Class MultipleAlignmentXMLParser


  • public class MultipleAlignmentXMLParser
    extends java.lang.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 Detail

      • MultipleAlignmentXMLParser

        public MultipleAlignmentXMLParser()
    • Method Detail

      • parseXMLfile

        public static java.util.List<MultipleAlignmentEnsemble> parseXMLfile​(java.lang.String xml)
                                                                      throws javax.xml.parsers.ParserConfigurationException,
                                                                             org.xml.sax.SAXException,
                                                                             java.io.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:
        javax.xml.parsers.ParserConfigurationException
        org.xml.sax.SAXException
        java.io.IOException
      • parseBlock

        public static Block parseBlock​(org.w3c.dom.Node root,
                                       BlockSet blockSet)
      • parseMatrix4d

        public static javax.vecmath.Matrix4d parseMatrix4d​(org.w3c.dom.Node node)
      • parseScoresCache

        public static void parseScoresCache​(org.w3c.dom.Node root,
                                            ScoresCache cache)