Package psidev.psi.mi.jami.commons

Class MIDataSourceOptionFactory

java.lang.Object

psidev.psi.mi.jami.commons.MIDataSourceOptionFactory

public class MIDataSourceOptionFactory
extends Object

The factory to populate the map of options for the DataSourceFactory

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Method Summary

Modifier and Type	Method	Description
Map<String,Object>	getDefaultFileOptions(MIFileType sourceType, Object inputData)	Create a map of default options depending on the provided sourceType.
Map<String,Object>	getDefaultMitabOptions(Object inputData)	Create the default options for the MITAB datasource.
Map<String,Object>	getDefaultOptions(File file)	Create a map with the default options to retrieve the default MI datasource that will read the file content.
Map<String,Object>	getDefaultOptions(InputStream streamToAnalyse)	Create a map with the default options to retrieve the default MI datasource that will read the inputstream content.
Map<String,Object>	getDefaultOptions(Reader readerToAnalyze)	Create a map with the default options to retrieve the default MI datasource that will read the reader content.
Map<String,Object>	getDefaultOptions(URL url)	Creates a map with the default options to retrieve MI datasource that will read the URL content
Map<String,Object>	getDefaultXmlOptions(Object inputData)	Create the default options for the Psi-XML 2.5 datasource.
static MIDataSourceOptionFactory	getInstance()	Getter for the field instance.
Map<String,Object>	getMitabOptions(boolean streaming, Object inputData)	Create the options for the MITAB datasource and specify if we want a Streaming MIFileDatasource.
Map<String,Object>	getMitabOptions(MIFileParserListener listener, Object inputData)	Create the options for the MITAB datasource using the provided MIFileParserListener.
Map<String,Object>	getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input)	Create the options for the MITAB datasource.
Map<String,Object>	getMitabOptions(InteractionCategory objectCategory, ComplexType complexType, Object inputData)	Create the options for the MITAB datasource using the provided objectCategory.
Map<String,Object>	getOptions(MIFileType type, InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input)	Create a map of options
Map<String,Object>	getXmlOptions(boolean streaming, Object inputData)	Create the options for the PSI-XML datasource and specify if we want a Streaming MIFileDatasource.
Map<String,Object>	getXmlOptions(MIFileParserListener listener, Object inputData)	Create the options for the Psi-XML datasource using the provided MIFileParserListener.
Map<String,Object>	getXmlOptions(InteractionCategory objectCategory, ComplexType complexType, boolean streaming, MIFileParserListener listener, Object input, ComplexExpansionMethod expansionMethod, PsiXmlIdCache objectCache)	Create the options for the PSI-XML datasource.
Map<String,Object>	getXmlOptions(InteractionCategory objectCategory, ComplexType complexType, Object inputData)	Create the options for the Psi-XML datasource using the provided objectCategory.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static MIDataSourceOptionFactory getInstance()

Getter for the field instance.

Returns:

a MIDataSourceOptionFactory object.

getDefaultOptions

public Map<String,Object> getDefaultOptions(File file)
                                           throws IOException

Create a map with the default options to retrieve the default MI datasource that will read the file content.

Parameters:

file - a File object.

Returns:

the default options for the MI datasource corresponding to this file

Throws:

IOException - if any.

getDefaultOptions

public Map<String,Object> getDefaultOptions(URL url)
                                           throws IOException

Creates a map with the default options to retrieve MI datasource that will read the URL content

Parameters:

url - a URL object.

Returns:

the default options for the MI datasource corresponding to this url

Throws:

IOException - if any.

getDefaultOptions

public Map<String,Object> getDefaultOptions(InputStream streamToAnalyse)
                                           throws IOException

Create a map with the default options to retrieve the default MI datasource that will read the inputstream content.

Parameters:

streamToAnalyse - : stream to be used to analyze the MIFileType

Returns:

the default options for the MI datasource corresponding to this source inputstream

Throws:

IOException - if any.

getDefaultOptions

public Map<String,Object> getDefaultOptions(Reader readerToAnalyze)
                                           throws IOException

Create a map with the default options to retrieve the default MI datasource that will read the reader content.

Parameters:

readerToAnalyze - : reader to be used to analyze the MIFileType

Returns:

the default options for the MI datasource corresponding to this source reader

Throws:

IOException - if any.

getDefaultFileOptions

public Map<String,Object> getDefaultFileOptions(MIFileType sourceType,
                                                      Object inputData)

Create a map of default options depending on the provided sourceType. It can recognize mitab, psi-xml and other

Parameters:

sourceType - a MIFileType object.

inputData - a Object object.

Returns:

the map of default options for this sourceType

getDefaultMitabOptions

public Map<String,Object> getDefaultMitabOptions(Object inputData)

Create the default options for the MITAB datasource. It will read InteractionEvidence elements in a streaming way. It will use the MitabParserLogger to listen to the MITAB parsing events

Parameters:

inputData - a Object object.

Returns:

the default options for the MITAB datasource

getMitabOptions

public Map<String,Object> getMitabOptions(InteractionCategory objectCategory,
                                                ComplexType complexType,
                                                Object inputData)

Create the options for the MITAB datasource using the provided objectCategory. It will read elements from this objectCategory in a streaming way. It will use the MitabParserLogger to listen to the MITAB parsing events

Parameters:

objectCategory - a InteractionCategory object.

complexType - : the kind of complex : n-ary or binary

inputData - a Object object.

Returns:

the options for the MITAB datasource using the provided objectCategory

getMitabOptions

public Map<String,Object> getMitabOptions(boolean streaming,
                                                Object inputData)

Create the options for the MITAB datasource and specify if we want a Streaming MIFileDatasource. It will read InteractionEvidence elements. It will use the MitabParserLogger to listen to the MITAB parsing events

Parameters:

streaming - : tru if we want to read the interactions in a streaming way

inputData - a Object object.

Returns:

the options for the MITAB datasource and specify if we want a Streaming MIFileDatasource

getMitabOptions

public Map<String,Object> getMitabOptions(MIFileParserListener listener,
                                                Object inputData)

Create the options for the MITAB datasource using the provided MIFileParserListener. It will read InteractionEvidence elements in a streaming way.

Parameters:

listener - a MIFileParserListener object.

inputData - is the mitab data to read

Returns:

the options for the MITAB datasource with the provided listener

getMitabOptions

public Map<String,Object> getMitabOptions(InteractionCategory objectCategory,
                                                ComplexType complexType,
                                                boolean streaming,
                                                MIFileParserListener listener,
                                                Object input)

Create the options for the MITAB datasource.

Parameters:

objectCategory - : interaction object type to load

complexType - : the kind of complex : n-ary or binary

streaming - : true if we want to load interactions in a streaming way

listener - : the listener to use for listening MITAB parsing events

input - a Object object.

Returns:

the MITAB datasource options

getDefaultXmlOptions

public Map<String,Object> getDefaultXmlOptions(Object inputData)

Create the default options for the Psi-XML 2.5 datasource. It will read InteractionEvidence elements in a streaming way. It will use the PsiXmlParserLogger to listen to the Psi-XML parsing events It will keep the parsed objects having an id in memory.

Parameters:

inputData - a Object object.

Returns:

the default options for the PSI-xml 2.5 datasource

getXmlOptions

public Map<String,Object> getXmlOptions(InteractionCategory objectCategory,
                                              ComplexType complexType,
                                              Object inputData)

Create the options for the Psi-XML datasource using the provided objectCategory. It will read elements from this objectCategory in a streaming way. It will use the PsiXmlParserLogger to listen to the Psi=XML parsing events It will keep the parsed objects having an id in memory.

Parameters:

objectCategory - a InteractionCategory object.

complexType - : the kind of complex : n-ary or binary

inputData - a Object object.

Returns:

the options for the Psi Xml datasource using the provided objectCategory

getXmlOptions

public Map<String,Object> getXmlOptions(boolean streaming,
                                              Object inputData)

Create the options for the PSI-XML datasource and specify if we want a Streaming MIFileDatasource. It will read InteractionEvidence elements. It will use the PsiXmlParserLogger to listen to the PSI-XML parsing events It will keep the parsed objects having an id in memory.

Parameters:

streaming - : tru if we want to read the interactions in a streaming way

inputData - a Object object.

Returns:

the options for the PSI-XML datasource and specify if we want a Streaming MIFileDatasource

getXmlOptions

public Map<String,Object> getXmlOptions(MIFileParserListener listener,
                                              Object inputData)

Create the options for the Psi-XML datasource using the provided MIFileParserListener. It will read InteractionEvidence elements in a streaming way. It will keep the parsed objects having an id in memory.

Parameters:

listener - a MIFileParserListener object.

inputData - is the mitab data to read

Returns:

the options for the PSI-XML datasource with the provided listener

getXmlOptions

public Map<String,Object> getXmlOptions(InteractionCategory objectCategory,
                                              ComplexType complexType,
                                              boolean streaming,
                                              MIFileParserListener listener,
                                              Object input,
                                              ComplexExpansionMethod expansionMethod,
                                              PsiXmlIdCache objectCache)

Create the options for the PSI-XML datasource.

Parameters:

objectCategory - : interaction object type to load

complexType - : the kind of complex : n-ary or binary

streaming - : true if we want to load interactions in a streaming way

listener - : the listener to use for listening XML parsing events

input - : the MI source containing data

expansionMethod - : the complex expansion method

objectCache - : cache for parsed objects having an id

Returns:

the Xml 2.5 datasource options

getOptions

public Map<String,Object> getOptions(MIFileType type,
                                           InteractionCategory objectCategory,
                                           ComplexType complexType,
                                           boolean streaming,
                                           MIFileParserListener listener,
                                           Object input)

Create a map of options

Parameters:

type - : MI source type (mitab, xml25, etc.)

objectCategory - : the kind of interactions to be returned by the datasource (interaction evidence, binary, modelled interaction, ...)

complexType - : the kind of complex : n-ary or binary

streaming - : boolean value to know if we want to stream the interactions or load the full interaction dataset

listener - : parser listener

input - : the MI source containing data

Returns:

the map of options