public final class Normalizer extends Object
| Modifier and Type | Field and Description |
|---|---|
static String |
PROPERTY_NORMALIZER_URI_STRATEGY |
static String |
VALUE_NORMALIZER_URI_STRATEGY_MD5 |
static String |
VALUE_NORMALIZER_URI_STRATEGY_SIMPLE |
| Constructor and Description |
|---|
Normalizer()
Constructor
|
| Modifier and Type | Method and Description |
|---|---|
static void |
autoName(Provenance pro)
Auto-generates standard and other names for the datasource
from either its ID (if URN) or one of its existing names (preferably - standard name)
|
static String |
convertToLevel3(String biopaxData)
Converts BioPAX L1 or L2 RDF/XML string data to BioPAX L3 string.
|
String |
getDescription()
Description of the model to normalize.
|
String |
getXmlBase() |
boolean |
isFixDisplayName() |
void |
normalize(Model model)
BioPAX normalization
(modifies the original Model)
|
String |
normalize(String biopaxOwlData)
Deprecated.
this method will fail if the data exceeds ~1Gb (max UTF8 java String length)
|
void |
setDescription(String description) |
void |
setFixDisplayName(boolean fixDisplayName) |
void |
setXmlBase(String xmlBase) |
static String |
uri(String xmlBase,
String dbName,
String idPart,
Class<? extends BioPAXElement> type)
Consistently generates a new BioPAX element URI
using given URI namespace (xml:base), BioPAX class,
and two different identifiers (at least one is required).
|
public static final String PROPERTY_NORMALIZER_URI_STRATEGY
public static final String VALUE_NORMALIZER_URI_STRATEGY_SIMPLE
public static final String VALUE_NORMALIZER_URI_STRATEGY_MD5
public String normalize(String biopaxOwlData)
biopaxOwlData - RDF/XML BioPAX content stringpublic static String uri(String xmlBase, String dbName, String idPart, Class<? extends BioPAXElement> type)
xmlBase - xml:base (common URI prefix for a BioPAX model), case-sensitivedbName - a bio data collection name or synonym, case-insensitiveidPart - optional (can be null), e.g., xref.id, case-sensitivetype - BioPAX classIllegalArgumentException - if either type is null or both 'dbName' and 'idPart' are all nulls.public String getDescription()
public void setDescription(String description)
description - the description to setpublic void normalize(Model model)
model - BioPAX model to normalizeNullPointerException - if model is nullIllegalArgumentException - if model is not Level3 BioPAXpublic static void autoName(Provenance pro)
pro - data source (BioPAX Provenance)public static String convertToLevel3(String biopaxData)
biopaxData - Stringpublic boolean isFixDisplayName()
public void setFixDisplayName(boolean fixDisplayName)
public String getXmlBase()
public void setXmlBase(String xmlBase)
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