Uses of Interface
org.biojava.nbio.core.sequence.template.SequenceView

Packages that use SequenceView

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.views

Uses of SequenceView in org.biojava.nbio.core.alignment

Methods in org.biojava.nbio.core.alignment that return SequenceView

Modifier and Type	Method and Description
SequenceView<C>	SimpleAlignedSequence.getInverse()
SequenceView<C>	SimpleAlignedSequence.getSubSequence(Integer start, Integer end)

Uses of SequenceView in org.biojava.nbio.core.sequence

Methods in org.biojava.nbio.core.sequence that return SequenceView

Modifier and Type	Method and Description
SequenceView<NucleotideCompound>	RNASequence.getComplement() Get the complement view of the RNA sequence
SequenceView<NucleotideCompound>	DNASequence.getComplement() Returns a Sequence which will complement every base
SequenceView<NucleotideCompound>	RNASequence.getInverse() Get the inverse view of the sequence.
SequenceView<NucleotideCompound>	DNASequence.getReverse() Returns a Sequence which runs in the current reverse order
SequenceView<NucleotideCompound>	RNASequence.getReverseComplement() Get reverse complement view of the sequence
SequenceView<NucleotideCompound>	DNASequence.getReverseComplement() Delegates to AbstractSequence.getInverse() for the reverse complement

Uses of SequenceView in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader that return SequenceView

Modifier and Type	Method and Description
SequenceView<C>	UniprotProxySequenceReader.getInverse()
SequenceView<C>	StringProxySequenceReader.getInverse()
SequenceView<C>	SequenceFileProxyLoader.getInverse()
SequenceView<C>	UniprotProxySequenceReader.getSubSequence(Integer bioBegin, Integer bioEnd)
SequenceView<C>	StringProxySequenceReader.getSubSequence(Integer bioBegin, Integer bioEnd)
SequenceView<C>	SequenceFileProxyLoader.getSubSequence(Integer bioBegin, Integer bioEnd)

Uses of SequenceView in org.biojava.nbio.core.sequence.storage

Methods in org.biojava.nbio.core.sequence.storage that return SequenceView

Modifier and Type	Method and Description
SequenceView<C>	SingleCompoundSequenceReader.getInverse()
SequenceView<C>	JoiningSequenceReader.getInverse()
SequenceView<C>	ArrayListSequenceReader.getInverse()
SequenceView<C>	BitSequenceReader.getInverse()
SequenceView<C>	SingleCompoundSequenceReader.getSubSequence(Integer start, Integer end) Creates a SequenceProxyView for the given coordinates
SequenceView<C>	JoiningSequenceReader.getSubSequence(Integer start, Integer end)
SequenceView<C>	ArrayListSequenceReader.getSubSequence(Integer bioBegin, Integer bioEnd)
SequenceView<C>	BitSequenceReader.getSubSequence(Integer start, Integer end)
SequenceView<C>	BitSequenceReader.getSubSequence(int start, int end) Returns a sub sequence view

Uses of SequenceView in org.biojava.nbio.core.sequence.template

Classes in org.biojava.nbio.core.sequence.template that implement SequenceView

Modifier and Type	Class and Description
class	SequenceProxyView<C extends Compound>

Methods in org.biojava.nbio.core.sequence.template that return SequenceView

Modifier and Type	Method and Description
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.
SequenceView<C>	Sequence.getInverse() Does the right thing to get the inverse of the current Sequence.
SequenceView<C>	AbstractSequence.getInverse()
SequenceView<C>	SequenceProxyView.getInverse()
SequenceView<C>	Sequence.getSubSequence(Integer start, Integer end) Returns a portion of the sequence from the different positions.
SequenceView<C>	AbstractSequence.getSubSequence(Integer bioStart, Integer bioEnd)
SequenceView<C>	SequenceProxyView.getSubSequence(Integer bioStart, Integer bioEnd)
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 complement

Methods in org.biojava.nbio.core.sequence.template that return types with arguments of type SequenceView

Modifier and Type	Method and Description
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.

Uses of SequenceView in org.biojava.nbio.core.sequence.views

Classes in org.biojava.nbio.core.sequence.views that implement SequenceView

Modifier and Type	Class and Description
class	ComplementSequenceView<C extends ComplementCompound> For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g. base A will become base T
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	RnaSequenceView Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

Methods in org.biojava.nbio.core.sequence.views that return SequenceView

Modifier and Type	Method and Description
SequenceView<C>	WindowedSequence.get(int index) Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.

Methods in org.biojava.nbio.core.sequence.views that return types with arguments of type SequenceView

Modifier and Type	Method and Description
Iterator<SequenceView<C>>	WindowedSequence.iterator() Returns an iterator which will return the windows in a sequence in sequential order.