fr.curie.BiNoM.pathways.utils
Class BioPAXNamingService

java.lang.Object
  fr.curie.BiNoM.pathways.utils.BioPAXNamingService

public class BioPAXNamingService
extends java.lang.Object

BioPAX Naming Service. Used to construct short, unique and 'meaningfull' names for BioPAX objects

Author:

Andrei Zinovyev

Field Summary

java.util.HashMap

genericUtilityName Names of utilities

Constructor Summary

BioPAXNamingService()

BioPAXNamingService(BioPAX biopax)

BioPAXNamingService(BioPAX biopax, boolean verbose)

Method Summary

java.lang.String	createEntityId(entity e) Creates entity id
java.lang.String	createEntityName(entity pe) Creates a name for entity pe
java.lang.String	createNameForComplex(complex compl) Generates a name for complex object
java.lang.String	createNameForParticipant(physicalEntityParticipant participant, boolean addCompartment) Creates a name for physicalEntityParticipant
static java.lang.String	createUtilityId(utilityClass e) Creates an id for utilityClass
java.lang.String	createUtilityName(utilityClass e) Creates a name for utilityClass object
void	generateNames(BioPAX biopax, boolean verbose) Function for generating names
java.lang.String	generateUniqueID(java.lang.String id, java.util.HashMap hm) Adds # symbols until the id will become unique
java.lang.String	getIdByUri(java.lang.String uri) Used to get id of the thing with uri
java.lang.String	getNameByUri(java.lang.String uri) Used to get name of the thing with uri
java.lang.String	getUriById(java.lang.String id)
java.lang.String	getUriByName(java.lang.String name)
static java.lang.String	getVocabularyTerm(java.util.Iterator it)
void	printEntityName(entity e)
void	printUtilityClassName(utilityClass e)
void	putEntity(entity e) Adds an entity for naming
void	putID(java.lang.String uri, java.lang.String id)
void	putName(java.lang.String uri, java.lang.String name) Adds a (uri,name) pair
void	putUtilityClass(utilityClass e) Adds an utilityClass for naming

Methods inherited from class java.lang.Object

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

Field Detail

genericUtilityName

public java.util.HashMap genericUtilityName

Names of utilities

Constructor Detail

BioPAXNamingService

public BioPAXNamingService()

BioPAXNamingService

public BioPAXNamingService(BioPAX biopax,
                           boolean verbose)
                    throws java.lang.Exception

Throws:

java.lang.Exception

BioPAXNamingService

public BioPAXNamingService(BioPAX biopax)
                    throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

generateNames

public void generateNames(BioPAX biopax,
                          boolean verbose)
                   throws java.lang.Exception

Function for generating names

Parameters:

biopax -

verbose - if true then some log is provided

Throws:

java.lang.Exception

putEntity

public void putEntity(entity e)
               throws java.lang.Exception

Adds an entity for naming

Parameters:

e -

Throws:

java.lang.Exception

putUtilityClass

public void putUtilityClass(utilityClass e)
                     throws java.lang.Exception

Adds an utilityClass for naming

Throws:

java.lang.Exception

printEntityName

public void printEntityName(entity e)

printUtilityClassName

public void printUtilityClassName(utilityClass e)

putID

public void putID(java.lang.String uri,
                  java.lang.String id)

putName

public void putName(java.lang.String uri,
                    java.lang.String name)

Adds a (uri,name) pair

Parameters:

uri -

name -

generateUniqueID

public java.lang.String generateUniqueID(java.lang.String id,
                                         java.util.HashMap hm)

Adds # symbols until the id will become unique

Parameters:

id -

hm -

Returns:

getNameByUri

public java.lang.String getNameByUri(java.lang.String uri)

Used to get name of the thing with uri

Parameters:

uri -

Returns:

getIdByUri

public java.lang.String getIdByUri(java.lang.String uri)

Used to get id of the thing with uri

Parameters:

uri -

Returns:

getUriById

public java.lang.String getUriById(java.lang.String id)

getUriByName

public java.lang.String getUriByName(java.lang.String name)

createEntityName

public java.lang.String createEntityName(entity pe)
                                  throws java.lang.Exception

Creates a name for entity pe

Parameters:

pe -

Returns:

Throws:

java.lang.Exception

createEntityId

public java.lang.String createEntityId(entity e)
                                throws java.lang.Exception

Creates entity id

Parameters:

e -

Returns:

Throws:

java.lang.Exception

createUtilityName

public java.lang.String createUtilityName(utilityClass e)
                                   throws java.lang.Exception

Creates a name for utilityClass object

Parameters:

e -

Returns:

Throws:

java.lang.Exception

createUtilityId

public static java.lang.String createUtilityId(utilityClass e)
                                        throws java.lang.Exception

Creates an id for utilityClass

Parameters:

e -

Returns:

Throws:

java.lang.Exception

createNameForComplex

public java.lang.String createNameForComplex(complex compl)
                                      throws java.lang.Exception

Generates a name for complex object

Parameters:

compl -

Returns:

Throws:

java.lang.Exception

createNameForParticipant

public java.lang.String createNameForParticipant(physicalEntityParticipant participant,
                                                 boolean addCompartment)
                                          throws java.lang.Exception

Creates a name for physicalEntityParticipant

Parameters:

participant -

addCompartment -

Returns:

Throws:

java.lang.Exception

getVocabularyTerm

public static java.lang.String getVocabularyTerm(java.util.Iterator it)