org.biojava.bio.structure.align.fatcat
Class FatCatFlexible

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.FatCat
      extended by org.biojava.bio.structure.align.fatcat.FatCatFlexible
All Implemented Interfaces:
StructureAlignment

public class FatCatFlexible
extends FatCat
implements StructureAlignment


Field Summary
static String algorithmName
           
 
Fields inherited from class org.biojava.bio.structure.align.fatcat.FatCat
newline, VERSION
 
Constructor Summary
FatCatFlexible()
           
 
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 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.bio.structure.align.fatcat.FatCat
align, alignFlexible, alignRigid, alignRigid, getFatCatAligner, main, printHelp, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment
printHelp
 

Field Detail

algorithmName

public static String algorithmName
Constructor Detail

FatCatFlexible

public FatCatFlexible()
Method Detail

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