Index (biojava-alignment 6.0.3 API)

A C D E F G H I K L M N O P Q R S T U V W X
All Classes All Packages

A

AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner which builds a score matrix during computation.
AbstractMatrixAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Before running an alignment, data must be sent in via calls to AbstractMatrixAligner.setGapPenalty(GapPenalty) and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractMatrixAligner(GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Prepares for an alignment.
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Sequences.
AbstractPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AbstractPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, boolean) - Constructor for class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Prepares for a pairwise sequence alignment.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements common code for an Aligner for a pair of Profiles.
AbstractProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
AbstractProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment.
AbstractScorer - Class in org.biojava.nbio.alignment.template: Implements common code for algorithms which compute a score.
AbstractScorer() - Constructor for class org.biojava.nbio.alignment.template.AbstractScorer
addActiveSite(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addAnchor(int, int) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Adds an additional anchor to the set of anchored compounds
addAnchors(AlignerHelper.Cut[], int[], boolean, int[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
addASPFamPredicted(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addASSwissProt(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addDBReference(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFBuildMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFFalseDiscoveryRate(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFNewHampshire(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGFTreeID(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addGSAccessionNumber(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSdbReference(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSDescription(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSLook(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSOrganismClassification(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addGSOrganismSpecies(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addIntron(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addLigandBinding(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addPosteriorProbability(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addSecondaryStructure(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addSurfaceAccessibility(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
addToGFComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
addToRefAuthor(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
addToRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
addTransMembrane(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
AFFINE - org.biojava.nbio.alignment.template.GapPenalty.Type
align() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Performs alignment
Aligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes an alignment Profile from a list of Sequences.
AlignerHelper - Class in org.biojava.nbio.alignment.routines: Static utility to construct alignment routines from a common library of methods.
AlignerHelper() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper
AlignerHelper.Anchor - Class in org.biojava.nbio.alignment.routines: Compounds in query and target sequences that must align
AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines
AlignerHelper.Cut - Class in org.biojava.nbio.alignment.routines: Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Last - Enum in org.biojava.nbio.alignment.routines: Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
AlignerHelper.Subproblem - Class in org.biojava.nbio.alignment.routines: Alignment subproblem.
Alignments - Class in org.biojava.nbio.alignment: Static utility to easily run alignment routines.
Alignments.PairInProfileScorerType - Enum in org.biojava.nbio.alignment: List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType - Enum in org.biojava.nbio.alignment: List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType - Enum in org.biojava.nbio.alignment: List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType - Enum in org.biojava.nbio.alignment: List of implemented profile-profile alignment routines.
Alignments.RefinerType - Enum in org.biojava.nbio.alignment: List of implemented profile refinement routines.
Anchor(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines: This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
AnchoredPairwiseSequenceAligner() - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S, S, GapPenalty, SubstitutionMatrix<C>, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Prepares for a pairwise global sequence alignment.
anchors - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
appendToSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
AV - org.biojava.nbio.phylo.TreeConstructorType: What does this stand for? (Aleix: Nov 2015)

C

call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a PairwiseSequenceAligner.
CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner: Creates a pairwise sequence alignment task for simplified parallel execution.
CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a PairwiseSequenceScorer.
CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer: Creates a pairwise sequence scoring task for simplified parallel execution.
CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template: Implements a concurrency wrapper for a ProfileProfileAligner.
CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner: Creates a profile-profile alignment task for simplified parallel execution.
children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Helper function to clone a forester symmetrical DistanceMatrix.
compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
Comparison - Class in org.biojava.nbio.phylo: This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
CONSTANT - org.biojava.nbio.alignment.template.GapPenalty.Type
convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a BioJava MultipleSequenceAlignment to a forester Msa.
CookbookMSA - Class in demo
CookbookMSA() - Constructor for class demo.CookbookMSA
Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

D

DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
DELETION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
demo - package demo
DemoAlignProteins - Class in demo
DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
DemoDistanceTree - Class in demo: This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
DemoLoadSubstMax - Class in demo
DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax
dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
DISTANCE - org.biojava.nbio.phylo.TreeType: Distance Tree
DistanceMatrixCalculator - Class in org.biojava.nbio.phylo: The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
DistanceTreeEvaluator - Class in org.biojava.nbio.phylo: Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
DYNAMIC - org.biojava.nbio.alignment.template.GapPenalty.Type

E

evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator: Evaluate the goodness of fit of a given tree to the original distance matrix.
EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

F

ForesterWrapper - Class in org.biojava.nbio.phylo: This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer: Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair.
FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer: Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer: Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer: Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer: Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer: Creates a fractional similarity scorer for an aligned pair of sequences.

G

gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
GapPenalty - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type - Enum in org.biojava.nbio.alignment.template: Defines the possible types of gap penalties.
getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAlignmentMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAllowsChildren() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getAllPairsAlignments(List<S>, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence alignment for all Sequence pairs in the given List.
getAllPairsScorers(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
getAllPairsScores() - Method in class org.biojava.nbio.alignment.GuideTree: Returns a sequence pair score for all Sequence pairs in the given List.
getAllPairsScores(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence pair score for all Sequence pairs in the given List.
getAnchors() - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Returns the list of anchors.
getAuthors() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure: used to retrieve sequences from the structure
getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: Because some database files have incorrectly small letters (e.g.
getBioSequences(boolean, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
getBuildMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getChild1() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChild1() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the first child node of this node.
getChild2() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChild2() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the second child node of this node.
getChildAt(int) - Method in class org.biojava.nbio.alignment.GuideTree.Node
getChildCount() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getClan() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getComputationTime() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getComputationTime() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getComputationTime() - Method in interface org.biojava.nbio.alignment.template.Aligner: Returns the computation time needed for an alignment computed in nanoseconds.
getConsAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getCuts(int, AlignerHelper.Subproblem, int[], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
getCutsPerSection() - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher: Returns the number of cuts added to each section during each pass.
getDatabase() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
getDbComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDbReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDefinition() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getDistance() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getDistance() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a distance between 0.0 and 1.0.
getDistance(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getDistance(double) - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a distance between 0.0 and scale.
getDistanceMatrix() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the distance matrix used to construct this guide tree.
getDistanceMatrix() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer: Returns the distance matrix used in clustering.
getDistanceToParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getDistanceToParent() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the difference in height of this node and it's parent node.
getEmbTrees() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getExtensionPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty: Returns the negative of the extension penalty passed to the constructor.
getExtensionPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns penalty given when an already open gap elongates by a single element
getFalseDiscoveryRate() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getFileAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getFormat() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getGapPenalty() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns the gap penalties.
getGatheringThreshs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getIdentification() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node
getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getMaxScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getMaxScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getMaxScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns maximum possible score.
getMembership() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getMinScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getMinScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getMinScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getMinScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getMinScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getMinScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns minimum possible score.
getMultipleSequenceAlignment(List<S>, Object...) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a multiple sequence alignment for the given List of Sequences.
getName() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getName() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the name of this node.
getNewickString(Phylogeny, boolean) - Static method in class org.biojava.nbio.phylo.ForesterWrapper: Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.
getNoiseCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getNumSequences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getOpenPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty: Returns the negative of the opening penalty passed to the constructor.
getOpenPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns penalty given when a deletion or insertion gap first opens
getPair() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getPair() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getPair() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceAligner: Returns sequence alignment pair.
getPair() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileAligner: Returns alignment profile pair.
getPairInProfileScorer() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getPairInProfileScorer() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner: Returns class type of pairwise scoring subroutine.
getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which constructs a pairwise sequence aligner.
getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method which computes a sequence alignment for the given Sequence pair.
getParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getPfamAccession() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getPreviousIDs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getProfile() - Method in class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
getProfile() - Method in class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
getProfile() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getProfile() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getProfile() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getProfile() - Method in interface org.biojava.nbio.alignment.template.Aligner: Returns the alignment Profile produced by this alignment algorithm.
getProfile() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the profile stored at this node.
getProfile() - Method in interface org.biojava.nbio.alignment.template.PairInProfileScorer: Returns the Profile from which the aligned pair originated.
getProfileFuture() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getProfileFuture() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the profile future stored at this node, but does not force the calculation, yet.
getProfileProfileAligner() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.PartitionRefiner: Returns class type of profile-profile alignment subroutine.
getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner: Returns class type of profile-profile alignment subroutine.
getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
getQuery() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getQuery() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getQuery() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getQuery() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer: Returns the first sequence of the pair.
getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the first profile of the pair.
getQueryEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
getQueryStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getReference() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getRefLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefMedline() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
getRoot() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the root GuideTree.Node which corresponds to the full multiple sequence alignment.
getRoot() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer: Returns the root node of the tree resulting from this clustering algorithm.
getScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
getScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScore() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score resulting from algorithm.
getScoreMatrix() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the similarity matrix used to construct this guide tree.
getScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrix() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner: Returns the entire score matrix built during alignment.
getScoreMatrixAsString() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner: Returns a depiction of the score matrix as a String.
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getSearchMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSequences() - Method in class org.biojava.nbio.alignment.GuideTree: Returns the Sequences which make up the leaves of this tree.
getSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
getSimilarity() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getSimilarity() - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a similarity between 0.0 and 1.0.
getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer: Returns score as a similarity between 0.0 and scale.
getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSubproblems(List<AlignerHelper.Anchor>, int, int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem: Convert a list of anchors into a subproblem list.
getSubstitutionMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns the substitution matrix.
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getSubstitutionScoreVector(int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns score for the alignment of the query column to all target columns
getSubstitutionScoreVector(int, AlignerHelper.Subproblem) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns score for the alignment of the query column to all target columns
getTarget() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
getTarget() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
getTarget() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getTarget() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer: Returns the second sequence of the pair.
getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the second profile of the pair.
getTargetEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getTargetIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
getTargetIndex(int) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
getTargetStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
getTrustedCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getType() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
getType() - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Returns GapPenalty.Type stored.
getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
GLOBAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
GLOBAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
GLOBAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
GLOBAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
GLOBAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
GLOBAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
GuanUberbacher<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines: Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
GuanUberbacher() - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Prepares for a pairwise global sequence alignment.
GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher: Prepares for a pairwise global sequence alignment.
GuideTree<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for a guide tree used during progressive multiple sequence alignment.
GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava.nbio.alignment.GuideTree: Creates a guide tree for use during progressive multiple sequence alignment.
GuideTree.Node - Class in org.biojava.nbio.alignment: Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
GuideTreeNode<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.

H

HierarchicalClusterer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a clustering algorithm that converts a distance matrix into a tree.
HOMSTRAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

I

IDENTITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
INFINITY - Static variable in class org.biojava.nbio.alignment.io.StockholmFileParser: indicates reading as much as possible, without limits
INSERTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
INTERPRO - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
isGap(char) - Static method in class org.biojava.nbio.phylo.Comparison: Method that determines if a character means a gap in the alignment.
isLeaf() - Method in class org.biojava.nbio.alignment.GuideTree.Node
isLocal() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns whether alignment finds a region of similarity rather than aligning every compound.
isPFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
isReady() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
isRFam() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
isStartAnchored() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem: Indicates whether the start query and start target index compounds are anchored to each other
isStoringScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
iterator() - Method in class org.biojava.nbio.alignment.GuideTree: Returns a post-order Iterator that traverses the tree from leaves to root.

K

kimuraDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.
KMERS - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

L

LINEAR - org.biojava.nbio.alignment.template.GapPenalty.Type
LOAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
LOCAL - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
LOCAL - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL_CONSENSUS - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL_IDENTITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
LOCAL_LINEAR_SPACE - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
LOCAL_SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

M

main(String[]) - Static method in class demo.CookbookMSA
main(String[]) - Static method in class demo.DemoAlignProteins
main(String[]) - Static method in class demo.DemoDistanceTree
main(String[]) - Static method in class demo.DemoLoadSubstMax
main(String[]) - Static method in class demo.TestDNANeedlemanWunsch
MatrixAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner which builds a score matrix during computation.
max - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
MIM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
min - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
ML - org.biojava.nbio.phylo.TreeType: Maximum Likelihood Tree

N

name - Variable in enum org.biojava.nbio.phylo.TreeType: Description name of the Tree Type
NeedlemanWunsch<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
NeedlemanWunsch() - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch: Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
NeedlemanWunsch(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.NeedlemanWunsch: Prepares for a pairwise global sequence alignment.
NJ - org.biojava.nbio.phylo.TreeConstructorType: Neighbor Joining Algorithm

O

org.biojava.nbio.alignment - package org.biojava.nbio.alignment
org.biojava.nbio.alignment.io - package org.biojava.nbio.alignment.io
org.biojava.nbio.alignment.routines - package org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template - package org.biojava.nbio.alignment.template
org.biojava.nbio.phylo - package org.biojava.nbio.phylo

P

pair - Variable in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
pair - Variable in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
PairInProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pair of sequences.
pamMLdistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.
parse(InputStream) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: parses InputStream and returns a the first contained alignment in a StockholmStructure object.
parse(InputStream, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: parses an InputStream and returns at maximum max objects contained in that file.
This method leaves the stream open for further calls of StockholmFileParser.parse(InputStream, int) (same function) or StockholmFileParser.parseNext(int).
parse(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Parses a Stockholm file and returns a StockholmStructure object with its content.
This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.
parse(String, int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Parses a Stockholm file and returns a StockholmStructure object with its content.
This function doesn't close the file after doing its assigned job; to allow for further calls of StockholmFileParser.parseNext(int).
parseNext(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileParser: Tries to parse and return as maximum as max structures in the last used file or input stream.
Please consider calling either StockholmFileParser.parse(InputStream), StockholmFileParser.parse(InputStream, int), or StockholmFileParser.parse(String, int) before calling this function.
PARSIMONY - org.biojava.nbio.phylo.TreeType: Parsimony Tree
PARTITION_SINGLE - org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_SINGLE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_TREE - org.biojava.nbio.alignment.Alignments.RefinerType
PARTITION_TREE_ALL - org.biojava.nbio.alignment.Alignments.RefinerType
PartitionRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
PDB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
percentageIdentity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: BioJava implementation for percentage of identity (PID).
PFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
PFAMB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PID(String, String) - Static method in class org.biojava.nbio.phylo.Comparison: this is a gapped PID calculation
PID(String, String, int, int) - Static method in class org.biojava.nbio.phylo.Comparison
poissonDistance(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:
PRINTS - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
profile - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
ProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an Aligner for a pair of Profiles.
ProfileProfileScorer<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score for a pairing of alignment profiles.
PROSITE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PROSITE_PROFILE - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

Q

QueryIndexComparator() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator

R

RESCORE_IDENTITIES - org.biojava.nbio.alignment.Alignments.RefinerType
RESCORE_SIMILARITIES - org.biojava.nbio.alignment.Alignments.RefinerType
RescoreRefiner<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.
reset() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Resets output fields; should be overridden to set max and min
reset() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
reset() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
RFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
runPairwiseScorers(List<PairwiseSequenceScorer<S, C>>) - Static method in class org.biojava.nbio.alignment.Alignments: Factory method to run a list of scorers concurrently.

S

SCOP - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
score - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Scorer - Interface in org.biojava.nbio.alignment.template: Defines an algorithm which computes a score.
scores - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Dynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)
setAlignmentMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setAnchors(int[]) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Sets the starting list of anchors before running the alignment routine.
setCuts(int, AlignerHelper.Subproblem, AlignerHelper.Last[][], AlignerHelper.Cut[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
setCutsPerSection(int) - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher: Sets the number of cuts added to each section during each pass.
setDbComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setDbReferences(Set<StockholmStructure.DatabaseReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setDefaultCutsPerSection(int) - Static method in class org.biojava.nbio.alignment.routines.GuanUberbacher: Sets the default number of cuts added to each section during each pass.
setDefaultExtensionPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty: Sets the default gap extension penalty.
setDefaultOpenPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty: Sets the default gap open penalty.
setExtensionPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
setExtensionPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Sets penalty given when an already open gap elongates by a single element
setFalseDiscoveryRate(float) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setFormat(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGapPenalty(GapPenalty) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Sets the gap penalties.
setGFAccessionNumber(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFAuthors(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFClan(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFDBComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFDefinition(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFGatheringThreshs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFIdentification(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFKeywords(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFMembership(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFNoiseCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFNumSequences(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFPfamAccession(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFPreviousIDs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFRefComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFSearchMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFSourceSeed(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFSourceStructure(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFTrustedCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFTypeField(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setGFWikipediaLink(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setNumSequences(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setOpenPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
setOpenPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty: Sets penalty given when a deletion or insertion gap first opens
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SimpleProfileProfileAligner
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SmithWaterman
setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
setProfile(Profile<S, C>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
setProfile(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Stores the given profile.
setProfileFuture(Future<ProfilePair<S, C>>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
setProfileFuture(Future<ProfilePair<S, C>>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Stores the given profile future.
setQuery(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Sets the query Profile.
setQuery(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Sets the query Sequence.
setRefAuthor(StringBuffer) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
setRefLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
setRefMedline(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
setRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
setScorePoint(int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
setScorePoint(int, int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
setScoreVector(int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score local alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score local alignment for a given position in the query sequence
setScoreVector(int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score global alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score local alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score global alignment for a given position in the query sequence
setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score local alignment for a given position in the query sequence
setScoreVector(int, AlignerHelper.Subproblem, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score global alignment for a given position in the query sequence for a linear gap penalty
setScoreVector(int, AlignerHelper.Subproblem, int, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Score global alignment for a given position in the query sequence
setSteps(AlignerHelper.Last[][][], boolean, int[], AlignerHelper.Last, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Find alignment path through traceback matrix
setSteps(AlignerHelper.Last[][][], int[][][], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Find global alignment path through traceback matrix
setSteps(AlignerHelper.Last[][][], int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper: Find local alignment path through traceback matrix
setStoringScoreMatrix(boolean) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
setSubstitutionMatrix(SubstitutionMatrix<C>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Sets the substitution matrix.
setTarget(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Sets the target Profile.
setTarget(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Sets the target Sequence.
setVersion(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
SIMILARITIES - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
SimpleGapPenalty - Class in org.biojava.nbio.alignment: Implements a data structure for the gap penalties used during a sequence alignment routine.
SimpleGapPenalty() - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty: Creates a new set of gap penalties using the defaults.
SimpleGapPenalty(int, int) - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty: Creates a new set of gap penalties.
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a simple (naive) Aligner for a pair of Profiles.
SimpleProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Prepares for a profile-profile alignment.
SMART - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
SmithWaterman<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).
SmithWaterman() - Constructor for class org.biojava.nbio.alignment.SmithWaterman: Before running a pairwise local sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
SmithWaterman(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SmithWaterman: Prepares for a pairwise local sequence alignment.
StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
StandardRescoreRefiner(Alignments.PairInProfileScorerType, Alignments.ProfileProfileAlignerType) - Constructor for class org.biojava.nbio.alignment.StandardRescoreRefiner
StockholmFileAnnotation - Class in org.biojava.nbio.alignment.io: Stores all the content parsed from the #=GF lines
StockholmFileAnnotation() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation
StockholmFileAnnotation.StockholmFileAnnotationReference - Class in org.biojava.nbio.alignment.io
StockholmFileAnnotationReference() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
StockholmFileParser - Class in org.biojava.nbio.alignment.io: Stockholm file parser.
for more information about the format refer to ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt. ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN. http://sonnhammer.sbc.su.se/Stockholm.html.
StockholmFileParser() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileParser
StockholmStructure - Class in org.biojava.nbio.alignment.io: Stores all the content of a Stockholm file.
StockholmStructure() - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure
StockholmStructure.DatabaseReference - Class in org.biojava.nbio.alignment.io
stringToFloats(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
structuralDistance(double[][], double, double, double) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator: The structural distance (d_S) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.
Subproblem(int, int, int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
Subproblem(int, int, int, int, boolean) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
SUBSTITUTION - org.biojava.nbio.alignment.routines.AlignerHelper.Last
SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Scores using a substitution matrix.
SubstitutionMatrixScorer(SequencePair<S, C>, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SubstitutionMatrixScorer

T

TestDNANeedlemanWunsch - Class in demo
TestDNANeedlemanWunsch() - Constructor for class demo.TestDNANeedlemanWunsch
time - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
toString() - Method in class org.biojava.nbio.alignment.GuideTree
toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
toString() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
tracebackToString(AlignerHelper.Last[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
TreeConstructor - Class in org.biojava.nbio.phylo: The TreeConstructor uses the forester library to build different types of phylogenetic trees.
TreeConstructorType - Enum in org.biojava.nbio.phylo: The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
TreeType - Enum in org.biojava.nbio.phylo: The TreeType specifies the optimization criteria used to generate the tree.

U

update(int, AlignerHelper.Subproblem, AlignerHelper.Last[][]) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
UPGMA - org.biojava.nbio.phylo.TreeConstructorType: Unweighted Pair-Group Method with Arithmetic mean
URL - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

V

valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructorType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.phylo.TreeConstructorType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava.nbio.phylo.TreeType: Returns an array containing the constants of this enum type, in the order they are declared.

W

WU_MANBER - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

X

xyMax - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: End position of the aligned sequence in the query and target respectively
xyStart - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Start position of the aligned sequence in the query and target respectively

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