Fixing a bug in WriteScores where random files and McBasc files were
getting confused...
Fixed issues with relative paths in some of the test suite, so that it
would use the packaged pnase.txt file regardless of other variables.
Fixed ability to append new start/stop information to
bestPfamLines_pfamToPDB.txt
Unclear to me what is happening with push-pull.  May have lost a family
or added one without knowing?
Would appear that excluding Energenetics.properties has caused issues
Merge branch 'master' of https://github.com/afodor/cobs

Conflicts:
	cobs/Energetics.properties
	cobs/test/SangerPDBpfamMappingTest.class
Shows output as a toString has been added, so the main method "proves"
the parsing is working.
Added logic to skip PFAM members that had no associated PDB.  Next, I
will eliminate the checking for the exhaustive list of PFAM families,
this seems like extra work to no end.
Hopefully I updated the correct columns here!  Not clear which of the 4
we are using for what...which is probably my fault.
Added logic to only test PFAM alignments we have in the paper.  Output
in console seems to run without issue.  Need to follow up on what
exactly we are looking for here.  Maybe some asserts should be added?
Merge branch 'master' into kyleBranch