Package org.biojava.nbio.structure.align.xml

Class MultipleAlignmentXMLConverter

java.lang.Object

org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

public class MultipleAlignmentXMLConverter
extends Object

Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.

To convert a MultipleAlignment to an XML String use the MultipleAlignmentWriter.toXML(MultipleAlignmentEnsemble) method.

Since:

4.1.1

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentXMLConverter()

Method Summary

Modifier and Type	Method	Description
static void	printXMLalignment(org.biojava.nbio.core.util.PrettyXMLWriter xml, MultipleAlignment msa)
static void	printXMLblock(org.biojava.nbio.core.util.PrettyXMLWriter xml, Block b)
static void	printXMLblockSet(org.biojava.nbio.core.util.PrettyXMLWriter xml, BlockSet bs)
static void	printXMLensemble(org.biojava.nbio.core.util.PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble)
static void	printXMLheader(org.biojava.nbio.core.util.PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble)
static void	printXMLmatrix4d(org.biojava.nbio.core.util.PrettyXMLWriter xml, javax.vecmath.Matrix4d transform)
static void	printXMLscoresCache(org.biojava.nbio.core.util.PrettyXMLWriter xml, ScoresCache cache)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultipleAlignmentXMLConverter

public MultipleAlignmentXMLConverter()

Method Detail

printXMLensemble

public static void printXMLensemble(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                    MultipleAlignmentEnsemble ensemble)
                             throws IOException

Throws:

IOException

printXMLalignment

public static void printXMLalignment(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                     MultipleAlignment msa)
                              throws IOException

Throws:

IOException

printXMLblockSet

public static void printXMLblockSet(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                    BlockSet bs)
                             throws IOException

Throws:

IOException

printXMLblock

public static void printXMLblock(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                 Block b)
                          throws IOException

Throws:

IOException

printXMLmatrix4d

public static void printXMLmatrix4d(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                    javax.vecmath.Matrix4d transform)
                             throws IOException

Throws:

IOException

printXMLscoresCache

public static void printXMLscoresCache(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                       ScoresCache cache)
                                throws IOException

Throws:

IOException

printXMLheader

public static void printXMLheader(org.biojava.nbio.core.util.PrettyXMLWriter xml,
                                  MultipleAlignmentEnsemble ensemble)
                           throws IOException

Throws:

IOException