public class BioPAXNamingService
extends java.lang.Object
Modifier and Type | Field and Description |
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java.util.HashMap |
genericUtilityName
Names of utilities
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Constructor and Description |
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BioPAXNamingService()
Empty constructor
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BioPAXNamingService(BioPAX biopax)
Constructor calling the constructor above (?!??), calling generateNames without printing anything.
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BioPAXNamingService(BioPAX biopax,
boolean verbose)
Constructor calling the generateNames function.
|
Modifier and Type | Method and Description |
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java.lang.String |
createEntityId(Entity e)
Creates entity id
|
java.lang.String |
createEntityName(Entity pe)
Creates a name for entity pe
|
void |
createEntityReferenceMap() |
java.lang.String |
createNameForComplex(Complex co)
Create a name for a Complex.
|
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 for BioPAX objects from a file.
|
java.lang.String |
generateUniqueID(java.lang.String id,
java.util.HashMap hm)
Adds # symbols until the id is 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)
Return the URI given an ID
|
java.lang.String |
getUriByName(java.lang.String name)
Return the URI for a given name
|
static java.lang.String |
getVocabularyTerm(java.util.Iterator it)
Return the first occurrence of a sorted Controlled Vocabulary list
|
java.lang.String |
ModifyIfSeveralEntitiesForTheSameReference(Entity pe,
java.lang.String name) |
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
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public BioPAXNamingService()
public BioPAXNamingService(BioPAX biopax, boolean verbose) throws java.lang.Exception
biopax
- BioPAX objectverbose
- boolean for printing out objects URI/namesjava.lang.Exception
public BioPAXNamingService(BioPAX biopax) throws java.lang.Exception
biopax
- java.lang.Exception
public void generateNames(BioPAX biopax, boolean verbose) throws java.lang.Exception
biopax
- BioPAX objectverbose
- if true then some log is providedjava.lang.Exception
public void putEntity(Entity e) throws java.lang.Exception
e
- java.lang.Exception
public void putUtilityClass(UtilityClass e) throws java.lang.Exception
java.lang.Exception
public void printEntityName(Entity e)
public void printUtilityClassName(UtilityClass e)
public void putID(java.lang.String uri, java.lang.String id)
public void putName(java.lang.String uri, java.lang.String name) throws java.lang.Exception
uri
- name
- java.lang.Exception
public java.lang.String generateUniqueID(java.lang.String id, java.util.HashMap hm)
id
- hm
- public java.lang.String getNameByUri(java.lang.String uri)
uri
- public java.lang.String getIdByUri(java.lang.String uri)
uri
- public java.lang.String getUriById(java.lang.String id)
String
- idpublic java.lang.String getUriByName(java.lang.String name)
String
- namepublic java.lang.String createEntityName(Entity pe) throws java.lang.Exception
Entity
- pejava.lang.Exception
public java.lang.String createEntityId(Entity e) throws java.lang.Exception
e
- java.lang.Exception
public java.lang.String createUtilityName(UtilityClass e) throws java.lang.Exception
UtilityClass
- ejava.lang.Exception
public static java.lang.String createUtilityId(UtilityClass e) throws java.lang.Exception
e
- java.lang.Exception
public java.lang.String createNameForComplex(Complex co)
Complex
- object.public static java.lang.String getVocabularyTerm(java.util.Iterator it)
ControlledVocabullary
- Iteratorpublic void createEntityReferenceMap()
public java.lang.String ModifyIfSeveralEntitiesForTheSameReference(Entity pe, java.lang.String name)