bringing the example into line with the new 'get_adaptor' method, rather than the old 'db adaptor' way

Altering the feature iteration code to while and shift rather than foreaching the array. It's far more memory efficient as we are dumping data once we are finished with it

ENSCORESW-140. Issue caused by 1 length sequences. Fixed by changing the logic in fasta serialiser. Test cases now assert for length 1 seqs and for other potential scenarios.

ENSCORESW-138. Fixed the encoded entities by de-encoding them. Code is untested though and should be treated with caution

ENSCORESW-137. Code could not handle empty lines nor attributes with multiple entries. Hope this isn't going to mess up anything else

[ENSCORESW-136]. Adding count methods to the API. Also triggered bug fixing of SqlHelper which was not behaving as expected. Test cases added

changes to provide multispecies support and also to use a unified command line processor (CliHelper)

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108

change to allow overriding of the default exonerate method for multiple sources with the same name http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-134

replaced methods ExonerateGappedBest1_agam and ExonerateGappedBest1_culex with ExonerateGappedBest1_55_perc_id

Added proper support for limiting the back-catalogue of patches that can be applied by --fix through the --oldest option.

Fixed PUBMED::culex_quinquefasciatus; added three plants species, setaria_italica solanum_lycopersicum oryza_brachyantha

Unbreaks bug where these options weren't used properly.

Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd results