bioscala 0.1 API
bio.Protein

class Sequence
[source: bio/Protein/Sequence.scala]
class Sequence(aalist : scala.List[AminoAcid], attributelist : scala.List[Attribute])
extends Sequence[AminoAcid]
The (immutable) Amino acid sequence class represents a list of Protiein amino acids. Each sequence can carry a list of attributes, including the ID(s) and description(s).

Contrasting with most Bio* implementations, the Sequence class represents the contained amino acids as a List, not as a String. Also a Sequence may be represented by multiple ID's and descriptions in the form of flexible attributes.

As each amino acid is a real object, it may contain additional information.

For gapped and ambiguous sequences see the relevant traits.

See Also
GappedSequence
IUPACSequence
Additional Constructor Summary
def this (str : java.lang.String) : Sequence
def this (sequence : Sequence) : Sequence
def this (list : scala.List[AminoAcid]) : Sequence
def this (id : java.lang.String, descr : java.lang.String, str : java.lang.String) : Sequence
def this (id : java.lang.String, str : java.lang.String) : Sequence
Type Summary
type SequenceType
Values and Variables inherited from Sequence
seq, attributes
Method Summary
def create (seqlist : scala.List[AminoAcid], attributelist : scala.List[Attribute]) : Sequence
Every derived class should have a factory, so methods like 'delete', defined in the abstract class, work in a type safe way.
Methods inherited from Sequence
apply, toString, toList, idList, descriptionList, id, length, delete, hasDescription, description, attrAdd, attrAdd
Methods inherited from AttributeAccess
attribList, attribValues, attribFirst
Methods inherited from AnyRef
getClass, hashCode, equals, clone, notify, notifyAll, wait, wait, wait, finalize, ==, !=, eq, ne, synchronized
Methods inherited from Any
==, !=, isInstanceOf, asInstanceOf
Additional Constructor Details
def this(list : scala.List[AminoAcid]) : Sequence
def this(str : java.lang.String) : Sequence
def this(id : java.lang.String, str : java.lang.String) : Sequence
def this(id : java.lang.String, descr : java.lang.String, str : java.lang.String) : Sequence
def this(sequence : Sequence) : Sequence
Type Details
type SequenceType
Method Details
def create(seqlist : scala.List[AminoAcid], attributelist : scala.List[Attribute]) : Sequence
Every derived class should have a factory, so methods like 'delete', defined in the abstract class, work in a type safe way.
Overrides
Sequence.create
bioscala 0.1 API