org.biojava.bio.structure.align.fatcat
Class FatCatFlexible

java.lang.Object
  org.biojava.bio.structure.align.fatcat.FatCat
      org.biojava.bio.structure.align.fatcat.FatCatFlexible

All Implemented Interfaces:

StructureAlignment

public class FatCatFlexible
extends FatCat
implements StructureAlignment

Field Summary

static java.lang.String

algorithmName

Fields inherited from class org.biojava.bio.structure.align.fatcat.FatCat

newline, VERSION

Constructor Summary

FatCatFlexible()

Method Summary

AFPChain	align(Atom[] ca1, Atom[] ca2) Run an alignment while specifying the atoms to be aligned.
AFPChain	align(Atom[] ca1, Atom[] ca2, java.lang.Object param) run an alignment and also send a bean containing the parameters.
java.lang.String	getAlgorithmName() Get the name of the Algorithm
ConfigStrucAligParams	getParameters() Return the paramers for this algorithm.
java.lang.String	getVersion() Get the Version information for this Algorithm.
void	setParameters(ConfigStrucAligParams parameters) Set the default parameters for this algorithm to use

Methods inherited from class org.biojava.bio.structure.align.fatcat.FatCat

align, alignFlexible, alignRigid, alignRigid, getFatCatAligner, main, printHelp, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment

printHelp

Field Detail

algorithmName

public static java.lang.String algorithmName

Constructor Detail

FatCatFlexible

public FatCatFlexible()

Method Detail

align

public AFPChain align(Atom[] ca1,
                      Atom[] ca2)
               throws StructureException

Description copied from interface: StructureAlignment

Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.

Specified by:

align in interface StructureAlignment

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

align

public AFPChain align(Atom[] ca1,
                      Atom[] ca2,
                      java.lang.Object param)
               throws StructureException

Description copied from interface: StructureAlignment

run an alignment and also send a bean containing the parameters.

Specified by:

align in interface StructureAlignment

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

getAlgorithmName

public java.lang.String getAlgorithmName()

Description copied from interface: StructureAlignment

Get the name of the Algorithm

Specified by:

getAlgorithmName in interface StructureAlignment

Returns:

the name of the algorithm

getVersion

public java.lang.String getVersion()

Description copied from interface: StructureAlignment

Get the Version information for this Algorithm.

Specified by:

getVersion in interface StructureAlignment

Returns:

the version of the algorithm

getParameters

public ConfigStrucAligParams getParameters()

Description copied from interface: StructureAlignment

Return the paramers for this algorithm.

Specified by:

getParameters in interface StructureAlignment

Returns:

The returned object will be a Java bean.

setParameters

public void setParameters(ConfigStrucAligParams parameters)

Description copied from interface: StructureAlignment

Set the default parameters for this algorithm to use

Specified by:

setParameters in interface StructureAlignment