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java.lang.Objectorg.biojava.bio.structure.align.AbstractStructureAlignment
org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
public class SmithWaterman3Daligner
provides a 3D superimposition based on the sequence alignment
Field Summary | |
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static String |
algorithmName
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Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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newline |
Constructor Summary | |
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SmithWaterman3Daligner()
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Method Summary | |
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AFPChain |
align(Atom[] ca1,
Atom[] ca2)
Run an alignment while specifying the atoms to be aligned. |
AFPChain |
align(Atom[] ca1,
Atom[] ca2,
Object parameters)
run an alignment and also send a bean containing the parameters. |
String |
getAlgorithmName()
Get the name of the Algorithm |
ConfigStrucAligParams |
getParameters()
Return the paramers for this algorithm. |
String |
getVersion()
Get the Version information for this Algorithm. |
static void |
main(String[] args)
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void |
setParameters(ConfigStrucAligParams parameters)
Set the default parameters for this algorithm to use |
Methods inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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printHelp |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment |
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printHelp |
Field Detail |
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public static final String algorithmName
Constructor Detail |
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public SmithWaterman3Daligner()
Method Detail |
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public static void main(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, Object parameters) throws StructureException
StructureAlignment
align
in interface StructureAlignment
align
in class AbstractStructureAlignment
StructureException
public String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
getAlgorithmName
in class AbstractStructureAlignment
public ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
getParameters
in class AbstractStructureAlignment
public 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
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