java.lang.Object

org.biojava.nbio.structure.align.AbstractStructureAlignment

org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

All Implemented Interfaces:: StructureAlignment

public class SmithWaterman3Daligner extends AbstractStructureAlignment implements StructureAlignment

provides a 3D superimposition based on the sequence alignment

Author:: Andreas Prlic

Field Summary

Fields

Modifier and Type

Field

Description

static final String

algorithmName

Fields inherited from class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline
Constructor Summary

Constructors

Constructor

Description

SmithWaterman3Daligner()
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 parameters)

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.

static void

main(String[] args)

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
- algorithmName
  
  public static final String algorithmName
  See Also:
  
  Constant Field Values
Constructor Details
- SmithWaterman3Daligner
  
  public SmithWaterman3Daligner()
Method Details
- main
  
  public static void main(String[] args) throws ConfigurationException
  
  Throws:
  
  ConfigurationException
- 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
  
  Specified by:
  
  align in class AbstractStructureAlignment
  
  Returns:
  
  the afpChain object that contains the alignment.
  
  Throws:
  
  StructureException
- align
  
  public AFPChain align(Atom[] ca1, Atom[] ca2, Object parameters) throws StructureException
  
  Description copied from interface: StructureAlignment
  
  run an alignment and also send a bean containing the parameters.
  
  Specified by:
  
  align in interface StructureAlignment
  
  Specified by:
  
  align in class AbstractStructureAlignment
  
  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
  
  Specified by:
  
  getAlgorithmName in class AbstractStructureAlignment
  
  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
  
  Specified by:
  
  getParameters in class AbstractStructureAlignment
  
  Returns:
  
  The returned object will be a Java bean.
- getVersion
  
  public String getVersion()
  
  Description copied from interface: StructureAlignment
  
  Get the Version information for this Algorithm.
  
  Specified by:
  
  getVersion in interface StructureAlignment
  
  Specified by:
  
  getVersion in class AbstractStructureAlignment
  
  Returns:
  
  the version of the algorithm
- 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
  
  Specified by:
  
  setParameters in class AbstractStructureAlignment

Class SmithWaterman3Daligner

Field Summary

Fields inherited from class org.biojava.nbio.structure.align.AbstractStructureAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

algorithmName

Constructor Details

SmithWaterman3Daligner

Method Details

main

align

align

getAlgorithmName

getParameters

getVersion

setParameters