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.gui
org.biojava.nbio.structure.align.gui.aligpanel
org.biojava.nbio.structure.align.gui.jmol	Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.quaternary
org.biojava.nbio.structure.align.xml	Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

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

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

Modifier and Type	Method	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.gui

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

Modifier and Type	Method	Description
static MultipleAlignmentJmol	MultipleAlignmentJmolDisplay.display(MultipleAlignment multAln)	Display a MultipleAlignment with a JmolPanel.
static JMenuBar	MenuCreator.getAlignmentPanelMenu(JFrame frame, ActionListener actionListener, AFPChain afpChain, MultipleAlignment msa)	Create the menu for the Alignment Panel representation of Structural Alignments.
static JMenuBar	MenuCreator.getAlignmentTextMenu(JFrame frame, ActionListener actionListener, AFPChain afpChain, MultipleAlignment msa)	Create the menu for the Text representations of Structural Alignments.
static List<String>	MultipleAlignmentJmolDisplay.getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca)	Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).
static JMenuItem	MenuCreator.getSaveAlignmentMenuItem(AFPChain afpChain, MultipleAlignment msa)
static JMenuBar	MenuCreator.initJmolMenu(JFrame frame, AbstractAlignmentJmol parent, AFPChain afpChain, MultipleAlignment msa)	Provide a JMenuBar that can be added to a JFrame containing a JmolPanel.
static void	MultipleAlignmentJmolDisplay.showAlignmentImage(MultipleAlignment multAln, String result)	Creates a new Frame with the String output representation of the MultipleAlignment.
static void	MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Deprecated. Replace with
static void	MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Creates a new Frame with the MultipleAlignment Sequence Panel.

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

Modifier	Constructor	Description
	MySaveFileListener(AFPChain afpChain, MultipleAlignment msa)	Constructor to avoid checking which of the two is null before instantiating this class.
	MySaveFileListener(MultipleAlignment msa)

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

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

Modifier and Type	Method	Description
MultipleAlignment	MultipleAligPanel.getMultipleAlignment()

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

Modifier	Constructor	Description
	MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm)	Constructor using a MultipleAlignment.

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

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

Modifier and Type	Method	Description
MultipleAlignment	MultipleAlignmentJmol.getMultipleAlignment()

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

Modifier and Type	Method	Description
static String	MultipleAlignmentJmol.getJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, org.jcolorbrewer.ColorBrewer colorPalette, boolean colorByBlocks)	Generate a Jmol command String that colors the aligned residues of every structure.
static String	MultipleAlignmentJmol.getMultiBlockJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, org.jcolorbrewer.ColorBrewer colorPalette, boolean colorByBlocks)	Colors every Block of the structures with a different color, following the palette.

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

Modifier	Constructor	Description
	MultipleAlignmentJmol(MultipleAlignment msa, List<Atom[]> rotatedAtoms)	The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.

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	Description
class	MultipleAlignmentImpl	A general implementation of a MultipleAlignment.

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

Modifier and Type	Method	Description
MultipleAlignment	MultipleAlignment.clone()	Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
MultipleAlignment	BlockSet.getMultipleAlignment()	Returns the parent MultipleAlignment of the BlockSet.
MultipleAlignment	BlockSetImpl.getMultipleAlignment()
MultipleAlignment	MultipleAlignmentEnsemble.getMultipleAlignment(int index)	Returns the MultipleAlignments at the specified index in the ensemble.
MultipleAlignment	MultipleAlignmentEnsembleImpl.getMultipleAlignment(int index)

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

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

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

Modifier and Type	Method	Description
void	MultipleAlignmentEnsemble.addMultipleAlignment(MultipleAlignment alignment)	Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
void	MultipleAlignmentEnsembleImpl.addMultipleAlignment(MultipleAlignment alignment)
void	BlockSet.setMultipleAlignment(MultipleAlignment parent)	Set the back-reference to its parent MultipleAlignment.
void	BlockSetImpl.setMultipleAlignment(MultipleAlignment parent)

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

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

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

Modifier	Constructor	Description
	BlockSetImpl(MultipleAlignment alignment)	Constructor.

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

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

Modifier and Type	Method	Description
MultipleAlignment	MultipleMcMain.align(List<Atom[]> atomArrays)
MultipleAlignment	MultipleMcMain.align(List<Atom[]> atomArrays, Object parameters)
MultipleAlignment	MultipleMcOptimizer.call()
MultipleAlignment	MultipleMcOptimizer.optimize()	Optimization method based in a Monte-Carlo approach.

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

Modifier	Constructor	Description
	MultipleMcOptimizer(MultipleAlignment seedAln, MultipleMcParameters params, int reference)	Constructor.

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

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

Modifier and Type	Method	Description
static void	MultipleAlignmentScorer.calculateScores(MultipleAlignment alignment)	Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
static Atom	MultipleAlignmentTools.getAtomForSequencePosition(MultipleAlignment msa, List<Integer> mapSeqToStruct, int str, int sequencePos)	Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
static Matrix	MultipleAlignmentTools.getAverageResidueDistances(MultipleAlignment msa)	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 of all the possible pairwise structure comparisons of the given alignment.
static int	MultipleAlignmentTools.getBlockForSequencePosition(MultipleAlignment multAln, List<Integer> mapSeqToStruct, int sequencePos)	Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.
static List<String>	MultipleAlignmentTools.getBlockSequenceAlignment(MultipleAlignment ma)	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 List<List<Integer>>	MultipleAlignmentTools.getEquivalentResidues(MultipleAlignment msa, boolean coreOnly)	Convert an MSA into a matrix of equivalent residues.
static org.forester.phylogeny.Phylogeny	MultipleAlignmentTools.getHSDMTree(MultipleAlignment msta)	Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.
static org.forester.phylogeny.Phylogeny	MultipleAlignmentTools.getKimuraTree(MultipleAlignment msta)	Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.
static double	MultipleAlignmentScorer.getMCScore(MultipleAlignment alignment, double gapOpen, double gapExtension, double dCutoff)	Calculates the MC score, specific for the MultipleAlignment algorithm.
static double	MultipleAlignmentScorer.getRefRMSD(MultipleAlignment alignment, int ref)	/** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
static double	MultipleAlignmentScorer.getRefTMScore(MultipleAlignment alignment, int ref)	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 Matrix	MultipleAlignmentTools.getRMSDMatrix(MultipleAlignment msa)	Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.
static List<Atom[]>	MultipleAlignmentDisplay.getRotatedAtoms(MultipleAlignment multAln)	New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the superposition information in the Multiple Alignment.
static List<String>	MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment msa)	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.
static org.forester.phylogeny.Phylogeny	MultipleAlignmentTools.getStructuralTree(MultipleAlignment msta)	Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.
void	CoreSuperimposer.superimpose(MultipleAlignment alignment)
void	MultipleSuperimposer.superimpose(MultipleAlignment alignment)	Superimpose all structures from a MultipleAlignment.
void	ReferenceSuperimposer.superimpose(MultipleAlignment alignment)
static String	MultipleAlignmentWriter.to3DFormat(MultipleAlignment alignment, int queryIndex, int templateIndex)	Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html
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 Structure	MultipleAlignmentTools.toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms)
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound>	MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta)	Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.
static String	MultipleAlignmentWriter.toTransformMatrices(MultipleAlignment alignment)	Converts the transformation Matrices of the alignment into a String output.
static List<Atom[]>	MultipleAlignmentTools.transformAtoms(MultipleAlignment alignment)	Transforms atoms according to the superposition stored in the alignment.

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

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

Modifier and Type	Method	Description
MultipleAlignment	QsAlignResult.getAlignment()	The alignment that specifies the residue equivalencies of the equivalent Subunits.

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

Modifier and Type	Method	Description
void	QsAlignResult.setAlignment(MultipleAlignment alignment)	The alignment that specifies the residue equivalencies of the equivalent Subunits.

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

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

Modifier and Type	Method	Description
static void	MultipleAlignmentXMLConverter.printXMLalignment(PrettyXMLWriter xml, MultipleAlignment msa)

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

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

Modifier and Type	Method	Description
MultipleAlignment	SubunitCluster.getMultipleAlignment()	The multiple alignment is calculated from the equivalent residues in the SubunitCluster.

Uses of MultipleAlignment in org.biojava.nbio.structure.symmetry.internal

Methods in org.biojava.nbio.structure.symmetry.internal that return MultipleAlignment

Modifier and Type	Method	Description
MultipleAlignment	CeSymmResult.getMultipleAlignment()
MultipleAlignment	SymmOptimizer.optimize()	Optimization method based in a Monte-Carlo approach.
MultipleAlignment	GraphComponentRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
MultipleAlignment	SequenceFunctionRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
MultipleAlignment	SymmetryRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)	Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

Methods in org.biojava.nbio.structure.symmetry.internal with parameters of type MultipleAlignment

Modifier and Type	Method	Description
void	CeSymmResult.setMultipleAlignment(MultipleAlignment multipleAlignment)

Uses of MultipleAlignment in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils that return MultipleAlignment

Modifier and Type	Method	Description
static MultipleAlignment	SymmetryTools.fromAFP(AFPChain symm, Atom[] atoms)	Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
static MultipleAlignment	SymmetryTools.toFullAlignment(CeSymmResult symm)	Method that converts a repeats symmetric alignment into an alignment of whole structures.
static MultipleAlignment	SymmetryTools.toRepeatsAlignment(CeSymmResult result)	Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.

Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type MultipleAlignment

Modifier and Type	Method	Description
static void	SymmetryTools.updateSymmetryScores(MultipleAlignment symm)	Update the scores (TM-score and RMSD) of a symmetry multiple alignment.
static void	SymmetryTools.updateSymmetryTransformation(SymmetryAxes axes, MultipleAlignment msa)	Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.