Interface MultipleAlignmentEnsemble

Method Details

• 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.