Class MultipleAlignmentXMLParser
java.lang.Object
org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic BlockparseBlock(Node root, BlockSet blockSet) static BlockSetparseBlockSet(Node root, MultipleAlignment msa) static MultipleAlignmentEnsembleparseEnsemble(Node root) static voidparseHeader(Node node, MultipleAlignmentEnsemble ensemble) static javax.vecmath.Matrix4dparseMatrix4d(Node node) static MultipleAlignmentparseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble) static voidparseScoresCache(Node root, ScoresCache cache) static voidparseStructures(Node root, MultipleAlignmentEnsemble ensemble) static List<MultipleAlignmentEnsemble>parseXMLfile(String xml) Creates a list of MultipleAlignment ensembles from an XML file.
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Constructor Details
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MultipleAlignmentXMLParser
public MultipleAlignmentXMLParser()
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Method Details
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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:
ParserConfigurationExceptionSAXExceptionIOException
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parseEnsemble
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parseMultipleAlignment
public static MultipleAlignment parseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble) -
parseBlockSet
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parseBlock
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parseMatrix4d
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parseScoresCache
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parseHeader
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parseStructures
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