org.biojava.bio.structure.align.seq
Class SmithWaterman3Daligner

java.lang.Object
  extended by org.biojava.bio.structure.align.AbstractStructureAlignment
      extended by org.biojava.bio.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
static String algorithmName
           
 
Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment
newline
 
Constructor Summary
SmithWaterman3Daligner()
           
 
Method Summary
 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 org.biojava.bio.structure.align.AbstractStructureAlignment
printHelp
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment
printHelp
 

Field Detail

algorithmName

public static final String algorithmName
See Also:
Constant Field Values
Constructor Detail

SmithWaterman3Daligner

public SmithWaterman3Daligner()
Method Detail

main

public static void main(String[] args)

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