org.biojava.bio.structure.align
Class AbstractStructureAlignment

java.lang.Object
  extended by org.biojava.bio.structure.align.AbstractStructureAlignment
All Implemented Interfaces:
StructureAlignment
Direct Known Subclasses:
CeMain, SmithWaterman3Daligner

public abstract class AbstractStructureAlignment
extends Object
implements StructureAlignment


Field Summary
static String newline
           
 
Constructor Summary
AbstractStructureAlignment()
           
 
Method Summary
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.
 String printHelp()
          Returns some documentation on the command line arguments 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 Detail

newline

public static String newline
Constructor Detail

AbstractStructureAlignment

public AbstractStructureAlignment()
Method Detail

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

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