Representation of a molecular sequence.

A unique identifier for this particular sequence instance.

Allows sequences to be distinguished and referenced.

The type of the Molecular Sequence (Amino Acid Sequence, DNA Sequence, RNA Sequence).

A literal representation of a Molecular Sequence.

The primary (linear) sequence, expressed as a literal string.

Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.

A Molecular Sequence that is represented as an ordered series of edits on a specified starting sequence.

The Molecular Sequence that serves as the starting sequence, on which edits will be applied.

An edit (change) made to a sequence.

Edits are applied sequentially. The sequence that results from one edit operation is used as the 'starting' sequence of the next edit operation.

The order of this edit, relative to other edits on the starting sequence.

The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based.

The start coordinate of the interval that will be edited.

The end coordinate of the interval that will be edited.

The sequence that defines the replacement sequence used in the edit operation.

The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit.

A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence.

The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted.

The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted.

The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted.

The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based.

A flag that indicates whether the extracted sequence should be reverse complemented.

This attribute might be needed in all sequence representation classes, so that any sequence representation could be reverseComplemented.

A Molecular Sequence that is represented as a repeated sequence motif.

This class represents motifs that occur in tandem (immediately adjacent to each other) and without edits (each copy of the motif is identical).

The sequence that defines the repeated motif.

The number of repeats (copies) of the sequence motif.

A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences.

One element of a concatenated Molecular Sequence.

At least two sequenceElement elements are required to represent a concatenated sequence.

The Molecular Sequence corresponding to this element.

The ordinal position of this sequence element within the concatenated Molecular Sequence.

0 or 1 based indices are possible, could potentially skip numbers in the sequence, suggest implementers sort numerically prior to concatenating