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 and Description
MultipleAlignmentXMLParser()

Method Summary

Modifier and Type	Method and Description
static Block	parseBlock(Node root, BlockSet blockSet)
static BlockSet	parseBlockSet(Node root, MultipleAlignment msa)
static MultipleAlignmentEnsemble	parseEnsemble(Node root)
static void	parseHeader(Node node, MultipleAlignmentEnsemble ensemble)
static javax.vecmath.Matrix4d	parseMatrix4d(Node node)
static MultipleAlignment	parseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble)
static void	parseScoresCache(Node root, ScoresCache cache)
static void	parseStructures(Node root, MultipleAlignmentEnsemble ensemble)
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 Detail

MultipleAlignmentXMLParser

public MultipleAlignmentXMLParser()

Method Detail

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

parseEnsemble

public static MultipleAlignmentEnsemble parseEnsemble(Node root)

parseMultipleAlignment

public static MultipleAlignment parseMultipleAlignment(Node root,
                                                       MultipleAlignmentEnsemble ensemble)

parseBlockSet

public static BlockSet parseBlockSet(Node root,
                                     MultipleAlignment msa)

parseBlock

public static Block parseBlock(Node root,
                               BlockSet blockSet)

parseMatrix4d

public static javax.vecmath.Matrix4d parseMatrix4d(Node node)

parseScoresCache

public static void parseScoresCache(Node root,
                                    ScoresCache cache)

parseHeader

public static void parseHeader(Node node,
                               MultipleAlignmentEnsemble ensemble)

parseStructures

public static void parseStructures(Node root,
                                   MultipleAlignmentEnsemble ensemble)