Package psidev.psi.mi.jami.utils

Class AliasUtils

java.lang.Object

psidev.psi.mi.jami.utils.AliasUtils

public class AliasUtils
extends Object

Utility class for aliases

Since:

01/02/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AliasUtils()

Method Summary

Modifier and Type	Method	Description
static Collection<Alias>	collectAllAliasesHavingType(Collection<? extends Alias> aliases, String typeId, String typeName)	Extract all the aliases having a specific type.
static Collection<Alias>	collectAllAliasesHavingTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	Extract all the aliases having a specific type.
static Alias	collectFirstAliasWithType(Collection<? extends Alias> aliases, String typeId, String typeName)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static Alias	collectFirstAliasWithTypeAndName(Collection<? extends Alias> aliases, String typeId, String typeName, String name)	This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name
static Alias	createAlias(String typeName, String name)	createAlias
static Alias	createAlias(String typeName, String typeMi, String name)	createAlias
static Alias	createAuthorAssignedName(String name)	createAuthorAssignedName
static Alias	createComplexSynonym(String name)	createComplexSynonym
static Alias	createGeneName(String name)	createGeneName
static Alias	createGeneNameSynonym(String name)	createGeneNameSynonym
static Alias	createIsoformSynonym(String name)	createIsoformSynonym
static Alias	createLocusName(String name)	createLocusName
static Alias	createOrfName(String name)	createOrfName
static boolean	doesAliasHaveType(Alias alias, String typeId, String typeName)	To know if an alias have a specific type.
static boolean	doesAliasHaveTypeAndName(Alias alias, String typeId, String typeName, String name)	To know if an alias have a specific type and name.
static void	removeAllAliasesWithType(Collection<? extends Alias> aliases, String typeId, String typeName)	Remove all Alias having this method name/method id from the collection of aliases
static void	removeAllAliasesWithTypeAndName(Collection<Alias> aliases, String typeId, String typeName, String name)	Remove all Alias having this method name/method id from the collection of aliases

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AliasUtils

public AliasUtils()

Method Detail

doesAliasHaveType

public static boolean doesAliasHaveType(Alias alias,
                                        String typeId,
                                        String typeName)

To know if an alias have a specific type.

Parameters:

alias - : the alias

typeId - : alias type MI identifier

typeName - : alias type name

Returns:

true if the alias has the type with given name/identifier

collectAllAliasesHavingType

public static Collection<Alias> collectAllAliasesHavingType(Collection<? extends Alias> aliases,
                                                            String typeId,
                                                            String typeName)

Extract all the aliases having a specific type.

Parameters:

aliases - : the aliases to analyse

typeId - : the alias type MI identifier

typeName - : the alias type name

Returns:

the selection of aliases having the specified type (typeId or typeName if no ids)

collectFirstAliasWithType

public static Alias collectFirstAliasWithType(Collection<? extends Alias> aliases,
                                              String typeId,
                                              String typeName)

This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name

Parameters:

aliases - : the collection of Alias

typeId - : the type id to look for

typeName - : the type name to look for

Returns:

the first alias having this type name/id, null if no Alias with this type name/id

removeAllAliasesWithType

public static void removeAllAliasesWithType(Collection<? extends Alias> aliases,
                                            String typeId,
                                            String typeName)

Remove all Alias having this method name/method id from the collection of aliases

Parameters:

aliases - : the collection of Checksum

typeId - : the method id to look for

typeName - : the method name to look for

doesAliasHaveTypeAndName

public static boolean doesAliasHaveTypeAndName(Alias alias,
                                               String typeId,
                                               String typeName,
                                               String name)

To know if an alias have a specific type and name.

Parameters:

alias - : the alias

typeId - : the alias type MI identifier

typeName - : the alias type name

name - : alias name

Returns:

true if the alias has the type with given name/identifier

collectAllAliasesHavingTypeAndName

public static Collection<Alias> collectAllAliasesHavingTypeAndName(Collection<? extends Alias> aliases,
                                                                   String typeId,
                                                                   String typeName,
                                                                   String name)

Extract all the aliases having a specific type.

Parameters:

aliases - : : the aliases to analyse

typeId - : : the alias type MI identifier

typeName - : : the alias type name

name - : alias name

Returns:

the selection of aliases having the specified type (typeId or typeName if no ids)

collectFirstAliasWithTypeAndName

public static Alias collectFirstAliasWithTypeAndName(Collection<? extends Alias> aliases,
                                                     String typeId,
                                                     String typeName,
                                                     String name)

This method will return the first Alias having this typeId/type name It will return null if there are no Alias with this type id/name

Parameters:

aliases - : the collection of Alias

typeId - : the type id to look for

typeName - : the type name to look for

name - : alias name

Returns:

the first alias having this type name/id, null if no Alias with this type name/id

removeAllAliasesWithTypeAndName

public static void removeAllAliasesWithTypeAndName(Collection<Alias> aliases,
                                                   String typeId,
                                                   String typeName,
                                                   String name)

Remove all Alias having this method name/method id from the collection of aliases

Parameters:

aliases - : the collection of Checksum

typeId - : the method id to look for

typeName - : the method name to look for

name - : alias name

createGeneName

public static Alias createGeneName(String name)

createGeneName

Parameters:

name - a String object.

Returns:

a Alias object.

createComplexSynonym

public static Alias createComplexSynonym(String name)

createComplexSynonym

Parameters:

name - a String object.

Returns:

a Alias object.

createAuthorAssignedName

public static Alias createAuthorAssignedName(String name)

createAuthorAssignedName

Parameters:

name - a String object.

Returns:

a Alias object.

createGeneNameSynonym

public static Alias createGeneNameSynonym(String name)

createGeneNameSynonym

Parameters:

name - a String object.

Returns:

a Alias object.

createIsoformSynonym

public static Alias createIsoformSynonym(String name)

createIsoformSynonym

Parameters:

name - a String object.

Returns:

a Alias object.

createOrfName

public static Alias createOrfName(String name)

createOrfName

Parameters:

name - a String object.

Returns:

a Alias object.

createLocusName

public static Alias createLocusName(String name)

createLocusName

Parameters:

name - a String object.

Returns:

a Alias object.

createAlias

public static Alias createAlias(String typeName,
                                String typeMi,
                                String name)

createAlias

Parameters:

typeName - a String object.

typeMi - a String object.

name - a String object.

Returns:

a Alias object.

createAlias

public static Alias createAlias(String typeName,
                                String name)

createAlias

Parameters:

typeName - a String object.

name - a String object.

Returns:

a Alias object.