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

Class AFPChainXMLConverter

java.lang.Object

org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

public class AFPChainXMLConverter
extends Object

Constructor Summary

Constructors

Constructor	Description
AFPChainXMLConverter()

Method Summary

Modifier and Type	Method	Description
static void	printXMLEQRInferPositions(PrettyXMLWriter xml, AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2)
static void	printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain)
static String	toXML(AFPChain afpChain)
static void	toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2)	Write the XML representation to a StringWriter
static String	toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2)	Convert an afpChain to a simple XML representation

Methods inherited from class java.lang.Object

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

Constructor Detail

AFPChainXMLConverter

public AFPChainXMLConverter()

Method Detail

toXML

public static String toXML(AFPChain afpChain,
                           Atom[] ca1,
                           Atom[] ca2)
                    throws IOException

Convert an afpChain to a simple XML representation

Parameters:

afpChain -

Returns:

XML representation of the AFPCHain

Throws:

IOException

toXML

public static void toXML(AFPChain afpChain,
                         StringWriter swriter,
                         Atom[] ca1,
                         Atom[] ca2)
                  throws IOException

Write the XML representation to a StringWriter

Parameters:

afpChain -

swriter -

Throws:

IOException

printXMLEQRInferPositions

public static void printXMLEQRInferPositions(PrettyXMLWriter xml,
                                             AFPChain afpChain,
                                             int bk,
                                             Atom[] ca1,
                                             Atom[] ca2)
                                      throws IOException

Throws:

IOException

toXML

public static String toXML(AFPChain afpChain)
                    throws IOException

Throws:

IOException

printXMLHeader

public static void printXMLHeader(PrettyXMLWriter xml,
                                  AFPChain afpChain)
                           throws IOException

Throws:

IOException