change Version{1,2} warning message

code-deduplication: mburnett, nnutter
extract reference_sequence_id method

code-deduplication: mburnett, nnutter
move _transcript_substruct_annotation to base

code-deduplication: mburnett, nnutter
delegate _transcript_substruct_annotation to base

code-deduplication: mburnett, nnutter
make base abstract

code-deduplication: mburnett, nnutter
extract should_update_variant_attributes method

code-deduplication: mburnett, nnutter
remove unused variable

code-deduplication: mburnett, nnutter
extract trv_type and protein_string calculation

code-deduplication: mburnett, nnutter
extract tnv_type and protein_string methods (V2)

code-deduplication: mburnett, nnutter
extract trv_type and protein_string methods (V3)

code-deduplication: mburnett, nnutter
move _transcript_annotation_for_cds_exon to base

code-deduplication: mburnett, nnutter