java.lang.Object
- psidev.psi.mi.jami.utils.XrefUtils

```
public class XrefUtils
extends Object
```
Utility class for Xrefs
Since:
```
24/01/13
```
Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors
Constructor Description

XrefUtils()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static Collection<Xref>`	`collectAllIdentifiersFrom(Collection<? extends Xref> refs)`	Method to return a sub collection of identifiers (qualifier identity or secondary) in a list of Xrefs
`static Collection<Xref>`	`collectAllXrefsHavingDatabase(Collection<? extends Xref> refs, String dbId, String dbName)`	Collect all cross references having a specific database
`static Collection<Xref>`	`collectAllXrefsHavingDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)`	Collect all cross references having a specific database
`static Collection<Xref>`	`collectAllXrefsHavingDatabaseAndQualifier(Collection<? extends Xref> refs, String dbId, String dbName, String qualifierId, String qualifierName)`	Collect all cross references having a specific database and qualifier
`static Collection<Xref>`	`collectAllXrefsHavingDatabaseQualifierAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id, String qualifierId, String qualifierName)`	Collect all cross references having a specific database and qualifier
`static Collection<Xref>`	`collectAllXrefsHavingQualifier(Collection<? extends Xref> refs, String qualifierId, String qualifierName)`	Collect all cross references having a specific qualifier
`static Collection<Xref>`	`collectAllXrefsHavingQualifierAndId(Collection<? extends Xref> refs, String qualifierId, String qualifierName, String id)`	Collect all cross references having a specific qualifier
`static Xref`	`collectFirstIdentifierWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName)`	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
`static Xref`	`collectFirstIdentifierWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)`	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
`static Xref`	`createChebiIdentity(String id)`	createChebiIdentity
`static Xref`	`createChebiSecondary(String id)`	createChebiSecondary
`static Xref`	`createDdbjEmblGenbankIdentity(String id)`	createDdbjEmblGenbankIdentity
`static Xref`	`createDdbjEmblGenbankSecondary(String id)`	createDdbjEmblGenbankSecondary
`static Xref`	`createDoiIdentity(String id)`	createDoiIdentity
`static Xref`	`createEnsemblGenomesIdentity(String ensembl)`	createEnsemblGenomesIdentity
`static Xref`	`createEnsemblGenomesSecondary(String ensembl)`	createEnsemblGenomesSecondary
`static Xref`	`createEnsemblIdentity(String ensembl)`	createEnsemblIdentity
`static Xref`	`createEnsemblSecondary(String ensembl)`	createEnsemblSecondary
`static Xref`	`createEntrezGeneIdIdentity(String geneId)`	createEntrezGeneIdIdentity
`static Xref`	`createEntrezGeneIdSecondary(String geneId)`	createEntrezGeneIdSecondary
`static Xref`	`createIdentityXref(String databaseName, String id)`	createIdentityXref
`static Xref`	`createIdentityXref(String databaseName, String databaseMi, String id)`	createIdentityXref
`static Xref`	`createPrimaryXref(String databaseName, String id)`	createPrimaryXref
`static Xref`	`createPrimaryXref(String databaseName, String databaseMi, String id)`	createPrimaryXref
`static Xref`	`createPsiMiIdentity(String id)`	createPsiMiIdentity
`static Xref`	`createPsiMiSecondary(String id)`	createPsiMiSecondary
`static Xref`	`createPsiModIdentity(String id)`	createPsiModIdentity
`static Xref`	`createPsiModSecondary(String id)`	createPsiModSecondary
`static Xref`	`createPubmedIdentity(String id)`	createPubmedIdentity
`static Xref`	`createRefseqIdentity(String refseq)`	createRefseqIdentity
`static Xref`	`createRefseqSecondary(String refseq)`	createRefseqSecondary
`static Xref`	`createSecondaryXref(String databaseName, String id)`	createSecondaryXref
`static Xref`	`createSecondaryXref(String databaseName, String databaseMi, String id)`	createSecondaryXref
`static Xref`	`createUniprotIdentity(String uniprot)`	createUniprotIdentity
`static Xref`	`createUniprotSecondary(String uniprot)`	createUniprotSecondary
`static Xref`	`createXref(String databaseName, String id)`	createXref
`static Xref`	`createXref(String databaseName, String databaseMi, String id)`	createXref
`static Xref`	`createXrefWithQualifier(String databaseName, String id, String qualifierName)`	createXrefWithQualifier
`static Xref`	`createXrefWithQualifier(String databaseName, String databaseMi, String id, String qualifierName, String qualifierMi)`	createXrefWithQualifier
`static Xref`	`createXrefWithQualifier(String databaseName, String databaseMi, String id, String version, String qualifierName, String qualifierMi)`	createXrefWithQualifierAndVersion
`static boolean`	`doesXrefHaveDatabaseAndId(Xref ref, String dbId, String dbName, String id)`	Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)
`static boolean`	`doesXrefHaveQualifier(Xref ref, String qualifierId, String qualifierName)`	Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)
`static boolean`	`doesXrefHaveQualifierAndId(Xref ref, String qualifierId, String qualifierName, String id)`	Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)
`static boolean`	`isXrefAnIdentifier(Xref ref)`	Method to know if a Xref is a potential identifier.
`static boolean`	`isXrefFromDatabase(Xref ref, String dbId, String dbName)`	Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)
`static void`	`removeAllXrefsWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName)`	Remove all Xrefs having this database name/database id from the collection of xrefs
`static void`	`removeAllXrefsWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)`	Remove all Xrefs having this database name/database id from the collection of xrefs
`static Collection<Xref>`	`searchAllXrefsHavingDatabaseAndQualifier(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs, Collection<String> typeMiRefs, Collection<String> typeRefs)`	Collect all cross references having specific databases and qualifiers
`static Collection<Xref>`	`searchAllXrefsHavingDatabases(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs)`	Collect all Xrefs having specific databases

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- XrefUtils
```
public XrefUtils()
```

Method Detail

isXrefAnIdentifier
```
public static boolean isXrefAnIdentifier(Xref ref)
```
Method to know if a Xref is a potential identifier. It can be an identity xref or a secondary xref.

Parameters:

ref - : the Xref

Returns:

true if the Xref has a qualifier identity or secondary-ac

isXrefFromDatabase
```
public static boolean isXrefFromDatabase(Xref ref,
                                         String dbId,
                                         String dbName)
```
Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)

Parameters:

ref - : the Xref

dbId - : the database MI identifier

dbName - : the database shortname

Returns:

true if the Xref has a database MI which is dbId or database shortname which is dbName

doesXrefHaveQualifier
```
public static boolean doesXrefHaveQualifier(Xref ref,
                                            String qualifierId,
                                            String qualifierName)
```
Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)

Parameters:

ref - : the Xref

qualifierId - : the qualifier MI identifier

qualifierName - : the qualifier shortname

Returns:

true if the Xref has a qualifier MI which is qualifierId or qualifier shortname which is qualifierName

doesXrefHaveDatabaseAndId

public static boolean doesXrefHaveDatabaseAndId(Xref ref,
                                                String dbId,
                                                String dbName,
                                                String id)

Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)

Parameters:: ref - : the Xref; dbId - : the database MI identifier; dbName - : the database shortname; id - : database id
Returns:: true if the Xref has a database MI which is dbId or database shortname which is dbName

doesXrefHaveQualifierAndId

public static boolean doesXrefHaveQualifierAndId(Xref ref,
                                                 String qualifierId,
                                                 String qualifierName,
                                                 String id)

Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)

Parameters:: ref - : the Xref; qualifierId - : the qualifier MI identifier; qualifierName - : the qualifier shortname; id - : database id
Returns:: true if the Xref has a qualifier MI which is qualifierId or qualifier shortname which is qualifierName

collectAllIdentifiersFrom
```
public static Collection<Xref> collectAllIdentifiersFrom(Collection<? extends Xref> refs)
```
Method to return a sub collection of identifiers (qualifier identity or secondary) in a list of Xrefs

Parameters:

refs - a Collection object.

Returns:

the sublist of identifiers (qualifier identity or secondary) from the list of Xrefs

collectAllXrefsHavingQualifier

public static Collection<Xref> collectAllXrefsHavingQualifier(Collection<? extends Xref> refs,
                                                              String qualifierId,
                                                              String qualifierName)

Collect all cross references having a specific qualifier

Parameters:: refs - a Collection object.; qualifierId - a String object.; qualifierName - a String object.
Returns:: a Collection object.

collectAllXrefsHavingDatabase

public static Collection<Xref> collectAllXrefsHavingDatabase(Collection<? extends Xref> refs,
                                                             String dbId,
                                                             String dbName)

Collect all cross references having a specific database

Parameters:: refs - a Collection object.; dbId - a String object.; dbName - a String object.
Returns:: a Collection object.

collectAllXrefsHavingDatabaseAndQualifier

public static Collection<Xref> collectAllXrefsHavingDatabaseAndQualifier(Collection<? extends Xref> refs,
                                                                         String dbId,
                                                                         String dbName,
                                                                         String qualifierId,
                                                                         String qualifierName)

Collect all cross references having a specific database and qualifier

Parameters:: refs - a Collection object.; dbId - a String object.; dbName - a String object.; qualifierId - a String object.; qualifierName - a String object.
Returns:: a Collection object.

collectAllXrefsHavingQualifierAndId

public static Collection<Xref> collectAllXrefsHavingQualifierAndId(Collection<? extends Xref> refs,
                                                                   String qualifierId,
                                                                   String qualifierName,
                                                                   String id)

Collect all cross references having a specific qualifier

Parameters:: refs - a Collection object.; qualifierId - a String object.; qualifierName - a String object.; id - a String object.
Returns:: a Collection object.

collectAllXrefsHavingDatabaseAndId

public static Collection<Xref> collectAllXrefsHavingDatabaseAndId(Collection<? extends Xref> refs,
                                                                  String dbId,
                                                                  String dbName,
                                                                  String id)

Collect all cross references having a specific database

Parameters:: refs - a Collection object.; dbId - a String object.; dbName - a String object.; id - a String object.
Returns:: a Collection object.

collectAllXrefsHavingDatabaseQualifierAndId

public static Collection<Xref> collectAllXrefsHavingDatabaseQualifierAndId(Collection<? extends Xref> refs,
                                                                           String dbId,
                                                                           String dbName,
                                                                           String id,
                                                                           String qualifierId,
                                                                           String qualifierName)

Collect all cross references having a specific database and qualifier

Parameters:: refs - a Collection object.; dbId - a String object.; dbName - a String object.; qualifierId - a String object.; qualifierName - a String object.; id - a String object.
Returns:: a Collection object.

searchAllXrefsHavingDatabaseAndQualifier

public static Collection<Xref> searchAllXrefsHavingDatabaseAndQualifier(Collection<Xref> xrefs,
                                                                        Collection<String> dbMiRefs,
                                                                        Collection<String> dbRefs,
                                                                        Collection<String> typeMiRefs,
                                                                        Collection<String> typeRefs)

Collect all cross references having specific databases and qualifiers

Parameters:: xrefs - a Collection object.; dbMiRefs - a Collection object.; dbRefs - a Collection object.; typeMiRefs - a Collection object.; typeRefs - a Collection object.
Returns:: a Collection object.

searchAllXrefsHavingDatabases

public static Collection<Xref> searchAllXrefsHavingDatabases(Collection<Xref> xrefs,
                                                             Collection<String> dbMiRefs,
                                                             Collection<String> dbRefs)

Collect all Xrefs having specific databases

Parameters:: xrefs - a Collection object.; dbMiRefs - a Collection object.; dbRefs - a Collection object.
Returns:: a Collection object.

collectFirstIdentifierWithDatabase
```
public static Xref collectFirstIdentifierWithDatabase(Collection<? extends Xref> refs,
                                                      String dbId,
                                                      String dbName)
```
This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name

Parameters:

refs - : the collection of Xrefs

dbId - : the database id to look for

dbName - : the database name to look for

Returns:

the first identifier having this database name/id, null if no Xrefs with this database name/id

removeAllXrefsWithDatabase

public static void removeAllXrefsWithDatabase(Collection<? extends Xref> refs,
                                              String dbId,
                                              String dbName)

Remove all Xrefs having this database name/database id from the collection of xrefs

Parameters:: refs - : the collection of Xrefs; dbId - : the database id to look for; dbName - : the database name to look for

collectFirstIdentifierWithDatabaseAndId
```
public static Xref collectFirstIdentifierWithDatabaseAndId(Collection<? extends Xref> refs,
                                                           String dbId,
                                                           String dbName,
                                                           String id)
```
This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name

Parameters:

refs - : the collection of Xrefs

dbId - : the database id to look for

dbName - : the database name to look for

id - a String object.

Returns:

the first identifier having this database name/id, null if no Xrefs with this database name/id

removeAllXrefsWithDatabaseAndId

public static void removeAllXrefsWithDatabaseAndId(Collection<? extends Xref> refs,
                                                   String dbId,
                                                   String dbName,
                                                   String id)

Remove all Xrefs having this database name/database id from the collection of xrefs

Parameters:: refs - : the collection of Xrefs; dbId - : the database id to look for; dbName - : the database name to look for; id - a String object.

createXref

public static Xref createXref(String databaseName,
                              String databaseMi,
                              String id)

createXref

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.
Returns:: a Xref object.

createXref

public static Xref createXref(String databaseName,
                              String id)

createXref

Parameters:: databaseName - a String object.; id - a String object.
Returns:: a Xref object.

createXrefWithQualifier

public static Xref createXrefWithQualifier(String databaseName,
                                           String databaseMi,
                                           String id,
                                           String version,
                                           String qualifierName,
                                           String qualifierMi)

createXrefWithQualifierAndVersion

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.; version - a String object.; qualifierName - a String object.; qualifierMi - a String object.
Returns:: a Xref object.

createXrefWithQualifier

public static Xref createXrefWithQualifier(String databaseName,
                                           String databaseMi,
                                           String id,
                                           String qualifierName,
                                           String qualifierMi)

createXrefWithQualifier

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.; qualifierName - a String object.; qualifierMi - a String object.
Returns:: a Xref object.

createXrefWithQualifier

public static Xref createXrefWithQualifier(String databaseName,
                                           String id,
                                           String qualifierName)

createXrefWithQualifier

Parameters:: databaseName - a String object.; id - a String object.; qualifierName - a String object.
Returns:: a Xref object.

createIdentityXref

public static Xref createIdentityXref(String databaseName,
                                      String databaseMi,
                                      String id)

createIdentityXref

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.
Returns:: a Xref object.

createIdentityXref

public static Xref createIdentityXref(String databaseName,
                                      String id)

createIdentityXref

Parameters:: databaseName - a String object.; id - a String object.
Returns:: a Xref object.

createSecondaryXref

public static Xref createSecondaryXref(String databaseName,
                                       String databaseMi,
                                       String id)

createSecondaryXref

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.
Returns:: a Xref object.

createSecondaryXref

public static Xref createSecondaryXref(String databaseName,
                                       String id)

createSecondaryXref

Parameters:: databaseName - a String object.; id - a String object.
Returns:: a Xref object.

createPrimaryXref

public static Xref createPrimaryXref(String databaseName,
                                     String databaseMi,
                                     String id)

createPrimaryXref

Parameters:: databaseName - a String object.; databaseMi - a String object.; id - a String object.
Returns:: a Xref object.

createPrimaryXref

public static Xref createPrimaryXref(String databaseName,
                                     String id)

createPrimaryXref

Parameters:: databaseName - a String object.; id - a String object.
Returns:: a Xref object.

createUniprotIdentity
```
public static Xref createUniprotIdentity(String uniprot)
```
createUniprotIdentity

Parameters:

uniprot - a String object.

Returns:

a Xref object.

createRefseqIdentity
```
public static Xref createRefseqIdentity(String refseq)
```
createRefseqIdentity

Parameters:

refseq - a String object.

Returns:

a Xref object.

createEnsemblIdentity
```
public static Xref createEnsemblIdentity(String ensembl)
```
createEnsemblIdentity

Parameters:

ensembl - a String object.

Returns:

a Xref object.

createEnsemblGenomesIdentity
```
public static Xref createEnsemblGenomesIdentity(String ensembl)
```
createEnsemblGenomesIdentity

Parameters:

ensembl - a String object.

Returns:

a Xref object.

createEntrezGeneIdIdentity
```
public static Xref createEntrezGeneIdIdentity(String geneId)
```
createEntrezGeneIdIdentity

Parameters:

geneId - a String object.

Returns:

a Xref object.

createDdbjEmblGenbankIdentity
```
public static Xref createDdbjEmblGenbankIdentity(String id)
```
createDdbjEmblGenbankIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createChebiIdentity
```
public static Xref createChebiIdentity(String id)
```
createChebiIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createPubmedIdentity
```
public static Xref createPubmedIdentity(String id)
```
createPubmedIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createDoiIdentity
```
public static Xref createDoiIdentity(String id)
```
createDoiIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createPsiMiIdentity
```
public static Xref createPsiMiIdentity(String id)
```
createPsiMiIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createPsiModIdentity
```
public static Xref createPsiModIdentity(String id)
```
createPsiModIdentity

Parameters:

id - a String object.

Returns:

a Xref object.

createUniprotSecondary
```
public static Xref createUniprotSecondary(String uniprot)
```
createUniprotSecondary

Parameters:

uniprot - a String object.

Returns:

a Xref object.

createRefseqSecondary
```
public static Xref createRefseqSecondary(String refseq)
```
createRefseqSecondary

Parameters:

refseq - a String object.

Returns:

a Xref object.

createEnsemblSecondary
```
public static Xref createEnsemblSecondary(String ensembl)
```
createEnsemblSecondary

Parameters:

ensembl - a String object.

Returns:

a Xref object.

createEnsemblGenomesSecondary
```
public static Xref createEnsemblGenomesSecondary(String ensembl)
```
createEnsemblGenomesSecondary

Parameters:

ensembl - a String object.

Returns:

a Xref object.

createEntrezGeneIdSecondary
```
public static Xref createEntrezGeneIdSecondary(String geneId)
```
createEntrezGeneIdSecondary

Parameters:

geneId - a String object.

Returns:

a Xref object.

createDdbjEmblGenbankSecondary
```
public static Xref createDdbjEmblGenbankSecondary(String id)
```
createDdbjEmblGenbankSecondary

Parameters:

id - a String object.

Returns:

a Xref object.

createChebiSecondary
```
public static Xref createChebiSecondary(String id)
```
createChebiSecondary

Parameters:

id - a String object.

Returns:

a Xref object.

createPsiMiSecondary
```
public static Xref createPsiMiSecondary(String id)
```
createPsiMiSecondary

Parameters:

id - a String object.

Returns:

a Xref object.

createPsiModSecondary
```
public static Xref createPsiModSecondary(String id)
```
createPsiModSecondary

Parameters:

id - a String object.

Returns:

a Xref object.

Class XrefUtils

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

XrefUtils

Method Detail

isXrefAnIdentifier

isXrefFromDatabase

doesXrefHaveQualifier

doesXrefHaveDatabaseAndId

doesXrefHaveQualifierAndId

collectAllIdentifiersFrom

collectAllXrefsHavingQualifier

collectAllXrefsHavingDatabase

collectAllXrefsHavingDatabaseAndQualifier

collectAllXrefsHavingQualifierAndId

collectAllXrefsHavingDatabaseAndId

collectAllXrefsHavingDatabaseQualifierAndId

searchAllXrefsHavingDatabaseAndQualifier

searchAllXrefsHavingDatabases

collectFirstIdentifierWithDatabase

removeAllXrefsWithDatabase

collectFirstIdentifierWithDatabaseAndId

removeAllXrefsWithDatabaseAndId

createXref

createXref

createXrefWithQualifier

createXrefWithQualifier

createXrefWithQualifier

createIdentityXref

createIdentityXref

createSecondaryXref

createSecondaryXref

createPrimaryXref

createPrimaryXref

createUniprotIdentity

createRefseqIdentity

createEnsemblIdentity

createEnsemblGenomesIdentity

createEntrezGeneIdIdentity

createDdbjEmblGenbankIdentity

createChebiIdentity

createPubmedIdentity

createDoiIdentity

createPsiMiIdentity

createPsiModIdentity

createUniprotSecondary

createRefseqSecondary

createEnsemblSecondary

createEnsemblGenomesSecondary

createEntrezGeneIdSecondary

createDdbjEmblGenbankSecondary

createChebiSecondary

createPsiMiSecondary

createPsiModSecondary