org.biojava.bio.structure.align.xml
Class AFPChainXMLConverter

java.lang.Object
  extended by org.biojava.bio.structure.align.xml.AFPChainXMLConverter

public class AFPChainXMLConverter
extends Object


Constructor Summary
AFPChainXMLConverter()
           
 
Method Summary
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 String toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
          Convert an afpChain to a simple XML representation
static void toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2)
          Write the XML representation to a StringWriter
 
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