public class MultipleAlignmentXMLParser
extends java.lang.Object
MultipleAlignmentEnsemble
, so
that the original alignment can be recovered.
Atoms need to be downloaded, either manually or using the method getAtomArrays() in MultipleAlignmentEnsemble.
Constructor | Description |
---|---|
MultipleAlignmentXMLParser() |
Modifier and Type | Method | Description |
---|---|---|
static Block |
parseBlock(org.w3c.dom.Node root,
BlockSet blockSet) |
|
static BlockSet |
parseBlockSet(org.w3c.dom.Node root,
MultipleAlignment msa) |
|
static MultipleAlignmentEnsemble |
parseEnsemble(org.w3c.dom.Node root) |
|
static void |
parseHeader(org.w3c.dom.Node node,
MultipleAlignmentEnsemble ensemble) |
|
static javax.vecmath.Matrix4d |
parseMatrix4d(org.w3c.dom.Node node) |
|
static MultipleAlignment |
parseMultipleAlignment(org.w3c.dom.Node root,
MultipleAlignmentEnsemble ensemble) |
|
static void |
parseScoresCache(org.w3c.dom.Node root,
ScoresCache cache) |
|
static void |
parseStructures(org.w3c.dom.Node root,
MultipleAlignmentEnsemble ensemble) |
|
static java.util.List<MultipleAlignmentEnsemble> |
parseXMLfile(java.lang.String xml) |
Creates a list of MultipleAlignment ensembles from an XML file.
|
public static java.util.List<MultipleAlignmentEnsemble> parseXMLfile(java.lang.String xml) throws javax.xml.parsers.ParserConfigurationException, org.xml.sax.SAXException, java.io.IOException
xml
- String XML file containing any number of ensemblesjavax.xml.parsers.ParserConfigurationException
org.xml.sax.SAXException
java.io.IOException
public static MultipleAlignmentEnsemble parseEnsemble(org.w3c.dom.Node root)
public static MultipleAlignment parseMultipleAlignment(org.w3c.dom.Node root, MultipleAlignmentEnsemble ensemble)
public static BlockSet parseBlockSet(org.w3c.dom.Node root, MultipleAlignment msa)
public static javax.vecmath.Matrix4d parseMatrix4d(org.w3c.dom.Node node)
public static void parseScoresCache(org.w3c.dom.Node root, ScoresCache cache)
public static void parseHeader(org.w3c.dom.Node node, MultipleAlignmentEnsemble ensemble)
public static void parseStructures(org.w3c.dom.Node root, MultipleAlignmentEnsemble ensemble)