Uses of Interface
org.biojava.nbio.core.sequence.template.Compound
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Uses of Compound in org.biojava.nbio.alignment
Classes in org.biojava.nbio.alignment with type parameters of type Compound Modifier and Type Class Description class
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignmentProfile
.class
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound>
Implements an algorithm which computes a score for a sequence alignment pair.class
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound>
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignmentProfile
.class
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound>
Implements an algorithm which computes a score for a sequence alignment pair.class
GuideTree<S extends Sequence<C>,C extends Compound>
Implements a data structure for a guide tree used during progressive multiple sequence alignment.class
NeedlemanWunsch<S extends Sequence<C>,C extends Compound>
class
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>
class
SmithWaterman<S extends Sequence<C>,C extends Compound>
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from eachSequence
).class
StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
class
SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound>
Scores using a substitution matrix.Methods in org.biojava.nbio.alignment with type parameters of type Compound Modifier and Type Method Description static <S extends Sequence<C>,C extends Compound>
List<SequencePair<S,C>>Alignments. getAllPairsAlignments(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
static <S extends Sequence<C>,C extends Compound>
List<PairwiseSequenceScorer<S,C>>Alignments. getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
static <S extends Sequence<C>,C extends Compound>
double[]Alignments. getAllPairsScores(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
static <S extends Sequence<C>,C extends Compound>
Profile<S,C>Alignments. getMultipleSequenceAlignment(List<S> sequences, Object... settings)
static <S extends Sequence<C>,C extends Compound>
PairwiseSequenceAligner<S,C>Alignments. getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Factory method which constructs a pairwise sequence aligner.static <S extends Sequence<C>,C extends Compound>
SequencePair<S,C>Alignments. getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Factory method which computes a sequence alignment for the givenSequence
pair.static <S extends Sequence<C>,C extends Compound>
Profile<S,C>Alignments. getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.static <S extends Sequence<C>,C extends Compound>
double[]Alignments. runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers)
Factory method to run a list of scorers concurrently. -
Uses of Compound in org.biojava.nbio.alignment.routines
Classes in org.biojava.nbio.alignment.routines with type parameters of type Compound Modifier and Type Class Description class
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
class
GuanUberbacher<S extends Sequence<C>,C extends Compound>
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Uses of Compound in org.biojava.nbio.alignment.template
Classes in org.biojava.nbio.alignment.template with type parameters of type Compound Modifier and Type Class Description class
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
Implements common code for anAligner
which builds a score matrix during computation.class
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
class
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>
interface
Aligner<S extends Sequence<C>,C extends Compound>
class
CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
Implements a concurrency wrapper for aPairwiseSequenceAligner
.class
CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
Implements a concurrency wrapper for aPairwiseSequenceScorer
.class
CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound>
Implements a concurrency wrapper for aProfileProfileAligner
.interface
GuideTreeNode<S extends Sequence<C>,C extends Compound>
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.interface
HierarchicalClusterer<S extends Sequence<C>,C extends Compound>
Defines a clustering algorithm that converts a distance matrix into a tree.interface
MatrixAligner<S extends Sequence<C>,C extends Compound>
Defines anAligner
which builds a score matrix during computation.interface
PairInProfileScorer<S extends Sequence<C>,C extends Compound>
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignmentProfile
.interface
PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
interface
PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
Defines an algorithm which computes a score for a pair of sequences.interface
PartitionRefiner<S extends Sequence<C>,C extends Compound>
Defines an algorithm which computes a new alignmentProfile
by splitting a current alignment and realigning.interface
ProfileProfileAligner<S extends Sequence<C>,C extends Compound>
Defines anAligner
for a pair ofProfile
s.interface
ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
Defines an algorithm which computes a score for a pairing of alignment profiles.interface
RescoreRefiner<S extends Sequence<C>,C extends Compound>
Defines an algorithm which computes a new alignmentProfile
by rescoring all pairs in an alignment and realigning. -
Uses of Compound in org.biojava.nbio.core.alignment
Classes in org.biojava.nbio.core.alignment with type parameters of type Compound Modifier and Type Class Description class
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>
Implements a data structure for aSequence
within an alignment.class
SimpleProfile<S extends Sequence<C>,C extends Compound>
Implements a data structure for the results of sequence alignment.class
SimpleProfilePair<S extends Sequence<C>,C extends Compound>
Implements a data structure for the results of the alignment of a pair ofProfile
s.class
SimpleSequencePair<S extends Sequence<C>,C extends Compound>
Implements a data structure for the results of pairwise sequence alignment.Methods in org.biojava.nbio.core.alignment with parameters of type Compound Modifier and Type Method Description int
SimpleAlignedSequence. countCompounds(C... compounds)
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Uses of Compound in org.biojava.nbio.core.alignment.matrices
Classes in org.biojava.nbio.core.alignment.matrices with type parameters of type Compound Modifier and Type Class Description class
SimpleSubstitutionMatrix<C extends Compound>
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of oneCompound
in a sequence for another. -
Uses of Compound in org.biojava.nbio.core.alignment.template
Classes in org.biojava.nbio.core.alignment.template with type parameters of type Compound Modifier and Type Interface Description interface
AlignedSequence<S extends Sequence<C>,C extends Compound>
Defines a data structure for aSequence
within an alignment.interface
MutableAlignedSequence<S extends Sequence<C>,C extends Compound>
Defines a mutable (editable) data structure for anAlignedSequence
.interface
MutableProfile<S extends Sequence<C>,C extends Compound>
Defines a mutable (editable) data structure for aProfile
.interface
MutableProfilePair<S extends Sequence<C>,C extends Compound>
Defines a mutable (editable) data structure for aProfilePair
.interface
MutableSequencePair<S extends Sequence<C>,C extends Compound>
Defines a mutable (editable) data structure for the results of pairwise sequence alignment.interface
Profile<S extends Sequence<C>,C extends Compound>
Defines a data structure for the results of sequence alignment.interface
ProfilePair<S extends Sequence<C>,C extends Compound>
Defines a data structure for the results of the alignment of a pair ofProfile
s.interface
ProfileView<S extends Sequence<C>,C extends Compound>
Defines a data structure for a view of sequence alignment.interface
SequencePair<S extends Sequence<C>,C extends Compound>
Defines a data structure for the results of pairwise sequence alignment.interface
SubstitutionMatrix<C extends Compound>
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of oneCompound
in a sequence for another. -
Uses of Compound in org.biojava.nbio.core.search.io
Classes in org.biojava.nbio.core.search.io with type parameters of type Compound Modifier and Type Class Description class
Hsp<S extends Sequence<C>,C extends Compound>
This class models a search Hsp. -
Uses of Compound in org.biojava.nbio.core.sequence
Classes in org.biojava.nbio.core.sequence with type parameters of type Compound Modifier and Type Class Description class
BasicSequence<C extends Compound>
Bare bones version of the Sequence object to be used sparingly.class
MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound>
Implements a minimal data structure for reading and writing a sequence alignment. -
Uses of Compound in org.biojava.nbio.core.sequence.compound
Classes in org.biojava.nbio.core.sequence.compound that implement Compound Modifier and Type Class Description class
AminoAcidCompound
Used to describe an Amino Acid.class
CodonCompound
Define a codonclass
NucleotideCompound
Methods in org.biojava.nbio.core.sequence.compound with parameters of type Compound Modifier and Type Method Description boolean
AminoAcidCompound. equalsIgnoreCase(Compound compound)
boolean
CodonCompound. equalsIgnoreCase(Compound compound)
boolean
NucleotideCompound. equalsIgnoreCase(Compound compound)
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Uses of Compound in org.biojava.nbio.core.sequence.edits
Classes in org.biojava.nbio.core.sequence.edits with type parameters of type Compound Modifier and Type Interface Description interface
Edit<C extends Compound>
Interface for carrying out edit operations on a Sequence.static class
Edit.AbstractEdit<C extends Compound>
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.static class
Edit.Delete<C extends Compound>
Implementation which allows for the deletion of bases from a Sequencestatic class
Edit.Insert<C extends Compound>
Edit implementation which allows us to insert a base at any position in a Sequence.static class
Edit.Substitute<C extends Compound>
Allows for the substitution of bases into an existing Sequence. -
Uses of Compound in org.biojava.nbio.core.sequence.features
Classes in org.biojava.nbio.core.sequence.features with type parameters of type Compound Modifier and Type Class Description class
AbstractFeature<S extends AbstractSequence<C>,C extends Compound>
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that featureclass
FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>
It isDBReferenceInfo
which implementsFeatureInterface
.interface
FeatureInterface<S extends AbstractSequence<C>,C extends Compound>
Interface class to handle describing arbitrary features.class
QualityFeature<S extends AbstractSequence<C>,C extends Compound>
DNA Sequences produced by modern sequencers usually have quality informaion attached to them.class
QuantityFeature<S extends AbstractSequence<C>,C extends Compound>
It is common to have a numerical value or values associated with a feature.class
TextFeature<S extends AbstractSequence<C>,C extends Compound>
A implmentation of AbstractFeature -
Uses of Compound in org.biojava.nbio.core.sequence.io
Classes in org.biojava.nbio.core.sequence.io with type parameters of type Compound Modifier and Type Class Description class
FastaReader<S extends Sequence<?>,C extends Compound>
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta filesclass
FastaWriter<S extends Sequence<?>,C extends Compound>
The FastaWriter writes a collection of sequences to an outputStream.class
GenbankReader<S extends AbstractSequence<C>,C extends Compound>
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank filesclass
GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
class
GenbankWriter<S extends Sequence<?>,C extends Compound>
class
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound>
We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.class
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>
The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterfaceclass
GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
class
GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>
class
GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
class
PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>
The plain fasta header takes everything in the header as a single entity. -
Uses of Compound in org.biojava.nbio.core.sequence.io.template
Classes in org.biojava.nbio.core.sequence.io.template with type parameters of type Compound Modifier and Type Interface Description interface
FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
interface
GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
interface
SequenceCreatorInterface<C extends Compound>
interface
SequenceHeaderParserInterface<S extends Sequence<?>,C extends Compound>
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Uses of Compound in org.biojava.nbio.core.sequence.io.util
Methods in org.biojava.nbio.core.sequence.io.util with type parameters of type Compound Modifier and Type Method Description static <S extends Sequence<C>,C extends Compound>
intIOUtils. getGCGChecksum(List<S> sequences)
Calculates GCG checksum for entire list of sequencesstatic <S extends Sequence<C>,C extends Compound>
intIOUtils. getGCGChecksum(S sequence)
Calculates GCG checksum for a given sequencestatic <S extends Sequence<C>,C extends Compound>
StringIOUtils. getGCGHeader(List<S> sequences)
Assembles a GCG file headerstatic <C extends Compound>
StringIOUtils. getGCGType(CompoundSet<C> cs)
Determines GCG typestatic <S extends Sequence<C>,C extends Compound>
StringIOUtils. getIDFormat(List<S> sequences)
Creates format String for accession IDs -
Uses of Compound in org.biojava.nbio.core.sequence.loader
Classes in org.biojava.nbio.core.sequence.loader with type parameters of type Compound Modifier and Type Class Description class
ArrayListProxySequenceReader<C extends Compound>
class
GenbankProxySequenceReader<C extends Compound>
class
SequenceFileProxyLoader<C extends Compound>
This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.class
StringProxySequenceReader<C extends Compound>
An example of a ProxySequenceReader that is created from a String.class
UniprotProxySequenceReader<C extends Compound>
Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.Methods in org.biojava.nbio.core.sequence.loader with type parameters of type Compound Modifier and Type Method Description static <C extends Compound>
UniprotProxySequenceReader<C>UniprotProxySequenceReader. parseUniprotXMLString(String xml, CompoundSet<C> compoundSet)
The passed in xml is parsed as a DOM object so we know everything about the protein.Methods in org.biojava.nbio.core.sequence.loader with parameters of type Compound Modifier and Type Method Description int
SequenceFileProxyLoader. countCompounds(C... compounds)
int
StringProxySequenceReader. countCompounds(C... compounds)
int
UniprotProxySequenceReader. countCompounds(C... compounds)
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Uses of Compound in org.biojava.nbio.core.sequence.location
Classes in org.biojava.nbio.core.sequence.location with type parameters of type Compound Modifier and Type Class Description class
InsdcParser<S extends AbstractSequence<C>,C extends Compound>
Parser for working with INSDC style locations.class
SequenceLocation<S extends AbstractSequence<C>,C extends Compound>
A location in a sequence that keeps a reference to its parent sequence -
Uses of Compound in org.biojava.nbio.core.sequence.location.template
Methods in org.biojava.nbio.core.sequence.location.template with type parameters of type Compound Modifier and Type Method Description protected <C extends Compound>
booleanAbstractLocation. canComplement(Sequence<C> sequence)
Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement<C extends Compound>
Sequence<C>AbstractLocation. getRelevantSubSequence(Sequence<C> sequence)
<C extends Compound>
Sequence<C>Location. getRelevantSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented<C extends Compound>
Sequence<C>AbstractLocation. getSubSequence(Sequence<C> sequence)
If circular this will return the sequence represented by the sub locations joined.<C extends Compound>
Sequence<C>Location. getSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which represents the outer bounds of this Locationprotected <C extends Compound>
Sequence<C>AbstractLocation. reverseSequence(Sequence<C> sequence)
Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).Methods in org.biojava.nbio.core.sequence.location.template that return types with arguments of type Compound Modifier and Type Method Description ProxySequenceReader<? extends Compound>
AccesionedLocation. getProxySequenceReader()
Return the proxy reader used to get sequence for this location. -
Uses of Compound in org.biojava.nbio.core.sequence.storage
Classes in org.biojava.nbio.core.sequence.storage with type parameters of type Compound Modifier and Type Class Description class
ArrayListSequenceReader<C extends Compound>
Stores a Sequence as a collection of compounds in an ArrayListclass
BitSequenceReader<C extends Compound>
An implementation of the popular bit encodings.static class
BitSequenceReader.BitArrayWorker<C extends Compound>
The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.class
FourBitSequenceReader<C extends Compound>
Four bit encoding of the bit formats.static class
FourBitSequenceReader.FourBitArrayWorker<C extends Compound>
A four bit per compound implementation of the bit array worker code.class
JoiningSequenceReader<C extends Compound>
This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence.class
SequenceAsStringHelper<C extends Compound>
This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.class
SingleCompoundSequenceReader<C extends Compound>
An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).Methods in org.biojava.nbio.core.sequence.storage with parameters of type Compound Modifier and Type Method Description int
ArrayListSequenceReader. countCompounds(C... compounds)
int
BitSequenceReader. countCompounds(C... compounds)
Counts the number of times a compound appears in this sequence storeint
JoiningSequenceReader. countCompounds(C... compounds)
int
SingleCompoundSequenceReader. countCompounds(C... compounds)
Delegates toSequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
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Uses of Compound in org.biojava.nbio.core.sequence.template
Classes in org.biojava.nbio.core.sequence.template with type parameters of type Compound Modifier and Type Class Description class
AbstractCompoundSet<C extends Compound>
class
AbstractCompoundTranslator<F extends Compound,T extends Compound>
class
AbstractCompoundTranslator<F extends Compound,T extends Compound>
class
AbstractSequence<C extends Compound>
The base class for DNA, RNA and Protein sequences.interface
CompoundSet<C extends Compound>
interface
CompoundTranslator<F extends Compound,T extends Compound>
interface
CompoundTranslator<F extends Compound,T extends Compound>
interface
LightweightProfile<S extends Sequence<C>,C extends Compound>
Defines a minimal data structure for reading and writing a sequence alignment.interface
ProxySequenceReader<C extends Compound>
interface
Sequence<C extends Compound>
Main interface for defining a collection of Compounds and accessing them using biological indexesstatic class
SequenceMixin.SequenceIterator<C extends Compound>
A basic sequence iterator which iterates over the given Sequence by biological index.class
SequenceProxyView<C extends Compound>
interface
SequenceReader<C extends Compound>
interface
SequenceView<C extends Compound>
Subinterfaces of Compound in org.biojava.nbio.core.sequence.template Modifier and Type Interface Description interface
ComplementCompound
Classes in org.biojava.nbio.core.sequence.template that implement Compound Modifier and Type Class Description class
AbstractCompound
The details of a CompoundMethods in org.biojava.nbio.core.sequence.template with type parameters of type Compound Modifier and Type Method Description static <C extends Compound>
StringSequenceMixin. checksum(Sequence<C> sequence)
Performs a simple CRC64 checksum on any given sequence.static <C extends Compound>
intSequenceMixin. countCompounds(Sequence<C> sequence, C... compounds)
For the given vargs of compounds this method counts the number of times those compounds appear in the given sequencestatic <C extends Compound>
Iterator<C>SequenceMixin. createIterator(Sequence<C> sequence)
Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.static <C extends Compound>
SequenceView<C>SequenceMixin. createSubSequence(Sequence<C> sequence, int start, int end)
Creates a simple sub sequence view delimited by the given start and end.static <C extends Compound>
Map<C,Integer>SequenceMixin. getComposition(Sequence<C> sequence)
Does a linear scan over the given Sequence and records the number of times each base appears.static <C extends Compound>
Map<C,Double>SequenceMixin. getDistribution(Sequence<C> sequence)
Analogous toSequenceMixin.getComposition(Sequence)
but returns the distribution of thatCompound
over the given sequence.static <C extends Compound>
intSequenceMixin. indexOf(Sequence<C> sequence, C compound)
Performs a linear search of the given Sequence for the given compound.static <C extends Compound>
SequenceView<C>SequenceMixin. inverse(Sequence<C> sequence)
A method which attempts to do the right thing when is comes to a reverse/reverse complementstatic <C extends Compound>
intSequenceMixin. lastIndexOf(Sequence<C> sequence, C compound)
Performs a reversed linear search of the given Sequence by wrapping it in aReversedSequenceView
and passing it intoSequenceMixin.indexOf(Sequence, Compound)
.static <C extends Compound>
List<SequenceView<C>>SequenceMixin. nonOverlappingKmers(Sequence<C> sequence, int kmer)
Produces kmers of the specified size e.g.static <C extends Compound>
List<SequenceView<C>>SequenceMixin. overlappingKmers(Sequence<C> sequence, int kmer)
Used to generate overlapping k-mers such i.e.static <C extends Compound>
booleanSequenceMixin. sequenceEquality(Sequence<C> source, Sequence<C> target)
A case-sensitive manner of comparing two sequence objects together.static <C extends Compound>
booleanSequenceMixin. sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target)
A case-insensitive manner of comparing two sequence objects together.static <C extends Compound>
Sequence<C>SequenceMixin. shuffle(Sequence<C> sequence)
Implements sequence shuffling by first materializing the givenSequence
into aList
, applyingCollections.shuffle(List)
and then returning the shuffled elements in a new instance ofSequenceBackingStore
which behaves as aSequence
.static <C extends Compound>
List<C>SequenceMixin. toList(Sequence<C> sequence)
static <C extends Compound>
StringSequenceMixin. toString(Sequence<C> sequence)
Shortcut toSequenceMixin.toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence)
which calls toString() on the resulting object.static <C extends Compound>
StringBuilderSequenceMixin. toStringBuilder(Sequence<C> sequence)
For the given Sequence this will return aStringBuilder
object filled with the results ofCompound#toString()
.static <C extends Compound>
voidSequenceMixin. write(Appendable appendable, Sequence<C> sequence)
Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data outMethods in org.biojava.nbio.core.sequence.template with parameters of type Compound Modifier and Type Method Description protected void
AbstractCompoundSet. addCompound(C compound, C lowerCasedCompound, C... equivalents)
protected void
AbstractCompoundTranslator. addCompounds(F source, T... targets)
int
AbstractSequence. countCompounds(C... compounds)
int
Sequence. countCompounds(C... compounds)
Returns the number of times we found a compound in the Sequencestatic <C extends Compound>
intSequenceMixin. countCompounds(Sequence<C> sequence, C... compounds)
For the given vargs of compounds this method counts the number of times those compounds appear in the given sequenceint
SequenceProxyView. countCompounds(C... compounds)
boolean
AbstractCompound. equalsIgnoreCase(Compound compound)
boolean
Compound. equalsIgnoreCase(Compound compound)
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Uses of Compound in org.biojava.nbio.core.sequence.transcription
Classes in org.biojava.nbio.core.sequence.transcription that implement Compound Modifier and Type Class Description class
CaseInsensitiveCompound
Attempts to wrap compounds so it is possible to view them in a case insensitive mannerstatic class
Table.Codon
Instance of a Codon which is 3NucleotideCompound
s, its correspondingAminoAcidCompound
and if it is a start or stop codon.Methods in org.biojava.nbio.core.sequence.transcription with parameters of type Compound Modifier and Type Method Description boolean
CaseInsensitiveCompound. equalsIgnoreCase(Compound compound)
boolean
Table.Codon. equalsIgnoreCase(Compound compound)
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Uses of Compound in org.biojava.nbio.core.sequence.views
Classes in org.biojava.nbio.core.sequence.views with type parameters of type Compound Modifier and Type Class Description class
ReversedSequenceView<C extends Compound>
For a given sequence this class will return the base at the reversed position i.e. in a sequence of size 10, if you request base 2 you will get back the base at position 9.class
WindowedSequence<C extends Compound>
A sliding window view of a sequence which does not implement any interfaces likeSequence
because they do not fit how this works. -
Uses of Compound in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo with type parameters of type Compound Modifier and Type Method Description static <C extends Sequence<D>,D extends Compound>
org.forester.msa.MsaForesterWrapper. convert(MultipleSequenceAlignment<C,D> msa)
Convert a BioJavaMultipleSequenceAlignment
to a foresterMsa
.static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. dissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M)
The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. fractionalDissimilarity(MultipleSequenceAlignment<C,D> msa)
The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. fractionalDissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M)
The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. kimuraDistance(MultipleSequenceAlignment<C,D> msa)
The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. pamMLdistance(MultipleSequenceAlignment<C,D> msa)
The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. percentageIdentity(MultipleSequenceAlignment<C,D> msa)
BioJava implementation for percentage of identity (PID).static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. poissonDistance(MultipleSequenceAlignment<C,D> msa)
The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:static <C extends Sequence<D>,D extends Compound>
org.forester.evoinference.matrix.distance.DistanceMatrixDistanceMatrixCalculator. structuralDistance(double[][] rmsdMat, double alpha, double rmsdMax, double rmsd0)
The structural distance (dS) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures. -
Uses of Compound in org.biojava.nbio.ws.alignment
Method parameters in org.biojava.nbio.ws.alignment with type arguments of type Compound Modifier and Type Method Description String
RemotePairwiseAlignmentService. sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa)
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object -
Uses of Compound in org.biojava.nbio.ws.alignment.qblast
Method parameters in org.biojava.nbio.ws.alignment.qblast with type arguments of type Compound Modifier and Type Method Description String
NCBIQBlastService. sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa)
Converts given sequence to String and callsNCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
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