The alignment can be thought of as a rectangular array of ISymbols. Each row is indexed by a label and each column is indexed by offset (counting from 1).

Alternatively, it can be thought of as a ISymbolList where each ISymbol is a list of ISymbols in that column.

To create gapped alignments, use ISymbolLists with gaps. The most flexible way to do this will be to leverage IGappedSymbolList objects.

Original BioJava version by Matthew Pocock and Nimesh Singh. Port to C# by Doug Swisher.