Package org.biojava.nbio.structure.align.xml

Class MultipleAlignmentXMLParser

java.lang.Object

org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser

public class MultipleAlignmentXMLParser
extends Object

Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.

Atoms need to be downloaded, either manually or using the method getAtomArrays() in MultipleAlignmentEnsemble.

Since:

4.1.1

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentXMLParser()

Method Summary

Modifier and Type	Method	Description
static List<MultipleAlignmentEnsemble>	parseXMLfile(String xml)	Creates a list of MultipleAlignment ensembles from an XML file.

Methods inherited from class java.lang.Object

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

Constructor Details

MultipleAlignmentXMLParser

public MultipleAlignmentXMLParser()

Method Details

parseXMLfile

public static List<MultipleAlignmentEnsemble> parseXMLfile(String xml)
                                                    throws ParserConfigurationException,
SAXException,
IOException

Creates a list of MultipleAlignment ensembles from an XML file. This recovers only the information that was previously stored. If the Atoms are needed, the method getAtomArrays() will automatically download the structures from the stored structure identifiers.

Parameters:

xml - String XML file containing any number of ensembles

Returns:

List of ensembles in the file

Throws:

ParserConfigurationException

SAXException

IOException