public abstract class AbstractStructureAlignment extends java.lang.Object implements StructureAlignment
Modifier and Type | Field and Description |
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static java.lang.String |
newline |
Constructor and Description |
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AbstractStructureAlignment() |
Modifier and Type | Method and Description |
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abstract AFPChain |
align(Atom[] ca1,
Atom[] ca2)
Run an alignment while specifying the atoms to be aligned.
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abstract AFPChain |
align(Atom[] ca1,
Atom[] ca2,
java.lang.Object params)
run an alignment and also send a bean containing the parameters.
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abstract java.lang.String |
getAlgorithmName()
Get the name of the Algorithm
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abstract ConfigStrucAligParams |
getParameters()
Return the paramers for this algorithm.
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abstract java.lang.String |
getVersion()
Get the Version information for this Algorithm.
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java.lang.String |
printHelp()
Returns some documentation on the command line arguments 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
public java.lang.String printHelp()
StructureAlignment
printHelp
in interface StructureAlignment