For a complete overview of the APIs provided by these packages, please consult the JavaDoc documentation . When biological sequence data first became available, it was necessary to find a convenient way to communicate it. When this data was entered into computers, it was logical to use the same scheme. Today's computational biology software is based on normal string handling APIs. It is possible to pass any string to a routine which is expecting a biological sequence.
Any validation has to be performed on an ad hoc basis.
The meaning of each symbol is not necessarily clear. This class, and the others described here, are part of the Java package org.biojava.bio.symbol . They may optionally have a second property, token which defines the entity's standard representation in a string. The set of Symbol objects which may be found in a particular type of sequence data are defined in an Alphabet . It it always possible to define custom Symbols and Alphabets, but BioJava supplies a set of predefined alphabets for representing biological molecules.