getCHEBI_Compounds() - Method in class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
getCHEBI_Compounds() - Method in interface uk.ac.ebi.ep.mm.app.ICompoundsDAO
 
getChebiAccession() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getChMBLXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getChMBLXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
retrieves a List of XRef with database name as ChEMBL.
getChMBLXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getChMBLXrefs(MmDatabase, String, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given accession where database name is CheMBL.
getCompound_id() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getCompounds() - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
getCompounds(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getCompounds(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getCompounds(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getCompounds(MmDatabase, String, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
 
getCompoundsCollection() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getCompoundsNew(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getConnection(String) - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
getCreatedBy() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getCreatedOn() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getCurrentXpath() - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
getCurrentXpath() - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
getDbName() - Method in class uk.ac.ebi.ep.mm.Entry
 
getDefinition() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getDisease(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getDisease(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getDisease(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getDisease(MmDatabase, String, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
 
getDiseaseNew(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getEntryAccessions() - Method in class uk.ac.ebi.ep.mm.Entry
 
getEntryForAccession(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getEntryForAccession(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
Retrieves an entry for a given accession.
getEntryForAccession(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getEntryForAccession(MmDatabase, String) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves an entry for a given accession.
getEntryId() - Method in class uk.ac.ebi.ep.mm.Entry
 
getEntryName() - Method in class uk.ac.ebi.ep.mm.Entry
 
getFromEntry() - Method in class uk.ac.ebi.ep.mm.XRef
 
getId() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getId() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getId() - Method in class uk.ac.ebi.ep.mm.Entry
 
getId() - Method in class uk.ac.ebi.ep.mm.XRef
 
getIdField() - Method in enum uk.ac.ebi.ep.mm.MmDatabase
 
getIndexDir(String) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getLocation_in_ref() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getMegaMapper() - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
getMergeType() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getModifiedBy() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getModifiedOn() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getName() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getNameField() - Method in enum uk.ac.ebi.ep.mm.MmDatabase
 
getParentId() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getReference() - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
getReference_id() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getReference_name() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
getRelationship() - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
getRelationship() - Method in class uk.ac.ebi.ep.mm.XRef
 
getSessionFactory() - Static method in class uk.ac.ebi.ep.mm.app.HibernateUtil
 
getSessionFactory() - Static method in class uk.ac.ebi.ep.mm.HibernateUtil
 
getSessionFactory(String) - Static method in class uk.ac.ebi.ep.mm.HibernateUtil
 
getSource() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getStar() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
getToEntry() - Method in class uk.ac.ebi.ep.mm.XRef
 
getValueOfEnum(Class<T>, String) - Static method in class uk.ac.ebi.ep.mm.app.CompoundsDAOImpl
 
getXrefs(Entry) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(Entry, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(Collection<Entry>, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
Retrieves cross references from the mega-map for a given accession (not ID) to/from the given database(s).
getXrefs(MmDatabase, String, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefs(Entry) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(Entry, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(Collection<Entry>, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(MmDatabase, String, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
getXrefs(Entry) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(Entry, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(Collection<Entry>, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(MmDatabase, String) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(MmDatabase, String, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, Relationship) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(MmDatabase, String, MegaMapper.Constraint, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefs(Entry) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map regardless of the referencing/referenced database.
getXrefs(Entry, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map.
getXrefs(Collection<Entry>, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for several entries.
getXrefs(MmDatabase, String) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given accession (not ID) regardless of the referencing/referenced database..
getXrefs(MmDatabase, String, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given accession (not ID) to/from the given database(s).
getXrefs(MmDatabase, String, Relationship) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given accession (not ID) given a concrete relationship.
getXrefs(MmDatabase, String, MegaMapper.Constraint, Relationship) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given text which matches an entry ID, who has a given relationship (if any).
This method is provided in order to search for UniProt ID prefixes (ex.
getXrefs(MmDatabase, String, MegaMapper.Constraint, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Retrieves cross references from the mega-map for a given text which matches an entry ID, who is related to the given databases.
This method is provided in order to search for UniProt ID prefixes (ex.
getXrefsSize(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
getXrefsSize(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
retrieves the total number of Xrefs found for a given accession.
getXrefsSize(MmDatabase, String, MmDatabase...) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
getXrefsSize(MmDatabase, String, MmDatabase...) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
retrieves the total number of Xrefs found for a given accession.

H

handleError() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
handleError() - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
handleError() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
handleError() - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Handles any errors which might affect the mega-map.
hashCode() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
hashCode() - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
hashCode() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
hashCode() - Method in class uk.ac.ebi.ep.mm.Entry
 
hashCode() - Method in class uk.ac.ebi.ep.mm.XRef
 
HibernateUtil - Class in uk.ac.ebi.ep.mm.app
Hibernate Utility class with a convenient method to get Session Factory object.
HibernateUtil() - Constructor for class uk.ac.ebi.ep.mm.app.HibernateUtil
 
HibernateUtil - Class in uk.ac.ebi.ep.mm
 
HibernateUtil() - Constructor for class uk.ac.ebi.ep.mm.HibernateUtil
 

I

ICompoundsDAO - Interface in uk.ac.ebi.ep.mm.app
 
ILLEGAL_COMPOUND - Static variable in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
isAccession - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isDbRef - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isEntry - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isEntryName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isOrgComName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isOrgSciName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isProperty - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
isProtRecName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

M

main(String...) - Static method in class uk.ac.ebi.ep.mm.app.ChebiCompounds
 
main(String...) - Static method in class uk.ac.ebi.ep.mm.app.EbeyeParser
Deprecated. Parses a EB-Eye XML file and indexes/stores the database identifiers corresponding to UniProt accessions.
main(String...) - Static method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
Parses a EB-Eye XML file and indexes/stores the entry IDs, accessions and xrefs into a mega-map.
main(String[]) - Static method in class uk.ac.ebi.ep.mm.app.Uniprot2DiseaseParser
Parses the HTML file and stores in the mega-map the xrefs from UniProt accessions to OMIM and MeSH terms, but only if the scores is equal or greater than Uniprot2DiseaseParser.minScore.
main(String...) - Static method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a mega-map.
MegaDbMapper - Class in uk.ac.ebi.ep.mm
Objects of this class write the mega-map to a database managed via hibernate.
MegaDbMapper(String, int) - Constructor for class uk.ac.ebi.ep.mm.MegaDbMapper
 
MegaJdbcMapper - Class in uk.ac.ebi.ep.mm
Plain JDBC implementation of MegaMapper.
MegaJdbcMapper(Connection) - Constructor for class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
MegaLuceneMapper - Class in uk.ac.ebi.ep.mm
Mega-mapper writing/reading to/from a lucene index.
MegaLuceneMapper(String) - Constructor for class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
MegaMapper - Interface in uk.ac.ebi.ep.mm
Interface for objects writing/reading entries and cross-references to/from the mega-map.
MegaMapper.Constraint - Enum in uk.ac.ebi.ep.mm
 
MmDatabase - Enum in uk.ac.ebi.ep.mm
Databases included in the mega-map (or encountered in some way during the process of building it).
MmParser - Interface in uk.ac.ebi.ep.mm.app
Interface for objects parsing data for the mega-mapper.

O

openMap() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
openMap() - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
Opens the mega-map for writing.
openMap() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
openMap() - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Opens the mega-map for writing.
orgComName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
orgSciName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

P

parse(String) - Method in class uk.ac.ebi.ep.mm.app.EbeyeParser
Deprecated.  
parse(String) - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
parse(String) - Method in interface uk.ac.ebi.ep.mm.app.MmParser
Parses a XML file and extracts interesting data into a mega-map.
parse(String) - Method in class uk.ac.ebi.ep.mm.app.Uniprot2DiseaseParser
 
parse(String) - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
Parses a UniProt XML file and indexes/stores the UniProt accessions, IDs and organisms into a lucene index.
This method is not thread safe.
parse(String) - Static method in enum uk.ac.ebi.ep.mm.MmDatabase
Parses a string into a MmDatabase value.
pdbCodes - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
protRecName - Variable in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

R

Reference - Class in uk.ac.ebi.ep.mm.app
 
Reference() - Constructor for class uk.ac.ebi.ep.mm.app.Reference
 
Reference(String, String, String) - Constructor for class uk.ac.ebi.ep.mm.app.Reference
 
Relationship - Enum in uk.ac.ebi.ep.mm
 
rollback() - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
rollback() - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
rollback() - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
rollback() - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Rolls back any pending changes to the underlying mega-map.

S

session - Variable in class uk.ac.ebi.ep.mm.MegaDbMapper
 
setAccession_number(String) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setAsciiName(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setChebiAccession(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setCompound_id(Long) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setCompoundsCollection(Collection<Compounds>) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setCreatedBy(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setCreatedOn(Date) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setDbName(String) - Method in class uk.ac.ebi.ep.mm.Entry
 
setDefinition(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setEntryAccessions(List<String>) - Method in class uk.ac.ebi.ep.mm.Entry
 
setEntryId(String) - Method in class uk.ac.ebi.ep.mm.Entry
 
setEntryName(String) - Method in class uk.ac.ebi.ep.mm.Entry
 
setFromEntry(Entry) - Method in class uk.ac.ebi.ep.mm.XRef
 
setId(Long) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setId(Long) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setId(Integer) - Method in class uk.ac.ebi.ep.mm.Entry
 
setId(Integer) - Method in class uk.ac.ebi.ep.mm.XRef
 
setLocation_in_ref(String) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setMergeType(Character) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setModifiedBy(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setModifiedOn(Date) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setName(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setParentId(Compounds) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setReference_id(String) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setReference_name(String) - Method in class uk.ac.ebi.ep.mm.app.Reference
 
setRelationship(String) - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
setRelationship(String) - Method in class uk.ac.ebi.ep.mm.XRef
 
setSource(String) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setStar(BigInteger) - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
setToEntry(Entry) - Method in class uk.ac.ebi.ep.mm.XRef
 
setWriter(MegaMapper) - Method in class uk.ac.ebi.ep.mm.app.EbeyeParser
Deprecated.  
setWriter(MegaMapper) - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
setWriter(MegaMapper) - Method in interface uk.ac.ebi.ep.mm.app.MmParser
Sets a writer to make the mega-map persistent.
setWriter(MegaMapper) - Method in class uk.ac.ebi.ep.mm.app.Uniprot2DiseaseParser
 
setWriter(MegaMapper) - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
startDocument() - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 
startElement(String, String, String, Attributes) - Method in class uk.ac.ebi.ep.mm.app.EbeyeSaxParser
 
startElement(String, String, String, Attributes) - Method in class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

T

toString() - Method in class uk.ac.ebi.ep.mm.app.Compounds
 
toString() - Method in class uk.ac.ebi.ep.mm.app.CustomEntity
 
toString() - Method in class uk.ac.ebi.ep.mm.app.Reference
 
toString() - Method in class uk.ac.ebi.ep.mm.Entry
 
toString() - Method in class uk.ac.ebi.ep.mm.XRef
 

U

uk.ac.ebi.ep.mm - package uk.ac.ebi.ep.mm
 
uk.ac.ebi.ep.mm.app - package uk.ac.ebi.ep.mm.app
 
Uniprot2DiseaseParser - Class in uk.ac.ebi.ep.mm.app
Class to parse the HTML file containing a table of equivalences from UniProt accessions to OMIM IDs and MeSH terms.
Uniprot2DiseaseParser() - Constructor for class uk.ac.ebi.ep.mm.app.Uniprot2DiseaseParser
 
UniprotSaxParser - Class in uk.ac.ebi.ep.mm.app
UniProt XML parser which takes into account only primary accessions, entry names (IDs), organisms, EC numbers and PDB codes, and indexes/stores them in a mega-map.
UniprotSaxParser() - Constructor for class uk.ac.ebi.ep.mm.app.UniprotSaxParser
 

V

valueOf(String) - Static method in enum uk.ac.ebi.ep.mm.MegaMapper.Constraint
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.ep.mm.MmDatabase
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.ep.mm.Relationship
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.ebi.ep.mm.MegaMapper.Constraint
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.ep.mm.MmDatabase
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.ep.mm.Relationship
Returns an array containing the constants of this enum type, in the order they are declared.

W

write(Collection<Entry>, Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
write(Collection<Entry>, Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
write(Collection<Entry>, Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
write(Collection<Entry>, Collection<XRef>) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Writes entries and relationships to the mega-map.
writeEntries(Collection<Entry>) - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
writeEntries(Collection<Entry>) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
writeEntries(Collection<Entry>) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
writeEntries(Collection<Entry>) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
writeEntries(Collection<Entry>) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
 
writeEntry(Entry) - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
writeEntry(Entry) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
writeEntry(Entry) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
writeEntry(Entry) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
writeEntry(Entry) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Writes one entry to the mega-map.
writeXref(XRef) - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
writeXref(XRef) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
writeXref(XRef) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
Writes one cross-reference to the mega-map.
writeXref(XRef) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
Writes one cross-reference to the mega-map.
writeXref(XRef) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
Writes one cross-reference to the mega-map.
writeXrefs(Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.app.DatabaseResources
 
writeXrefs(Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaDbMapper
 
writeXrefs(Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaJdbcMapper
 
writeXrefs(Collection<XRef>) - Method in class uk.ac.ebi.ep.mm.MegaLuceneMapper
 
writeXrefs(Collection<XRef>) - Method in interface uk.ac.ebi.ep.mm.MegaMapper
 

X

XRef - Class in uk.ac.ebi.ep.mm
This class is one case of triple, same as found in RDF.
XRef() - Constructor for class uk.ac.ebi.ep.mm.XRef
 

A B C D E F G H I M O P R S T U V W X

Copyright © 2012 EMBL-EBI. All Rights Reserved.