cannot read FASTA with small caps letters

[rwst]

One output option at PFAM is usage of small caps to indicate non-conserved residues in multiple seq alignments. Trying to read such a file using BioJava results in an exception. It should be possible to read such files and treat small caps as normal AminoAcidCompound, leaving its interpretation to the user

[sbliven]

I've written some code to do this for one of my projects. I'll push it back into BioJava for you.