Class MultipleAlignmentXMLParser
- java.lang.Object
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- org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
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public class MultipleAlignmentXMLParser extends Object
Parse an XML file representing aMultipleAlignmentEnsemble
, 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 Constructor Description MultipleAlignmentXMLParser()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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.
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Constructor Detail
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MultipleAlignmentXMLParser
public MultipleAlignmentXMLParser()
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Method Detail
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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:
ParserConfigurationException
SAXException
IOException
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parseEnsemble
public static MultipleAlignmentEnsemble parseEnsemble(Node root)
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parseMultipleAlignment
public static MultipleAlignment parseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble)
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parseBlockSet
public static BlockSet parseBlockSet(Node root, MultipleAlignment msa)
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parseBlock
public static Block parseBlock(Node root, BlockSet blockSet)
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parseMatrix4d
public static javax.vecmath.Matrix4d parseMatrix4d(Node node)
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parseScoresCache
public static void parseScoresCache(Node root, ScoresCache cache)
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parseHeader
public static void parseHeader(Node node, MultipleAlignmentEnsemble ensemble)
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parseStructures
public static void parseStructures(Node root, MultipleAlignmentEnsemble ensemble)
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