All Superinterfaces:

ScoresCache

All Known Implementing Classes:

MultipleAlignmentEnsembleImpl
```
public interface MultipleAlignmentEnsemble
extends ScoresCache
```
A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).
This class is the top level of the hierarchy and allows the storage of a set of alignment alternatives created by a multiple structure alignment algorithm, so that only one object is returned with more than one alignment option.

Since:

4.1.0

Author:

Aleix Lafita, Spencer Bliven

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`addMultipleAlignment(MultipleAlignment alignment)`	Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
`void`	`clear()`	Clear scores and other properties which depend on the specific alignment.
`MultipleAlignmentEnsemble`	`clone()`	Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
`String`	`getAlgorithmName()`	Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
`List<Atom[]>`	`getAtomArrays()`	Get an array of representative atoms for each structure (CA atoms for proteins).
`Long`	`getCalculationTime()`	Returns the running time of the structure alignment calculation, in milliseconds.
`List<Matrix>`	`getDistanceMatrix()`	Returns the List containing the interatomic distance Matrix of each structure.
`Long`	`getIoTime()`	Returns the io time for this object, in milliseconds.
`MultipleAlignment`	`getMultipleAlignment(int index)`	Returns the MultipleAlignments at the specified index in the ensemble.
`List<MultipleAlignment>`	`getMultipleAlignments()`	Returns the List of MultipleAlignments in the ensemble.
`List<StructureIdentifier>`	`getStructureIdentifiers()`	Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
`String`	`getVersion()`	Returns the version of the algorithm used to generate the MultipleAlignment objects.
`void`	`setAlgorithmName(String algorithmName)`	Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
`void`	`setAtomArrays(List<Atom[]> atomArrays)`	Sets the List of Atom arrays.
`void`	`setCalculationTime(Long millis)`	Set the running time spent to calculate this alignment.
`void`	`setIoTime(Long millis)`	Set the IO time to load this object
`void`	`setMultipleAlignments(List<MultipleAlignment> alignments)`	Set the List of MultipleAlignments in the ensemble.
`void`	`setStructureIdentifiers(List<StructureIdentifier> structureIdentifiers)`	Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
`void`	`setVersion(String version)`	Sets the version of the algorithm used to generate the MultipleAlignment objects.
`int`	`size()`	Returns the number of aligned structures in the MultipleAlignments.

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache
getScore, getScores, putScore

- Method Detail
  - clone
```
MultipleAlignmentEnsemble clone()
```
    Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
    
    Returns:
    
    MultipleAlignmentEnsemble identical copy of this object.
  - getAlgorithmName
```
String getAlgorithmName()
```
    Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
    
    Returns:
    
    String name of the algorithm.
    
    See Also:
    
    setAlgorithmName(String)
  - setAlgorithmName
```
void setAlgorithmName(String algorithmName)
```
    Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
    
    Parameters:
    
    algorithmName - name of the algorithm.
    
    See Also:
    
    getAlgorithmName()
  - getVersion
```
String getVersion()
```
    Returns the version of the algorithm used to generate the MultipleAlignment objects.
    
    Returns:
    
    String version of the algorithm.
    
    See Also:
    
    setVersion(String)
  - setVersion
```
void setVersion(String version)
```
    Sets the version of the algorithm used to generate the MultipleAlignment objects.
    
    Parameters:
    
    version - the version of the algorithm.
    
    See Also:
    
    getVersion()
  - getStructureIdentifiers
```
List<StructureIdentifier> getStructureIdentifiers()
```
    Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
    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).
    
    Returns:
    
    List of String names of the structures
    
    See Also:
    
    setStructureIdentifiers(List), getAtomArrays()
  - setStructureIdentifiers
```
void setStructureIdentifiers(List<StructureIdentifier> structureIdentifiers)
```
    Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
    The names are structure identifiers of the structures.
    
    Parameters:
    
    structureIdentifiers - names of the structures, structure identifiers
    
    See Also:
    
    getStructureIdentifiers(), setAtomArrays(List)
  - getAtomArrays
```
List<Atom[]> getAtomArrays()
```
    Get an array of representative atoms for each structure (CA atoms for proteins).
    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 setAtomArrays(List), attempts to load representative atoms based on getStructureIdentifiers(). If it fails to load the Atoms it gives a NullPointerException before returning null.
    
    Returns:
    
    List of Atom[].
    
    See Also:
    
    setAtomArrays(List)
  - setAtomArrays
```
void setAtomArrays(List<Atom[]> atomArrays)
```
    Sets the List of Atom arrays. Every structure has an Atom array associated. Note that this should be called in conjunction with setStructureIdentifiers(List).
    Setting the atom arrays to null will cause them to be automatically regenerated based on getStructureIdentifiers() during the next call to getAtomArrays().
    
    Parameters:
    
    atomArrays - the List of representative (C-alpha) atom arrays
    
    See Also:
    
    getAtomArrays(), setStructureIdentifiers(List)
  - getDistanceMatrix
```
List<Matrix> getDistanceMatrix()
```
    Returns the List containing the interatomic distance Matrix of each structure.
    
    Returns:
    
    List of Matrix interatomic distance matrices.
    
    See Also:
    
    #updateDistanceMatrix()
  - getMultipleAlignments
```
List<MultipleAlignment> getMultipleAlignments()
```
    Returns the List of MultipleAlignments in the ensemble.
    
    Returns:
    
    List of MultipleAlignment in the ensemble.
    
    See Also:
    
    #setMultipleAlignments()
  - getMultipleAlignment
```
MultipleAlignment getMultipleAlignment(int index)
```
    Returns the MultipleAlignments at the specified index in the ensemble. Throws an exception equivalently to accessing an index of a List
    
    Returns:
    
    MultipleAlignment at the index in the ensemble.
    
    See Also:
    
    #setMultipleAlignments()
  - setMultipleAlignments
```
void setMultipleAlignments(List<MultipleAlignment> alignments)
```
    Set the List of MultipleAlignments in the ensemble.
    
    Parameters:
    
    alignments - List of MultipleAlignments that are part of the ensemble.
    
    See Also:
    
    addMultipleAlignment(MultipleAlignment)
  - addMultipleAlignment
```
void addMultipleAlignment(MultipleAlignment alignment)
```
    Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
    
    Parameters:
    
    alignment -
  - size
```
int size()
```
    Returns the number of aligned structures in the MultipleAlignments.
    
    Returns:
    
    int number of aligned structures.
    
    See Also:
    
    getStructureIdentifiers(), getAtomArrays()
  - getIoTime
```
Long getIoTime()
```
    Returns the io time for this object, in milliseconds.
    
    Returns:
    
    long creation time, or null if unset
  - setIoTime
```
void setIoTime(Long millis)
```
    Set the IO time to load this object
    
    Parameters:
    
    millis -
  - getCalculationTime
```
Long getCalculationTime()
```
    Returns the running time of the structure alignment calculation, in milliseconds.
    
    Returns:
    
    long running time of the calculation, or null if unset
    
    See Also:
    
    getIoTime()
  - setCalculationTime
```
void setCalculationTime(Long millis)
```
    Set the running time spent to calculate this alignment.
    
    Parameters:
    
    millis -
  - clear
```
void clear()
```
    Clear scores and other properties which depend on the specific alignment. This frees memory and ensures consistency of the cached variables.
    Recursively clears the member MultipleAlignments.

Interface MultipleAlignmentEnsemble

Method Summary

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache

Method Detail

clone

getAlgorithmName

setAlgorithmName

getVersion

setVersion

getStructureIdentifiers

setStructureIdentifiers

getAtomArrays

setAtomArrays

getDistanceMatrix

getMultipleAlignments

getMultipleAlignment

setMultipleAlignments

addMultipleAlignment

size

getIoTime

setIoTime

getCalculationTime

setCalculationTime

clear