aln2plot(): New function for alignment plotting

[Barry Grant]

I would like a plot() output equivalent of aln2html() with options for colored text and background. This aln2plot() function would allow coloring by property, conservation scores, etc. as well as residue number annotations and eventually our prototype fancy SSE annotations. Outputting to a PDF would result in useful alignment visualizations.

Printing from seaview, pfat, and boxshade are often not sufficiently flexible.

[Lars Skjærven]

I agree. I made an attempt some time ago with the plot.fasta function, but I'm not very satisfied with it. We should definitively revisit this.