Uses of Interface
org.biojava.nbio.structure.align.multiple.MultipleAlignment
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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 -
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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 theMultipleAlignmentJmol
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 theMultipleAlignment
.static void
MultipleAlignmentJmolDisplay. showMultipleAligmentPanel(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 Constructor Description MySaveFileListener(AFPChain afpChain, MultipleAlignment msa)
Constructor to avoid checking which of the two is null before instantiating this class.MySaveFileListener(MultipleAlignment msa)
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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 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 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 aMultipleAlignment
.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 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 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 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 aMultipleAlignment
.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.htmlstatic 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 theMultipleAlignment
into a multiple sequence alignment String in FASTA format.static String
MultipleAlignmentWriter. toFatCat(MultipleAlignment alignment)
Converts theMultipleAlignment
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 that return MultipleAlignment Modifier and Type Method Description static MultipleAlignment
MultipleAlignmentXMLParser. parseMultipleAlignment(Node root, MultipleAlignmentEnsemble ensemble)
Methods in org.biojava.nbio.structure.align.xml with parameters of type MultipleAlignment Modifier and Type Method Description static BlockSet
MultipleAlignmentXMLParser. parseBlockSet(Node root, MultipleAlignment msa)
static void
MultipleAlignmentXMLConverter. printXMLalignment(PrettyXMLWriter xml, MultipleAlignment msa)
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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)
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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.
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