Package fr.ens.biologie.genomique.aozan.aozan3.recipe

Class ConfigurationXMLParser

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.recipe.ConfigurationXMLParser

public class ConfigurationXMLParser
extends Object

This class define a XML parser for configuration.

Since:

3.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
ConfigurationXMLParser(String rootTagName, String sectionName, Configuration parentConfiguration, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected Path	getIncludePath(Element element, String source)	Get the path of a file to include.
protected fr.ens.biologie.genomique.kenetre.log.GenericLogger	getLogger()	Get the logger.
protected String	getRootTagName()	Get the root tag name
E	parse(InputStream is)	Parse XML as an input stream.
E	parse(InputStream is, String source)	Parse XML as an input stream.
E	parse(Path path)	Parse XML as an input stream.
protected Configuration	parse(NodeList nList, String source)	Parse a run step XML tag.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConfigurationXMLParser

public ConfigurationXMLParser(String rootTagName,
                              String sectionName,
                              Configuration parentConfiguration,
                              fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Constructor.

Parameters:

rootTagName - root tag name

sectionName - name of the section in the recipe file

parentConfiguration - parent configuration

logger - logger to use

Method Detail

parse

protected Configuration parse(NodeList nList,
                              String source)
                       throws Aozan3Exception

Parse a run step XML tag.

Parameters:

nList - node list

source - XML source description

Returns:

a list with step objects

Throws:

Aozan3Exception - if an error occurs while parsing the XML

getLogger

protected fr.ens.biologie.genomique.kenetre.log.GenericLogger getLogger()

Get the logger.

Returns:

the logger

getRootTagName

protected String getRootTagName()

Get the root tag name

Returns:

the root tag name

parse

public E parse(Path path)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

path - file path

Returns:

a list of Step

Throws:

Aozan3Exception - if an error occurs while parsing the file

parse

public E parse(InputStream is)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

is - input stream

Returns:

a Recipe object

Throws:

Aozan3Exception - if an error occurs while parsing the file

parse

public E parse(InputStream is,
               String source)
        throws Aozan3Exception

Parse XML as an input stream.

Parameters:

is - input stream

source - XML source description

Returns:

a Recipe object

Throws:

Aozan3Exception - if an error occurs while parsing the file

getIncludePath

protected Path getIncludePath(Element element,
                              String source)
                       throws Aozan3Exception

Get the path of a file to include.

Parameters:

element - element to parse

Returns:

a Path object if the element to include exists or null

Throws:

Aozan3Exception - if other attribute than include exists for the tag