org.biojava.nbio.structure.align.multiple

Interface MultipleAlignmentEnsemble

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.

Author:

Aleix Lafita, Spencer Bliven

Method Summary

Methods

Modifier and Type	Method and 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.
java.lang.String	getAlgorithmName() Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
int	getAlignmentNum() Return the number of alternative alignments stored in the Ensemble.
java.util.List<Atom[]>	getAtomArrays() Get an array of representative atoms for each structure (CA atoms for proteins).
java.lang.Long	getCalculationTime() public Returns the running time of the structure alignment calculation, in milliseconds.
java.util.List<Matrix>	getDistanceMatrix() Returns the List containing the interatomic distance Matrix of each structure.
java.lang.Long	getIoTime() Returns the io time for this object, in milliseconds.
java.util.List<MultipleAlignment>	getMultipleAlignments() Returns the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
java.util.List<java.lang.String>	getStructureNames() Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
java.lang.String	getVersion() Returns the version of the algorithm used to generate the MultipleAlignment objects.
void	setAlgorithmName(java.lang.String algorithmName) Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
void	setAtomArrays(java.util.List<Atom[]> atomArrays) Sets the List of Atom arrays.
void	setCalculationTime(java.lang.Long millis) Set the time needed to calculate this alignment
void	setIoTime(java.lang.Long millis) Set the IO time to load this object
void	setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments) Set the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
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.).
void	setVersion(java.lang.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

java.lang.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(java.lang.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

java.lang.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(java.lang.String version)

Sets the version of the algorithm used to generate the MultipleAlignment objects.

Parameters:

version - the version of the algorithm.

See Also:

getVersion()

getStructureNames

java.util.List<java.lang.String> getStructureNames()

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:

setStructureNames(List), getAtomArrays()

setStructureNames

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.).

The names are structure identifiers of the structures.

Parameters:

structureNames - names of the structures, structure identifiers

See Also:

getStructureNames(), setAtomArrays(List)

getAtomArrays

java.util.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 getStructureNames(). 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(java.util.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 setStructureNames(List)

Setting the atom arrays to null will cause them to be automatically regenerated based on getStructureNames() during the next call to getAtomArrays()

Parameters:

atomArrays - the List of representative (C-alpha) atom arrays

See Also:

getAtomArrays(), setStructureNames(List)

getAlignmentNum

int getAlignmentNum()

Return the number of alternative alignments stored in the Ensemble.

Returns:

int number of alternative alignments.

See Also:

size()

getDistanceMatrix

java.util.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

java.util.List<MultipleAlignment> getMultipleAlignments()

Returns the List of MultipleAlignments in the MultipleAlignmentEnsemble object.

Returns:

List of MultipleAlignment in the MultipleAlignmentEnsemble.

See Also:

#setMultipleAlignments(), #getOptimalMultipleAlignment()

setMultipleAlignments

void setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments)

Set the List of MultipleAlignments in the MultipleAlignmentEnsemble object.

Parameters:

List - of MultipleAlignments that are part of the ensemble.

See Also:

getMultipleAlignments(), #getOptimalMultipleAlignment()

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:

getStructureNames(), getAtomArrays()

getIoTime

java.lang.Long getIoTime()

Returns the io time for this object, in milliseconds.

Returns:

long creation time, or null if unset

setIoTime

void setIoTime(java.lang.Long millis)

Set the IO time to load this object

Parameters:

millis -

getCalculationTime

java.lang.Long getCalculationTime()

public 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()L

setCalculationTime

void setCalculationTime(java.lang.Long millis)

Set the time needed to calculate this alignment

Parameters:

millis -

clear

void clear()

Clear scores and other properties which depend on the specific alignment.

This can free memory and ensures consistency for cached variables.