org.biojava.bio.structure.align

Interface StructureAlignment

All Known Implementing Classes:

AbstractStructureAlignment, BioJavaStructureAlignment, CeCPMain, CeMain, CeSideChainMain, FatCatFlexible, FatCatRigid, OptimalCECPMain, SmithWaterman3Daligner

public interface StructureAlignment

Method Summary

Methods

Modifier and Type	Method and Description
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 parameters) Set the default parameters for this algorithm to use

Method Detail

align

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

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

Parameters:

ca1 -

ca2 -

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

align

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

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

Parameters:

ca1 -

ca2 -

params -

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

getParameters

ConfigStrucAligParams getParameters()

Return the paramers for this algorithm.

Returns:

The returned object will be a Java bean.

setParameters

void setParameters(ConfigStrucAligParams parameters)

Set the default parameters for this algorithm to use

Parameters:

parameters -

getAlgorithmName

String getAlgorithmName()

Get the name of the Algorithm

Returns:

the name of the algorithm

getVersion

String getVersion()

Get the Version information for this Algorithm.

Returns:

the version of the algorithm

printHelp

String printHelp()

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

Returns:

the help string