org.biojava.bio.structure.align.seq
public class SmithWaterman3Daligner extends AbstractStructureAlignment implements StructureAlignment
Modifier and Type | Field and Description |
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static java.lang.String |
algorithmName |
newline
Constructor and Description |
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SmithWaterman3Daligner() |
Modifier and Type | Method and Description |
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AFPChain |
align(Atom[] ca1,
Atom[] ca2)
Run an alignment while specifying the atoms to be aligned.
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AFPChain |
align(Atom[] ca1,
Atom[] ca2,
java.lang.Object parameters)
run an alignment and also send a bean containing the parameters.
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java.lang.String |
getAlgorithmName()
Get the name of the Algorithm
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ConfigStrucAligParams |
getParameters()
Return the paramers for this algorithm.
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java.lang.String |
getVersion()
Get the Version information for this Algorithm.
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static void |
main(java.lang.String[] args) |
void |
setParameters(ConfigStrucAligParams parameters)
Set the default parameters for this algorithm to use
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printHelp
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
printHelp
public static final java.lang.String algorithmName
public static void main(java.lang.String[] args)
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