Sequence

Sequences are the core data of the Bio++ libraries. They come as character chains, from text files or from a database. In order to be able to interpret a sequence, an alphabet is required. It will be used to encode the sequence en ensure the trnaslation between computer representation and human representation. A sequence can in some cases be associated with several features, like gene annotations or quality scores.

Depending on the user's need, there are several ways to manipulate sequences in Bio++.

Sequences as strings
The simplest way to manipulate sequences is to store them as character strings (using std::string). The class StringSequenceTools offers several methods to process such sequences. while being the easiest way to process sequences, this option is rather limited as it comes to perform more complexe data manipulation, particularly when states have more than one character (for instance: codon sequences).

Sequences as dedicated objects
Most methods in Bio++ will required a full object implementation of sequence data. In Bio++ 2.00, the class hierarchy has been rewritten in order to accomodate several implementations. It is however to a large extent backward compatible with previous versions of Bio++.