This object is able to read a substitution matrix file and constructs an int matrix to store the matrix. Every single element of the matrix can be accessed by the method GetValueAt with the parameters being two biosharp symbols. This is why it is not necessary to access the matrix directly. If there is no value for the two specified ISymbols an Exception is thrown.

Substitution matrix files, are available at the NCBI FTP directory - ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/.

Original BioJava version by Andreas Dräger. Port to C# by Doug Swisher.