Merging major change to master, resolves issue #29

[cerebis]

Resolving issue #29 was accomplished by definition a community profile object hierarchy, to include the notion of a Molecule which contains Segments. This replaces the bottom-most object which was merely the sequence records.

Now, users must specify in the community profile the molecule to which each sequence belongs. This allows the use of draft genomes -- which dominate the public sequence databases.

The tab-delimited flat community profile table now included a 4th mandatory column. The keys used for molecules are not special and can be whatever the user chooses. The header column is not required and any line beginning with a # is treated as a comment.

#chrom    cell     molecule      abundance    copy_number
contig1   e.coli   chromosome    0.6           1
contig2   e.coli   chromosome    0.2           1
contig3   e.coli   plasmid       0.1           4
contig4   b.subt   chrom_xyz     0.05          1
contig5   s.aur    foobar        0.05          1