org.biojava.bio.structure.align
Class BioJavaStructureAlignment

java.lang.Object
  extended by org.biojava.bio.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
static String algorithmName
           
 
Constructor Summary
BioJavaStructureAlignment()
           
 
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 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()
          Returns some documentation on the command line arguments for this algorithm.
 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 Detail

algorithmName

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

BioJavaStructureAlignment

public BioJavaStructureAlignment()
Method Detail

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()
Description copied from interface: StructureAlignment
Returns some documentation on the command line arguments for this algorithm.

Specified by:
printHelp in interface StructureAlignment
Returns:
the help string

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