| Modifier and Type | Class and Description |
|---|---|
class |
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>
Implements a data structure for a
Sequence within an alignment. |
| Modifier and Type | Interface and Description |
|---|---|
interface |
AlignedSequence<S extends Sequence<C>,C extends Compound>
Defines a data structure for a
Sequence within an alignment. |
interface |
MutableAlignedSequence<S extends Sequence<C>,C extends Compound>
Defines a mutable (editable) data structure for an
AlignedSequence. |
| Modifier and Type | Class and Description |
|---|---|
class |
BasicSequence<C extends Compound>
Bare bones version of the Sequence object to be used sparingly.
|
class |
CDSSequence
Represents a exon or coding sequence in a gene.
|
class |
ChromosomeSequence
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
|
class |
DNASequence
This is class should model the attributes associated with a DNA sequence
|
class |
ExonSequence
A gene contains a collection of Exon sequences
|
class |
GeneSequence |
class |
IntronSequence |
class |
ProteinSequence
The representation of a ProteinSequence
|
class |
RNASequence
RNASequence where RNACompoundSet are the allowed values
|
class |
StartCodonSequence
Used to map the start codon feature on a gene
|
class |
StopCodonSequence
Used to map the stop codon sequence on a gene
|
class |
TranscriptSequence
This is the sequence if you want to go from a gene sequence to a protein sequence.
|
| Modifier and Type | Class and 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.
|
| Modifier and Type | Class and Description |
|---|---|
static class |
InsdcLocations.BondLocation
Used to represent bond locations equivalent to bond(7,8) or bond(7).
|
static class |
InsdcLocations.GroupLocation
Deprecated in INSDC yet still appears; equivalent to the order()
directive except no 5' to 3' ordering is defined.
|
static class |
InsdcLocations.OneOfLocation
Deprecated in INSDC; refers to a set of locations of which one
location could be valid e.g. one-of(location, location, location).
|
static class |
InsdcLocations.OrderLocation
Used to describe a 5' to 3' ordering but no firm assurance it is correct
|
class |
SequenceLocation<S extends AbstractSequence<C>,C extends Compound>
A location in a sequence that keeps a reference to its parent sequence
|
class |
SimpleLocation
Very basic implementation of the Location interface which defines a series
of simple constructors.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
AccesionedLocation
A location which is bound to an AccessionID.
|
interface |
Location
Sets of integers used to represent the location of features on sequence.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractLocation
Base abstraction of a location which encodes for the majority of important
features about a location such as the start, end and strand
|
| Modifier and Type | Class and Description |
|---|---|
class |
ArrayListSequenceReader<C extends Compound>
Stores a Sequence as a collection of compounds in an ArrayList
|
class |
BitSequenceReader<C extends Compound>
An implementation of the popular bit encodings.
|
class |
FourBitSequenceReader<C extends Compound>
Four bit encoding of the bit formats.
|
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 |
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).
|
class |
TwoBitSequenceReader<C extends NucleotideCompound>
Implementation of the 2bit encoding.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
ProxySequenceReader<C extends Compound> |
interface |
Sequence<C extends Compound>
Main interface for defining a collection of Compounds and accessing them
using biological indexes
|
interface |
SequenceReader<C extends Compound> |
interface |
SequenceView<C extends Compound> |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSequence<C extends Compound>
The base class for DNA, RNA and Protein sequences.
|
class |
SequenceProxyView<C extends Compound> |
| 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.
|
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