org.biojava.bio.structure.align
Class AbstractStructureAlignment

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

All Implemented Interfaces:

StructureAlignment

Direct Known Subclasses:

CeMain, SmithWaterman3Daligner

public abstract class AbstractStructureAlignment
extends Object
implements StructureAlignment

Field Summary

static String

newline

Constructor Summary

AbstractStructureAlignment()

Method Summary

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

newline

public static String newline

Constructor Detail

AbstractStructureAlignment

public AbstractStructureAlignment()

Method Detail

align

public abstract 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 abstract 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

getAlgorithmName

public abstract 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 abstract 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.

getVersion

public abstract 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

setParameters

public abstract void setParameters(ConfigStrucAligParams parameters)

Description copied from interface: StructureAlignment

Set the default parameters for this algorithm to use

Specified by:

setParameters in interface StructureAlignment

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