org.biojava.bio.structure.align
Class BioJavaStructureAlignment

java.lang.Object
  org.biojava.bio.structure.align.BioJavaStructureAlignment

All Implemented Interfaces:

StructureAlignment

public class BioJavaStructureAlignment
extends Object
implements StructureAlignment

Wrapper for the BioJava Structure Alignment Implementation

Author:

Andreas Prlic

Field Summary

static String

algorithmName

Constructor Summary

BioJavaStructureAlignment()

Method Summary

AFPChain	align(Atom[] ca1, Atom[] ca2) Run an alignment while specifying the atoms to be aligned.
AFPChain	align(Atom[] ca1, Atom[] ca2, Object params) run an alignment and also send a bean containing the parameters.
String	getAlgorithmName() Get the name of the Algorithm
ConfigStrucAligParams	getParameters() Return the paramers for this algorithm.
String	getVersion() Get the Version information for this Algorithm.
String	printHelp() Returns some documentation on the command line arguments for this algorithm.
void	setParameters(ConfigStrucAligParams o) Set the default parameters for this algorithm to use

Methods inherited from class java.lang.Object

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

Field Detail

algorithmName

public static final String algorithmName

See Also:

Constant Field Values

Constructor Detail

BioJavaStructureAlignment

public BioJavaStructureAlignment()

Method Detail

getAlgorithmName

public 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

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 o)

Description copied from interface: StructureAlignment

Set the default parameters for this algorithm to use

Specified by:

setParameters in interface StructureAlignment

getVersion

public 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

printHelp

public String printHelp()

Description copied from interface: StructureAlignment

Returns some documentation on the command line arguments for this algorithm.

Specified by:

printHelp in interface StructureAlignment

Returns:

the help string

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,
                      Object params)
               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