add_indel_coordinates subroutine was defined twice. Probably the result of a mistaken copy/paste or related

added section to deal with alleles and transcripts on different strands.  Changed  creating consequenc type using allele strand to creating the consequenceType using the transcript strand.  Changed code so empty object is added to the array rather than none so the number of ConsequenceType Objects matches the number of allele objects

Also refactoring.

Extended xref.display_label to 255 chars (from 40) to deal with "[from ..." suffix for projected names.

Added the "regulated_object_info" to enble access of the regulatory_feature_object.evidence and regulatory_feature_object.influence attributes.

change to api version

 Added warning to fix the error message <Can't locate object method "warn" via package "Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor">

Bug fix: is_known() was returning true if the transcript had a display_xref set, which is both incorrect and inconsitent with the is_known() method in Gene.pm. New behaviour is to return true if the transcript's status is KNOWN.