Package psidev.psi.mi.jami.crosslink

Class CrossLinkCsvOptionFactory

java.lang.Object

psidev.psi.mi.jami.crosslink.CrossLinkCsvOptionFactory

public class CrossLinkCsvOptionFactory
extends Object

The factory to populate the map of options for the DataSourceFactory for crosslink csv datasources

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Method Summary

Modifier and Type	Method	Description
Map<String,Object>	getCsvOptions(boolean streaming, Object inputData)	Create the options for the CSV datasource and specify if we want a Streaming MIFileDatasource.
Map<String,Object>	getCsvOptions(CsvType csvType, ComplexType complexType, Boolean streaming, MIFileParserListener listener, Object input)	Create a map of options
Map<String,Object>	getCsvOptions(CsvType csvType, ComplexType complexType, Object inputData)	Create the options for the CSV datasource using the provided csvtype.
Map<String,Object>	getCsvOptions(MIFileParserListener listener, Object inputData)	Create the options for the CSV datasource using the provided MIFileParserListener.
Map<String,Object>	getDefaultCsvOptions(Reader readerToAnalyze)	Create a map with the default options to retrieve the default MI datasource that will read the reader content.
Map<String,Object>	getDefaultCsvOptions(Object inputData)	Create the default options for the CSV datasource.
Map<String,Object>	getDefaultFileOptions(CsvType csvType, Object inputData)	Create a map of default options depending on the provided sourceType.
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(URL url)	Creates a map with the default options to retrieve MI datasource that will read the URL content
static CrossLinkCsvOptionFactory	getInstance()	Getter for the field instance.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static CrossLinkCsvOptionFactory getInstance()

Getter for the field instance.

Returns:

a CrossLinkCsvOptionFactory 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.

getDefaultCsvOptions

public Map<String,Object> getDefaultCsvOptions(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(CsvType csvType,
                                                      Object inputData)

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

Parameters:

csvType - a CsvType object.

inputData - a Object object.

Returns:

the map of default options for this sourceType

getDefaultCsvOptions

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

Create the default options for the CSV datasource. It will read InteractionEvidence elements usingCsvType.mix. It will use the CsvParserLogger to listen to the CSV parsing events

Parameters:

inputData - a Object object.

Returns:

the default options for the CSV datasource

getCsvOptions

public Map<String,Object> getCsvOptions(CsvType csvType,
                                              ComplexType complexType,
                                              Object inputData)

Create the options for the CSV datasource using the provided csvtype. It will read elements from this objectCategory. It will use the CsvParserLogger to listen to the CSV parsing events

Parameters:

csvType - a CsvType object.

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

inputData - a Object object.

Returns:

the options for the CSV datasource using the provided objectCategory

getCsvOptions

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

Create the options for the CSV datasource and specify if we want a Streaming MIFileDatasource. It will read InteractionEvidence elements using CsvType.binary_only. It will use the CsvParserLogger to listen to the Csv 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

getCsvOptions

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

Create the options for the CSV datasource using the provided MIFileParserListener. It will read InteractionEvidence elements and use CsvType.mix by default.

Parameters:

listener - a MIFileParserListener object.

inputData - is the mitab data to read

Returns:

the options for the MITAB datasource with the provided listener

getCsvOptions

public Map<String,Object> getCsvOptions(CsvType csvType,
                                              ComplexType complexType,
                                              Boolean streaming,
                                              MIFileParserListener listener,
                                              Object input)

Create a map of options

Parameters:

csvType - : Crosslink Csv type (mix, binary_only, single_nary, etc.)

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