StructureAlignment
CeMain
, SmithWaterman3Daligner
public abstract class AbstractStructureAlignment extends java.lang.Object implements StructureAlignment
Modifier and Type | Field | Description |
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static java.lang.String |
newline |
Constructor | Description |
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AbstractStructureAlignment() |
Modifier and Type | Method | Description |
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abstract AFPChain |
align(Atom[] ca1,
Atom[] ca2) |
Run an alignment while specifying the atoms to be aligned.
|
abstract AFPChain |
align(Atom[] ca1,
Atom[] ca2,
java.lang.Object params) |
run an alignment and also send a bean containing the parameters.
|
abstract java.lang.String |
getAlgorithmName() |
Get the name of the Algorithm
|
abstract ConfigStrucAligParams |
getParameters() |
Return the paramers for this algorithm.
|
abstract java.lang.String |
getVersion() |
Get the Version information for this Algorithm.
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abstract void |
setParameters(ConfigStrucAligParams parameters) |
Set the default parameters for this algorithm to use
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public abstract AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
StructureAlignment
align
in interface StructureAlignment
StructureException
public abstract AFPChain align(Atom[] ca1, Atom[] ca2, java.lang.Object params) throws StructureException
StructureAlignment
align
in interface StructureAlignment
StructureException
public abstract java.lang.String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
public abstract ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
public abstract java.lang.String getVersion()
StructureAlignment
getVersion
in interface StructureAlignment
public abstract void setParameters(ConfigStrucAligParams parameters)
StructureAlignment
setParameters
in interface StructureAlignment