org.biopax.paxtools.io

Class SimpleIOHandler

java.lang.Object

org.biopax.paxtools.io.BioPAXIOHandlerAdapter

org.biopax.paxtools.io.SimpleIOHandler

All Implemented Interfaces:

BioPAXIOHandler

public final class SimpleIOHandler
extends BioPAXIOHandlerAdapter

Simple BioPAX reader/writer. This class provides a JAXP based I/O handler. As compared to Jena based implementation it offers ~10x performance, significantly less memory requirements when reading large files and a lightweight deployement. It, however, is not as robust as the Jena based reader and can not read non-RDF/XML OWL formats or non-UTF encodings.For those, you might want to use the JenaIOHandler class

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	SimpleIOHandler.Triple

Field Summary

Fields inherited from class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

base, bp, editorMap, factory, level, namespaces, owl, rdf, rdfs, xsd

Constructor Summary

Constructors

Constructor and Description
SimpleIOHandler() Basic constructor, defaults to Level 3 and default BioPAXFactory
SimpleIOHandler(BioPAXFactory factory, BioPAXLevel level) Full constructor
SimpleIOHandler(BioPAXLevel level) Basic constructor, defaults to level.defaultFactory

Method Summary

Modifier and Type	Method and Description
void	absoluteUris(boolean absoluteUris) Sets the flag used when exporting a BioPAX model to RDF/XML: true - to always write full URI in rdf:resource and use rdf:about instead rdf:ID (does not matter xml:base is set or not).
void	checkRestrictions(boolean checkRestrictions) If set to true, property editors will check restrictions at the subclass level and throw an exception if violated.
static String	convertToOwl(Model model) Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string.
void	convertToOWL(Model model, OutputStream outputStream) Converts a model into BioPAX (OWL) format, and writes it into the outputStream.
protected void	createAndBind(Model model) This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.
String	getId()
String	getXmlStreamInfo() This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.
protected void	init(InputStream in) This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.
boolean	isAbsoluteUris()
boolean	isMergeDuplicates()
boolean	isNormalizeNameSpaces()
void	mergeDuplicates(boolean mergeDuplicates) If set to true, the reader will merge duplicate individuals, i.e.
void	normalizeNameSpaces(boolean normalizeNameSpaces) Sets the flag used when exporting a BioPAX model to RDF/XML: true - to clean up current namespaces (e.g., those read from a file) and use defaults instead (prefixes: 'rdf', 'rdfs', 'owl', 'xsd')
protected Map<String,String>	readNameSpaces() This method provides a hook for the implementers of this abstract class to set the namespaces of the model.
protected void	reset(InputStream in)
protected void	resetEditorMap() This method resets the editor map.
void	writeObject(Writer out, BioPAXElement bean) Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete).

Methods inherited from class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

bindValue, convertFromOWL, convertToOWL, createAndAdd, fixReusedPEPs, getEditorMap, getFactory, getLevel, getRDFCommentEditor, getReusedPEPHelper, isFixReusedPEPs, resetLevel, resourceFixes, setEditorMap, setFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleIOHandler

public SimpleIOHandler()

Basic constructor, defaults to Level 3 and default BioPAXFactory

SimpleIOHandler

public SimpleIOHandler(BioPAXLevel level)

Basic constructor, defaults to level.defaultFactory

Parameters:

level - BioPAXLevel to handle.

SimpleIOHandler

public SimpleIOHandler(BioPAXFactory factory,
                       BioPAXLevel level)

Full constructor

Parameters:

factory - to create BioPAX objects

level - BioPAX level to handle.

Method Detail

mergeDuplicates

public void mergeDuplicates(boolean mergeDuplicates)

If set to true, the reader will merge duplicate individuals, i.e. individuals that has the same ID. Otherwise it will throw an exception. By default it is set to false.

Parameters:

mergeDuplicates - true/false

checkRestrictions

public void checkRestrictions(boolean checkRestrictions)

If set to true, property editors will check restrictions at the subclass level and throw an exception if violated. This is true by default. WARNING: This is a static parameter and will change behaviour for the whole thread. Do not change unless you need to read a (relatively exotic) BioPAX export that violates subclass level restrictions.

Parameters:

checkRestrictions - true/false

resetEditorMap

protected void resetEditorMap()

This method resets the editor map. Editor maps are used to map property names to property editors. Resetting the editor map might be required to switch between levels.

Specified by:

resetEditorMap in class BioPAXIOHandlerAdapter

getXmlStreamInfo

public String getXmlStreamInfo()

This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.

Returns:

current XML stream state summary

init

protected void init(InputStream in)

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.

Specified by:

init in class BioPAXIOHandlerAdapter

Parameters:

in - BioPAX RDF/XML input stream

reset

protected void reset(InputStream in)

Overrides:

reset in class BioPAXIOHandlerAdapter

readNameSpaces

protected Map<String,String> readNameSpaces()

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to set the namespaces of the model.

Specified by:

readNameSpaces in class BioPAXIOHandlerAdapter

Returns:

a map of namespaces.

createAndBind

protected void createAndBind(Model model)

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.

Specified by:

createAndBind in class BioPAXIOHandlerAdapter

Parameters:

model - to be populated

getId

public String getId()

convertToOWL

public void convertToOWL(Model model,
                         OutputStream outputStream)

Converts a model into BioPAX (OWL) format, and writes it into the outputStream. Saved data can be then read via BioPAXIOHandler interface (e.g., SimpleIOHandler). Note: When the model is incomplete (i.e., contains elements that refer externals, dangling BioPAX elements) and is exported by this method, it works; however one will find corresponding object properties set to NULL later, after converting such data back to Model. Note: if the model is very very large, and the output stream is a byte array stream, then you can eventually get OutOfMemoryError "Requested array size exceeds VM limit" (max. array size is 2Gb)

Parameters:

model - model to be converted into OWL format

outputStream - output stream into which the output will be written

Throws:

BioPaxIOException - in case of I/O problems

writeObject

public void writeObject(Writer out,
                        BioPAXElement bean)
                 throws IOException

Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete). Note: use BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) convertToOWL(org.biopax.paxtools.model.Model, Object)} instead if you have a model and want to save and later restore it.

Parameters:

out - output

bean - BioPAX object

Throws:

IOException - when the output writer throws

absoluteUris

public void absoluteUris(boolean absoluteUris)

Sets the flag used when exporting a BioPAX model to RDF/XML: true - to always write full URI in rdf:resource and use rdf:about instead rdf:ID (does not matter xml:base is set or not). This is good for the data loading a RDF/SPARQL servers, such as Virtuoso, so they generate correct and resolvable links from BioPAX URIs (use of rdf:ID="localId" and rdf:resource="#localID" is known to make them insert extra '#' between xml:base and localId).

Parameters:

absoluteUris - true/false - whether to force writing absolute URIs (thus, never use rdf:ID)

isAbsoluteUris

public boolean isAbsoluteUris()

Returns:

true/false

See Also:

absoluteUris(boolean)

normalizeNameSpaces

public void normalizeNameSpaces(boolean normalizeNameSpaces)

Sets the flag used when exporting a BioPAX model to RDF/XML: true - to clean up current namespaces (e.g., those read from a file) and use defaults instead (prefixes: 'rdf', 'rdfs', 'owl', 'xsd')

Parameters:

normalizeNameSpaces - true/false

isNormalizeNameSpaces

public boolean isNormalizeNameSpaces()

Returns:

true/false

See Also:

normalizeNameSpaces()

isMergeDuplicates

public boolean isMergeDuplicates()

Returns:

true/false

See Also:

mergeDuplicates(boolean)

convertToOwl

public static String convertToOwl(Model model)

Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string.

Parameters:

model - a BioPAX object model to convert to the RDF/XML format

Returns:

the BioPAX data in the RDF/XML format

Throws:

IllegalArgumentException - if model is null

OutOfMemoryError - when it cannot be stored in a byte array (max 2Gb).