Package org.biopax.paxtools.normalizer

Class Normalizer

java.lang.Object

org.biopax.paxtools.normalizer.Normalizer

public final class Normalizer
extends Object

BioPAX (Level 3) Normalizer, an advanced BioPAX utility to help pathway data integrating and linking.

Author:

rodche

Field Summary

Fields

Modifier and Type	Field	Description
static final String	PROPERTY_NORMALIZER_URI_STRATEGY
static final String	VALUE_NORMALIZER_URI_STRATEGY_MD5
static final String	VALUE_NORMALIZER_URI_STRATEGY_SIMPLE

Constructor Summary

Constructors

Constructor	Description
Normalizer()	Constructor

Method Summary

Modifier and Type	Method	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()
String	normalize(String biopaxOwlData)	Deprecated. this method will fail if the data exceeds ~1Gb (max UTF8 java String length)
void	normalize(Model model)	BioPAX normalization (modifies the original Model)
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).

Methods inherited from class java.lang.Object

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

Field Details

PROPERTY_NORMALIZER_URI_STRATEGY

public static final String PROPERTY_NORMALIZER_URI_STRATEGY

See Also:

• Constant Field Values

VALUE_NORMALIZER_URI_STRATEGY_SIMPLE

public static final String VALUE_NORMALIZER_URI_STRATEGY_SIMPLE

See Also:

• Constant Field Values

VALUE_NORMALIZER_URI_STRATEGY_MD5

public static final String VALUE_NORMALIZER_URI_STRATEGY_MD5

See Also:

• Constant Field Values

Constructor Details

Normalizer

public Normalizer()

Constructor

Method Details

normalize

public String normalize(String biopaxOwlData)

Deprecated.

this method will fail if the data exceeds ~1Gb (max UTF8 java String length)

Normalizes BioPAX OWL data and returns the result as BioPAX OWL (string). This public method is actually intended to use outside the BioPAX Validator framework, with not too large models.

Parameters:

biopaxOwlData - RDF/XML BioPAX content string

Returns:

normalized BioPAX RDF/XML

uri

public 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). Miriam registry is used to get the standard db name and identifiers.org URI, if possible, only for relationship type vocabulary, publication xref, and entity reference types.

Parameters:

xmlBase - xml:base (common URI prefix for a BioPAX model), case-sensitive

dbName - a bio data collection name or synonym, case-insensitive

idPart - optional (can be null), e.g., xref.id, case-sensitive

type - BioPAX class

Returns:

URI

Throws:

IllegalArgumentException - if either type is null or both 'dbName' and 'idPart' are all nulls.

getDescription

public String getDescription()

Description of the model to normalize.

Returns:

info about the BioPAX model

setDescription

public void setDescription(String description)

Parameters:

description - the description to set

normalize

public void normalize(Model model)

BioPAX normalization (modifies the original Model)

Parameters:

model - BioPAX model to normalize

Throws:

NullPointerException - if model is null

IllegalArgumentException - if model is not Level3 BioPAX

autoName

public 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)

Parameters:

pro - data source (BioPAX Provenance)

convertToLevel3

public static String convertToLevel3(String biopaxData)

Converts BioPAX L1 or L2 RDF/XML string data to BioPAX L3 string. WARN: this is not for huge (larger than 1GB) BioPAX RDF/XML data due to use of (UTF-8) String and Byte Array internally. This can be and is used by online web apps, such as the BioPAX Validator.

Parameters:

biopaxData - String

Returns:

BioPAX Level3 RDF/XML string

isFixDisplayName

public boolean isFixDisplayName()

setFixDisplayName

public void setFixDisplayName(boolean fixDisplayName)

getXmlBase

public String getXmlBase()

setXmlBase

public void setXmlBase(String xmlBase)