org.biojava.nbio.structure.align.xml

Class AFPChainXMLParser

java.lang.Object

org.biojava.nbio.structure.align.xml.AFPChainXMLParser

public class AFPChainXMLParser
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_ALGORITHM_NAME

Constructor Summary

Constructors

Constructor and Description
AFPChainXMLParser()

Method Summary

Modifier and Type	Method and Description
static String	flipAlignment(String xml) Takes an XML representation of the alignment and flips the positions of name1 and name2
static AFPChain	fromXML(String xml, Atom[] ca1, Atom[] ca2)
static AFPChain	fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
static boolean	isErrorXML(String xml) returns true if the alignment XML contains an error message
static AFPChain[]	parseMultiXML(String xml)
static void	rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) replace the PDB res nums with atom positions:

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_ALGORITHM_NAME

public static final String DEFAULT_ALGORITHM_NAME

See Also:

Constant Field Values

Constructor Detail

AFPChainXMLParser

public AFPChainXMLParser()

Method Detail

fromXML

public static AFPChain fromXML(String xml,
                               String name1,
                               String name2,
                               Atom[] ca1,
                               Atom[] ca2)
                        throws IOException,
                               StructureException

new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed

Parameters:

xml -

name1 -

name1 -

ca1 -

ca2 -

Returns:

Throws:

IOException

StructureException

fromXML

public static AFPChain fromXML(String xml,
                               Atom[] ca1,
                               Atom[] ca2)
                        throws IOException

Throws:

IOException

isErrorXML

public static boolean isErrorXML(String xml)

returns true if the alignment XML contains an error message

Parameters:

xml -

Returns:

flag if there was an Error while processing the alignment.

flipAlignment

public static String flipAlignment(String xml)
                            throws IOException,
                                   StructureException

Takes an XML representation of the alignment and flips the positions of name1 and name2

Parameters:

xml - String representing the alignment

Returns:

XML representation of the flipped alignment

Throws:

IOException

StructureException

rebuildAFPChain

public static void rebuildAFPChain(AFPChain afpChain,
                                   Atom[] ca1,
                                   Atom[] ca2)

replace the PDB res nums with atom positions:

Parameters:

afpChain -

ca1 -

ca2 -

parseMultiXML

public static AFPChain[] parseMultiXML(String xml)
                                throws IOException

Throws:

IOException