Index (biojava-alignment 4.1.0 API)

A C D E F G H I L M N O P R S T U V X

A

AAindexFactory - Class in org.biojava.nbio.alignment.aaindex: Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava.nbio.alignment.aaindex.AAindexFactory
AAIndexFileParser - Class in org.biojava.nbio.alignment.aaindex
AAIndexFileParser() - Constructor for class org.biojava.nbio.alignment.aaindex.AAIndexFileParser
AAIndexProvider - Interface in org.biojava.nbio.alignment.aaindex
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(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Prepares for a profile-profile alignment.
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(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(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.
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
addSequence(String, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: Deprecated.
Use StockholmStructure.appendToSequence(String,String) instead
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
align() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner: Performs alignment
AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step - Enum in org.biojava.nbio.alignment.template: Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
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(int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
AlignerHelper.Anchor.QueryIndexComparator - Class in org.biojava.nbio.alignment.routines
AlignerHelper.Anchor.QueryIndexComparator() - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
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.Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
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.
AlignerHelper.Subproblem(int, int, int, int) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
AlignerHelper.Subproblem(int, int, int, int, boolean) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.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.
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

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
clearCache() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
clearCache() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Nullifies cached arrays/objects.
compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
CookbookMSA - Class in demo
CookbookMSA() - Constructor for class demo.CookbookMSA
countCompounds(C...) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner

D

DefaultAAIndexProvider - Class in org.biojava.nbio.alignment.aaindex: The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider
demo - package demo
DemoAlignProteins - Class in demo
DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
DemoLoadSubstMax - Class in demo
DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax

E

EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

F

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.
getAAIndexProvider() - Static method in class org.biojava.nbio.alignment.aaindex.AAindexFactory
getAccession() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getAlignedSequence(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getAlignedSequence(S) - Method in class org.biojava.nbio.alignment.SimpleProfile
getAlignedSequence(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns AlignedSequence at given index.
getAlignedSequence(S) - Method in interface org.biojava.nbio.alignment.template.Profile: Searches for the given Sequence within this alignment profile.
getAlignedSequences() - Method in class org.biojava.nbio.alignment.SimpleProfile
getAlignedSequences(int...) - Method in class org.biojava.nbio.alignment.SimpleProfile
getAlignedSequences(S...) - Method in class org.biojava.nbio.alignment.SimpleProfile
getAlignedSequences() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a List containing the individual AlignedSequences of this alignment.
getAlignedSequences(int...) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences(S...) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignmentIndexAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getAlignmentIndexAt(int) - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the column index within an alignment corresponding to the given index in the original Sequence.
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(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.
getAllPairsScores() - Method in class org.biojava.nbio.alignment.GuideTree: Returns a sequence pair score for all Sequence pairs in the given List.
getAminoAcidSubstitutionMatrix(String) - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns a substitution matrix for amino acids given by the name name.
getAnchors() - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner: Returns the list of anchors.
getAsList() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
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, 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).
getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure: Because some database files have incorrectly small letters (e.g.
getBlosum100() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 100 matrix by Henikoff & Henikoff
getBlosum30() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 30 matrix by Henikoff & Henikoff
getBlosum35() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 35 matrix by Henikoff & Henikoff
getBlosum40() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 40 matrix by Henikoff & Henikoff
getBlosum45() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 45 matrix by Henikoff & Henikoff
getBlosum50() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 50 matrix by Henikoff & Henikoff
getBlosum55() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 55 matrix by Henikoff & Henikoff
getBlosum60() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 60 matrix by Henikoff & Henikoff
getBlosum62() - Static method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getBlosum62() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 62 matrix by Henikoff & Henikoff
getBlosum65() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 65 matrix by Henikoff & Henikoff
getBlosum70() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 70 matrix by Henikoff & Henikoff
getBlosum75() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 75 matrix by Henikoff & Henikoff
getBlosum80() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 80 matrix by Henikoff & Henikoff
getBlosum85() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 85 matrix by Henikoff & Henikoff
getBlosum90() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Blosum 90 matrix by Henikoff & Henikoff
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
getCols() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getColumn(C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getColumn(C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
getComment() - Static method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getCompoundAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getCompoundAt(int, int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundAt(S, int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundAt(int, int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(S, int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundCountsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundCountsAt(int, List<C>) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundCountsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the number of each Compound in the given column for all compounds in CompoundSet.
getCompoundCountsAt(int, List<C>) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the number of each Compound in the given column only for compounds in the given list.
getCompoundInQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getCompoundInQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the Compound in query sequence at given column index in alignment.
getCompoundInTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getCompoundInTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the Compound in target sequence at given column index in alignment.
getCompoundsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the Compound elements of the original Sequences at the given column.
getCompoundSet() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
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
getCompoundSet() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns CompoundSet of all AlignedSequences
getCompoundSet() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns the CompoundSet on which the matrix is defined.
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
getCompoundWeightsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundWeightsAt(int, List<C>) - Method in class org.biojava.nbio.alignment.SimpleProfile
getCompoundWeightsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the fraction of each Compound in the given column only for compounds in the given list.
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
getDescription() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getDescription() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getDescription() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns the description of this matrix.
getDistance() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
getDistance(double) - 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 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
getEnd() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getEnd() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the Point within an alignment of the last element of the original Sequence.
getEnd() - Method in interface org.biojava.nbio.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the final element in this view
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.
getGonnet250() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns PAM 250 matrix by Gonnet, Cohen & Benner
getIdentification() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getIdentity() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node
getIndexInQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getIndexInQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the query index corresponding to a given alignment column.
getIndexInQueryForTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getIndexInQueryForTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the query index corresponding to a given target index.
getIndexInTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getIndexInTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the target index corresponding to a given alignment column.
getIndexInTargetForQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getIndexInTargetForQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the target index corresponding to a given query index.
getIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleProfile
getIndexOf(C) - Method in interface org.biojava.nbio.alignment.template.Profile: Searches for the given Compound within this alignment profile.
getIndicesAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
getIndicesAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the indices in the original Sequences corresponding to the given column.
getInputStreamToAAindexFile() - Method in class org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider
getInverse() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getLastIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getLastIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleProfile
getLastIndexOf(C) - Method in interface org.biojava.nbio.alignment.template.Profile: Searches for the given Compound within this alignment profile.
getLength() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getLength() - Method in class org.biojava.nbio.alignment.SimpleProfile
getLength() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the number of columns in the alignment profile.
getLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getLocationInAlignment() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getLocationInAlignment() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the Location of the original Sequence within an alignment.
getMatrices() - Method in class org.biojava.nbio.alignment.aaindex.AAIndexFileParser
getMatrix(String) - Method in interface org.biojava.nbio.alignment.aaindex.AAIndexProvider
getMatrix(String) - Method in class org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider
getMatrix() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getMatrix() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getMatrix() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns entire matrix.
getMatrixAsString() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getMatrixAsString() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns this matrix as a formatted String with Compound labels along the axes.
getMatrixFromAAINDEX(String) - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns any matrix from the AAINDEX database file
getMax() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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.
getMaxValue() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getMaxValue() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getMaxValue() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns the maximum value in this matrix.
getMembership() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getMin() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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.
getMinValue() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getMinValue() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getMinValue() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns the minimum value in this matrix.
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.aaindex.ScaledSubstitutionMatrix
getName() - Method in class org.biojava.nbio.alignment.GuideTree.Node
getName() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getName() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode: Returns the name of this node.
getName() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns the name (short description) of this matrix.
getNoiseCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation: Not always 2.
It may undergo further change.
getNuc4_2() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
getNuc4_4() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
getNumGaps() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getNumGaps() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns number of gaps in the sequence.
getNumIdenticals() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getNumIdenticals() - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have an identical Compound.
getNumSequences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getNumSimilars() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
getNumSimilars() - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have a similar Compound.
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
getOriginalSequence() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getOriginalSequence() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the original Sequence before alignment.
getOriginalSequences() - Method in class org.biojava.nbio.alignment.SimpleProfile
getOriginalSequences() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a List containing the original Sequences used for alignment.
getOverlapCount() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getOverlapCount() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the maximum number of elements contributed to a column of an alignment by this Sequence.
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.
getPAM250() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper: Returns PAM 250 matrix by Dayhoff
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.SimpleProfilePair
getQuery() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
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.ProfilePair: Returns the first Profile of the pair.
getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the first profile of the pair.
getQuery() - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the first AlignedSequence 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.
getRow(AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getRow(C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getRow(C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
getRows() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getScale() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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
getSequenceAsString() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getSequenceIndexAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getSequenceIndexAt(int) - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the index in the original Sequence corresponding to the given index within an alignment.
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(double) - 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 interface org.biojava.nbio.alignment.template.Scorer: Returns score as a similarity between 0.0 and scale.
getSize() - Method in class org.biojava.nbio.alignment.SimpleProfile
getSize() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns the number of rows in this profile.
getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getStart() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
getStart() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns the Point within an alignment of the first element of the original Sequence.
getStart() - Method in interface org.biojava.nbio.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the first element in this view
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.
getSubProfile(Location) - Method in class org.biojava.nbio.alignment.SimpleProfile
getSubProfile(Location) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a ProfileView windowed to contain only the given Location.
getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
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.SimpleProfilePair
getTarget() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
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.ProfilePair: Returns the second Profile of the pair.
getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer: Returns the second profile of the pair.
getTarget() - Method in interface org.biojava.nbio.alignment.template.SequencePair: Returns the second AlignedSequence 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
getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
getValue(C, C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
getValue(C, C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Returns value in matrix for conversion from first Compound to the second.
getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
getViewedProfile() - Method in interface org.biojava.nbio.alignment.template.ProfileView: Returns the entire Profile being viewed
getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
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

hasGap(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
hasGap(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns true if any AlignedSequence has a gap at the given index.
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

INFINITY - Static variable in class org.biojava.nbio.alignment.io.StockholmFileParser: indicates reading as much as possible, without limits
INTERPRO - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
isCircular() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
isCircular() - Method in class org.biojava.nbio.alignment.SimpleProfile
isCircular() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns true if this Sequence wraps around from the last alignment column back to the first.
isCircular() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns true if any AlignedSequence is circular.
isGap(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
isGap(int) - Method in interface org.biojava.nbio.alignment.template.AlignedSequence: Returns true if this Sequence has a gap at a particular alignment column.
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.
iterator() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
iterator() - Method in class org.biojava.nbio.alignment.SimpleProfile

L

LOAD - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference

M

main(String[]) - Static method in class demo.CookbookMSA
main(String[]) - Static method in class demo.DemoAlignProteins
main(String[]) - Static method in class demo.DemoLoadSubstMax
main(String[]) - Static method in class demo.TestDNANeedlemanWunsch
matrix - Static variable in class org.biojava.nbio.alignment.SimpleProfile
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
MutableAlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a mutable (editable) data structure for the results of pairwise sequence alignment.

N

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.
normalizeMatrix(short) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
normalizeMatrix(short) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
normalizeMatrix(short) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.

O

org.biojava.nbio.alignment - package org.biojava.nbio.alignment
org.biojava.nbio.alignment.aaindex - package org.biojava.nbio.alignment.aaindex
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

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.
parse(InputStream) - Method in class org.biojava.nbio.alignment.aaindex.AAIndexFileParser: parse an inputStream that points to an AAINDEX database file
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).
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).
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.
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
PFAM - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure
PFAMB - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
PRINTS - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
profile - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
Profile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the results of sequence alignment.
Profile.StringFormat - Enum in org.biojava.nbio.alignment.template: List of output formats.
ProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the results of the alignment of a pair of Profiles.
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.
ProfileView<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for a view of sequence alignment.
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

R

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

ScaledSubstitutionMatrix - Class in org.biojava.nbio.alignment.aaindex: The biojava-alignment module represents substitution matrices with short values.
ScaledSubstitutionMatrix() - Constructor for class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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)
SequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure for the results of pairwise sequence alignment.
setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava.nbio.alignment.aaindex.AAindexFactory
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.
setCols(List<AminoAcidCompound>) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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.
setDescription(String) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setDescription(String) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
setDescription(String) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Sets the description of this matrix.
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
setLocationInAlignment(Location) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence: Sets the position of the AlignedSequence to the given Location (start, gaps, end).
setMatrix(short[][]) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setMax(short) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setMin(short) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setName(String) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setName(String) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
setName(String) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix: Sets the name (short description) of this matrix.
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
setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair: Sets both Profiles of the pair.
setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair: Sets both AlignedSequences of the pair.
setProfile(Profile<S, C>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
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 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(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Sets the query Sequence.
setQuery(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Sets the query Profile.
setQuery(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair: Sets the first Profile of the pair.
setQuery(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair: Sets the first AlignedSequence of the pair.
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
setRows(List<AminoAcidCompound>) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
setScale(int) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
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
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
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
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, 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, 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[], 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, 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[], 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[], 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
setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava.nbio.alignment.template.MutableProfile: Sets entirely new set of AlignedSequences.
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(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner: Sets the target Sequence.
setTarget(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner: Sets the target Profile.
setTarget(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair: Sets the second Profile of the pair.
setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair: Sets the second AlignedSequence of the pair.
setVersion(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence: Slides a part of the AlignedSequence.
shiftAtSequenceLocation(Location, int) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence: Slides a part of the AlignedSequence.
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for a Sequence within an alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence: Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence: Creates an AlignedSequence for the given Sequence in a local alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence: Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence: Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
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.
SimpleProfile<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for the results of sequence alignment.
SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile: Creates a pair profile for the given already aligned sequences.
SimpleProfile(S) - Constructor for class org.biojava.nbio.alignment.SimpleProfile: Creates a profile from a single sequence.
SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleProfile: Creates a pair profile for the given sequences.
SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile: Creates a pair profile for the given profiles.
SimpleProfile(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile: Creates a profile for the already aligned sequences.
SimpleProfilePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for the results of the alignment of a pair of Profiles.
SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleProfilePair: Creates a pair profile for the given profiles.
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(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner: Prepares for a profile-profile alignment.
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(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(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.
SimpleSequencePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure for the results of pairwise sequence alignment.
SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair: Creates a pair profile for the given already aligned sequences.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair: Creates a pair profile for the given sequences with a global alignment.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair: Creates a pair profile for the given sequences with a local alignment.
SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava.nbio.alignment: Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix: Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix: Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix: Creates a substitution matrix by parsing a String.
SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix: Creates an identity substitution matrix from match and replace values.
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
StockholmFileAnnotation.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
StockholmStructure.DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
StockholmStructure.DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
stringToFloats(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
SubstitutionMatrix<C extends Compound> - Interface in org.biojava.nbio.alignment.template: Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SubstitutionMatrixHelper - Class in org.biojava.nbio.alignment: Static utility to access substitution matrices that come bundled with BioJava.
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.aaindex.ScaledSubstitutionMatrix: Returns in a format similar to the standard NCBI files.
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
toString() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence: Provides standard Java language access to results of SimpleAlignedSequence.getSequenceAsString().
toString(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
toString(Profile.StringFormat) - Method in class org.biojava.nbio.alignment.SimpleProfile
toString() - Method in class org.biojava.nbio.alignment.SimpleProfile
toString() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix: Returns in a format similar to the standard NCBI files.
toString() - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a simple view of the alignment profile.
toString(int) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a formatted view of the alignment profile.
toString(Profile.StringFormat) - Method in interface org.biojava.nbio.alignment.template.Profile: Returns a formatted view of the alignment profile.
tracebackToString(AlignerHelper.Last[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper

U

update(int, AlignerHelper.Subproblem, AlignerHelper.Last[][]) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
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.AlignedSequence.Step: 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.alignment.template.Profile.StringFormat: 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.AlignedSequence.Step: 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.alignment.template.Profile.StringFormat: Returns an array containing the constants of this enum type, in the order they are declared.

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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