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Modified to deal with alt_scaffold_placement.txt ori=b, to process the files from GRC (skipping previously loaded patches) and load the patches into the supercontig level of the assembly (as well as chromosome and contig) along with the chrom-supercontig and supercontig-chrom mappings.

Clean up comment code that had unbalanced quotes and parens (causing
Pdoc to break).

sb23: fixed get_species_and_object_type - check port as well as host. Also, don't die. Die is bad. Why would you die when you can return undef and not totally break the web code?

ensembl-61'.

Sprout from master 2011-01-18 13:58:26 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Generate code to remove master table entries marked with is_current = 0.'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Added ensembl_object_type and ensembl_id methods so that IF the dbentry is connected to a specific Ensembl entity (Gene/Transcript/Translation) then we can easily find out which one it is

Asking for a a GOTerm adaptor, or a SOTerm adaptor, still works, but the
correct call to get_adaptor() should request an OntologyTerm adaptor.

  the array objects instead of dereferencing using integer indexes from
  for-loops, and use [-1] instead of [$#$ea].

the form "host:port", with ":port" being optional (default is 3306).