public class BioJavaStructureAlignment extends java.lang.Object implements StructureAlignment
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
algorithmName |
Constructor and Description |
---|
BioJavaStructureAlignment() |
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 o)
Set the default parameters for this algorithm to use
|
public static final java.lang.String algorithmName
public java.lang.String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
public ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
public void setParameters(ConfigStrucAligParams o)
StructureAlignment
setParameters
in interface StructureAlignment
public java.lang.String getVersion()
StructureAlignment
getVersion
in interface StructureAlignment
public java.lang.String printHelp()
StructureAlignment
printHelp
in interface StructureAlignment
public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
StructureAlignment
align
in interface StructureAlignment
StructureException
public AFPChain align(Atom[] ca1, Atom[] ca2, java.lang.Object params) throws StructureException
StructureAlignment
align
in interface StructureAlignment
StructureException