java.lang.Object

org.biojava.nbio.structure.align.fatcat.FatCat

org.biojava.nbio.structure.align.fatcat.FatCatFlexible

All Implemented Interfaces:: StructureAlignment

public class FatCatFlexible extends FatCat implements StructureAlignment

Field Summary

Fields

Modifier and Type

Field

Description

static final String

algorithmName

Fields inherited from class org.biojava.nbio.structure.align.fatcat.FatCat
newline, VERSION
Constructor Summary

Constructors

Constructor

Description

FatCatFlexible()
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 param)

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.

void

setParameters(ConfigStrucAligParams parameters)

Set the default parameters for this algorithm to use

Methods inherited from class org.biojava.nbio.structure.align.fatcat.FatCat
align, alignFlexible, alignRigid, alignRigid, getFatCatAligner, main, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

Class FatCatFlexible

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Details

algorithmName

Constructor Details

FatCatFlexible

Method Details

align

align

getAlgorithmName

getVersion

getParameters

setParameters