java.lang.Object

org.biojava.nbio.structure.align.AbstractStructureAlignment

All Implemented Interfaces:: StructureAlignment

Direct Known Subclasses:: CeMain, SmithWaterman3Daligner

public abstract class AbstractStructureAlignment extends Object implements StructureAlignment

Field Summary

Fields

Modifier and Type

Field

Description

static String

newline
Constructor Summary

Constructors

Constructor

Description

AbstractStructureAlignment()
Method Summary

Modifier and Type

Method

Description

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.

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 Details
- newline
  
  public static String newline
Constructor Details
- AbstractStructureAlignment
  
  public AbstractStructureAlignment()
Method Details
- 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

Class AbstractStructureAlignment

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

newline

Constructor Details

AbstractStructureAlignment

Method Details

align

align

getAlgorithmName

getParameters

getVersion

setParameters