org.biojava.spark.function

Class AlignmentTools

java.lang.Object

org.biojava.spark.function.AlignmentTools

All Implemented Interfaces:

Serializable

public class AlignmentTools
extends Object
implements Serializable

Class to calculate the TM Score between two Atom arrays.

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AlignmentTools()

Method Summary

Modifier and Type	Method and Description
static org.biojava.nbio.structure.align.model.AFPChain	getBiojavaAlignment(org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2, String alignmentMethod) Performs an alignment and returns the AFPChain scores between two C-alpha Atom arrays.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentTools

public AlignmentTools()

Method Detail

getBiojavaAlignment

public static org.biojava.nbio.structure.align.model.AFPChain getBiojavaAlignment(org.biojava.nbio.structure.Atom[] ca1,
                                                                                  org.biojava.nbio.structure.Atom[] ca2,
                                                                                  String alignmentMethod)

Performs an alignment and returns the AFPChain scores between two C-alpha Atom arrays.

Parameters:

ca1 - the first C-alpha array

ca2 - the second C-alpha array

alignmentMethod - the string specifying the alignment method

Returns:

the AFPChain pf the scores between the two input Atom array