org.biojava.bio.structure.align
public interface StructureAlignment
Modifier and Type | Method and Description |
---|---|
AFPChain |
align(Atom[] ca1,
Atom[] ca2)
Run an alignment while specifying the atoms to be aligned.
|
AFPChain |
align(Atom[] ca1,
Atom[] ca2,
java.lang.Object params)
run an alignment and also send a bean containing the parameters.
|
java.lang.String |
getAlgorithmName()
Get the name of the Algorithm
|
ConfigStrucAligParams |
getParameters()
Return the paramers for this algorithm.
|
java.lang.String |
getVersion()
Get the Version information for this Algorithm.
|
java.lang.String |
printHelp()
Returns some documentation on the command line arguments for this algorithm.
|
void |
setParameters(ConfigStrucAligParams parameters)
Set the default parameters for this algorithm to use
|
AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
ca1
- ca2
- StructureException
AFPChain align(Atom[] ca1, Atom[] ca2, java.lang.Object params) throws StructureException
ca1
- ca2
- params
- StructureException
ConfigStrucAligParams getParameters()
void setParameters(ConfigStrucAligParams parameters)
parameters
- java.lang.String getAlgorithmName()
java.lang.String getVersion()
java.lang.String printHelp()