Uses of Interface
org.biojava.nbio.structure.align.multiple.MultipleAlignment

Packages that use MultipleAlignment

Package	Description
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.cemc
org.biojava.nbio.structure.align.multiple

Uses of MultipleAlignment in org.biojava.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return MultipleAlignment

Modifier and Type	Method and Description
MultipleAlignment	MultipleStructureAligner.align(List<Atom[]> atomArrays) Run an alignment while specifying the atoms to be aligned.
MultipleAlignment	MultipleStructureAligner.align(List<Atom[]> atomArrays, Object params) Run an alignment and also send a bean containing the parameters.

Uses of MultipleAlignment in org.biojava.nbio.structure.align.cemc

Methods in org.biojava.nbio.structure.align.cemc that return MultipleAlignment

Modifier and Type	Method and Description
MultipleAlignment	CeMcMain.align(List<Atom[]> atomArrays)
MultipleAlignment	CeMcMain.align(List<Atom[]> atomArrays, Object params)
MultipleAlignment	CeMcOptimizer.call()

Constructors in org.biojava.nbio.structure.align.cemc with parameters of type MultipleAlignment

Constructor and Description
CeMcOptimizer(MultipleAlignment seedAln, long randomSeed, int reference) Constructor.

Uses of MultipleAlignment in org.biojava.nbio.structure.align.multiple

Classes in org.biojava.nbio.structure.align.multiple that implement MultipleAlignment

Modifier and Type	Class and Description
class	MultipleAlignmentImpl A general implementation of a MultipleAlignment.

Methods in org.biojava.nbio.structure.align.multiple that return MultipleAlignment

Modifier and Type	Method and Description
MultipleAlignment	MultipleAlignment.clone() Creates and returns an identical copy of this alignment, including a deep clone of all constituent blocks sets.
MultipleAlignment	BlockSetImpl.getMultipleAlignment()
MultipleAlignment	BlockSet.getMultipleAlignment() Returns the parent MultipleAlignment of the BlockSet.

Methods in org.biojava.nbio.structure.align.multiple that return types with arguments of type MultipleAlignment

Modifier and Type	Method and Description
List<MultipleAlignment>	MultipleAlignmentEnsembleImpl.getMultipleAlignments()
List<MultipleAlignment>	MultipleAlignmentEnsemble.getMultipleAlignments() Returns the List of MultipleAlignments in the MultipleAlignmentEnsemble object.

Methods in org.biojava.nbio.structure.align.multiple with parameters of type MultipleAlignment

Modifier and Type	Method and Description
void	MultipleAlignmentEnsembleImpl.addMultipleAlignment(MultipleAlignment alignment)
void	MultipleAlignmentEnsemble.addMultipleAlignment(MultipleAlignment alignment) Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
static void	MultipleAlignmentScorer.calculateScores(MultipleAlignment alignment) Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
static Atom	MultipleAlignmentTools.getAtomForSequencePosition(MultipleAlignment multAln, List<Integer> mapSeqToStruct, int structure, int sequencePos) Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
static Matrix	MultipleAlignmentTools.getAverageResidueDistances(MultipleAlignment alignment) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static double	MultipleAlignmentScorer.getAvgTMScore(MultipleAlignment alignment) Calculates the average TMScore all the possible pairwise structure comparisons of the given MultipleAlignment.
static int	MultipleAlignmentTools.getBlockForSequencePosition(MultipleAlignment multAln, List<Integer> mapSeqToStruct, int sequencePos) Returns the block number of a specified position in the sequence alignment.
static List<String>	MultipleAlignmentTools.getBlockSequenceAlignment(MultipleAlignment alignment) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static List<String>	MultipleAlignmentTools.getBlockSequenceAlignment(MultipleAlignment alignment, List<Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static double	MultipleAlignmentScorer.getCEMCScore(MultipleAlignment alignment) Calculates the CEMC score, specific for the MultipleAlignment algorithm.
static double	MultipleAlignmentScorer.getRefRMSD(MultipleAlignment alignment, int reference)
static double	MultipleAlignmentScorer.getRefTMScore(MultipleAlignment alignment, int reference) Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
static double	MultipleAlignmentScorer.getRMSD(MultipleAlignment alignment) Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.
static List<String>	MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment alignment) Calculate the sequence alignment Strings for the whole alignment.
static List<String>	MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment alignment, List<Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the whole alignment.
void	BlockSetImpl.setMultipleAlignment(MultipleAlignment parent)
void	BlockSet.setMultipleAlignment(MultipleAlignment parent) Set the back-reference to its parent MultipleAlignment.
void	MultipleSuperimposer.superimpose(MultipleAlignment alignment) Superimpose all structures from a MultipleAlignment.
void	ReferenceSuperimposer.superimpose(MultipleAlignment alignment) Superimpose all structures in a MultipleAlignment to the reference structure.
static String	MultipleAlignmentWriter.toAlignedResidues(MultipleAlignment multAln) Converts the alignment to its simplest form: a list of groups of aligned residues.
static String	MultipleAlignmentWriter.toFASTA(MultipleAlignment alignment) Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.
static String	MultipleAlignmentWriter.toFatCat(MultipleAlignment alignment) Converts the MultipleAlignment into a FatCat String format.
static String	MultipleAlignmentWriter.toTransformMatrices(MultipleAlignment alignment) Converts the transformation Matrices of the alignment into a String output.
static List<Atom[]>	MultipleAlignmentScorer.transformAtoms(MultipleAlignment alignment) Transforms atoms according to the superposition stored in the alignment.

Method parameters in org.biojava.nbio.structure.align.multiple with type arguments of type MultipleAlignment

Modifier and Type	Method and Description
void	MultipleAlignmentEnsembleImpl.setMultipleAlignments(List<MultipleAlignment> multipleAlignments)
void	MultipleAlignmentEnsemble.setMultipleAlignments(List<MultipleAlignment> multipleAlignments) Set the List of MultipleAlignments in the MultipleAlignmentEnsemble object.

Constructors in org.biojava.nbio.structure.align.multiple with parameters of type MultipleAlignment

Constructor and Description
BlockSetImpl(MultipleAlignment multipleAlignment) Constructor.