java.lang.Object

org.biojava.nbio.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

Fields

Modifier and Type

Field

Description

static final String

algorithmName
Constructor Summary

Constructors

Constructor

Description

BioJavaStructureAlignment()
Method Summary

Modifier and Type

Method

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()

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 Details
- algorithmName
  
  public static final String algorithmName
  See Also:
  
  Constant Field Values
Constructor Details
- BioJavaStructureAlignment
  
  public BioJavaStructureAlignment()
Method Details
- 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()
- 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

Class BioJavaStructureAlignment

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

algorithmName

Constructor Details

BioJavaStructureAlignment

Method Details

getAlgorithmName

getParameters

setParameters

getVersion

printHelp

align

align