StructureAlignment
public class SmithWaterman3Daligner extends AbstractStructureAlignment implements StructureAlignment
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
algorithmName |
newline
Constructor | Description |
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SmithWaterman3Daligner() |
Modifier and Type | Method | 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 parameters) |
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.
|
static void |
main(java.lang.String[] args) |
|
void |
setParameters(ConfigStrucAligParams parameters) |
Set the default parameters for this algorithm to use
|
public static final java.lang.String algorithmName
public static void main(java.lang.String[] args) throws ConfigurationException
ConfigurationException
public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
StructureAlignment
align
in interface StructureAlignment
align
in class AbstractStructureAlignment
StructureException
public AFPChain align(Atom[] ca1, Atom[] ca2, java.lang.Object parameters) throws StructureException
StructureAlignment
align
in interface StructureAlignment
align
in class AbstractStructureAlignment
StructureException
public java.lang.String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
getAlgorithmName
in class AbstractStructureAlignment
public ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
getParameters
in class AbstractStructureAlignment
public java.lang.String getVersion()
StructureAlignment
getVersion
in interface StructureAlignment
getVersion
in class AbstractStructureAlignment
public void setParameters(ConfigStrucAligParams parameters)
StructureAlignment
setParameters
in interface StructureAlignment
setParameters
in class AbstractStructureAlignment