public class MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements MultipleAlignmentEnsemble, java.io.Serializable, java.lang.Cloneable
MultipleAlignmentEnsemble
.Constructor and Description |
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MultipleAlignmentEnsembleImpl()
Default Constructor.
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MultipleAlignmentEnsembleImpl(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
Constructor from an AFPChain instance.
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MultipleAlignmentEnsembleImpl(java.util.List<java.lang.String> structureNames)
Constructor using structure identifiers.
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MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e)
Copy constructor.
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Modifier and Type | Method and Description |
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void |
addMultipleAlignment(MultipleAlignment alignment)
Add a new MultipleAlignment to the end of the ensemble and set its
parent ensemble to this.
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void |
clear()
Resets all scores
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MultipleAlignmentEnsembleImpl |
clone()
Creates and returns an identical copy of this ensemble, including a deep
clone of all constituent alignments.
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java.lang.String |
getAlgorithmName()
Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
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int |
getAlignmentNum()
Return the number of alternative alignments stored in the Ensemble.
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java.util.List<Atom[]> |
getAtomArrays()
Get an array of representative atoms for each structure (CA atoms for proteins).
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java.lang.Long |
getCalculationTime()
public
Returns the running time of the structure alignment calculation, in milliseconds.
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java.util.List<Matrix> |
getDistanceMatrix()
Returns the List containing the interatomic distance Matrix of each structure.
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java.lang.Long |
getIoTime()
Returns the io time for this object, in milliseconds.
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java.util.List<MultipleAlignment> |
getMultipleAlignments()
Returns the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
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java.util.List<java.lang.String> |
getStructureNames()
Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
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java.lang.String |
getVersion()
Returns the version of the algorithm used to generate the MultipleAlignment objects.
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void |
setAlgorithmName(java.lang.String algorithmName)
Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
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void |
setAtomArrays(java.util.List<Atom[]> atomArrays)
Sets the List of Atom arrays.
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void |
setCalculationTime(java.lang.Long millis)
Set the time needed to calculate this alignment
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void |
setIoTime(java.lang.Long millis)
Set the IO time to load this object
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void |
setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments)
Set the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
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void |
setStructureNames(java.util.List<java.lang.String> structureNames)
Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
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void |
setVersion(java.lang.String version)
Sets the version of the algorithm used to generate the MultipleAlignment objects.
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int |
size()
Returns the number of aligned structures in the MultipleAlignments.
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void |
updateAtomArrays()
Force the atom arrays to regenerate based on
getStructureNames() |
void |
updateDistanceMatrix()
Force recalculation of the distance matrices
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clone, getScore, getScores, putScore
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getScore, getScores, putScore
public MultipleAlignmentEnsembleImpl()
public MultipleAlignmentEnsembleImpl(java.util.List<java.lang.String> structureNames)
structureNames
- List of Structure names, that can be parsed by AtomCache.public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e)
e
- MultipleAlignmentEnsembleImpl to copy.public MultipleAlignmentEnsembleImpl clone()
MultipleAlignmentEnsemble
clone
in interface MultipleAlignmentEnsemble
clone
in class java.lang.Object
public java.lang.String getAlgorithmName()
MultipleAlignmentEnsemble
getAlgorithmName
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.setAlgorithmName(String)
public void setAlgorithmName(java.lang.String algorithmName)
MultipleAlignmentEnsemble
setAlgorithmName
in interface MultipleAlignmentEnsemble
algorithmName
- name of the algorithm.MultipleAlignmentEnsemble.getAlgorithmName()
public java.lang.String getVersion()
MultipleAlignmentEnsemble
getVersion
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.setVersion(String)
public void setVersion(java.lang.String version)
MultipleAlignmentEnsemble
setVersion
in interface MultipleAlignmentEnsemble
version
- the version of the algorithm.MultipleAlignmentEnsemble.getVersion()
public java.lang.Long getIoTime()
MultipleAlignmentEnsemble
getIoTime
in interface MultipleAlignmentEnsemble
public void setIoTime(java.lang.Long millis)
MultipleAlignmentEnsemble
setIoTime
in interface MultipleAlignmentEnsemble
public java.lang.Long getCalculationTime()
MultipleAlignmentEnsemble
getCalculationTime
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.getIoTime()L
public void setCalculationTime(java.lang.Long millis)
MultipleAlignmentEnsemble
setCalculationTime
in interface MultipleAlignmentEnsemble
public java.util.List<java.lang.String> getStructureNames()
MultipleAlignmentEnsemble
The names are structure identifiers of the structures. They are in the same order as in the alignment Blocks (same index number for same structure).
getStructureNames
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.setStructureNames(List)
,
MultipleAlignmentEnsemble.getAtomArrays()
public void setStructureNames(java.util.List<java.lang.String> structureNames)
MultipleAlignmentEnsemble
The names are structure identifiers of the structures.
setStructureNames
in interface MultipleAlignmentEnsemble
structureNames
- names of the structures, structure identifiersMultipleAlignmentEnsemble.getStructureNames()
,
MultipleAlignmentEnsemble.setAtomArrays(List)
public java.util.List<Atom[]> getAtomArrays()
MultipleAlignmentEnsemble
Atoms should be unrotated. Thus, to obtain a superimposed set of structures, each atom array should be cloned and then rotated according to the transformation matrix.
If atoms have not previously been set using MultipleAlignmentEnsemble.setAtomArrays(List)
,
attempts to load representative atoms based on MultipleAlignmentEnsemble.getStructureNames()
.
If it fails to load the Atoms it gives a NullPointerException before returning null.
getAtomArrays
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.setAtomArrays(List)
public void setAtomArrays(java.util.List<Atom[]> atomArrays)
MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.setStructureNames(List)
Setting the atom arrays to null will cause them to be automatically
regenerated based on MultipleAlignmentEnsemble.getStructureNames()
during the next call to
MultipleAlignmentEnsemble.getAtomArrays()
setAtomArrays
in interface MultipleAlignmentEnsemble
atomArrays
- the List of representative (C-alpha) atom arraysMultipleAlignmentEnsemble.getAtomArrays()
,
MultipleAlignmentEnsemble.setStructureNames(List)
public void updateAtomArrays() throws java.io.IOException, StructureException
getStructureNames()
java.io.IOException
StructureException
public int getAlignmentNum()
MultipleAlignmentEnsemble
getAlignmentNum
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.size()
public java.util.List<Matrix> getDistanceMatrix()
MultipleAlignmentEnsemble
getDistanceMatrix
in interface MultipleAlignmentEnsemble
#updateDistanceMatrix()
public void updateDistanceMatrix()
public java.util.List<MultipleAlignment> getMultipleAlignments()
MultipleAlignmentEnsemble
getMultipleAlignments
in interface MultipleAlignmentEnsemble
#setMultipleAlignments()
,
#getOptimalMultipleAlignment()
public void setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments)
MultipleAlignmentEnsemble
setMultipleAlignments
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.getMultipleAlignments()
,
#getOptimalMultipleAlignment()
public void addMultipleAlignment(MultipleAlignment alignment)
MultipleAlignmentEnsemble
addMultipleAlignment
in interface MultipleAlignmentEnsemble
public int size()
MultipleAlignmentEnsemble
size
in interface MultipleAlignmentEnsemble
MultipleAlignmentEnsemble.getStructureNames()
,
MultipleAlignmentEnsemble.getAtomArrays()
public void clear()
AbstractScoresCache
clear
in interface MultipleAlignmentEnsemble
clear
in class AbstractScoresCache