GitLab

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.

added 2 new attributes in protein and dna alignFeatures to get the name of the external database and the displayable name

query and target (respectively) covered by the feature

Added methods: hseq_region_name, hseq_region_strand, hseq_region_start and hseq_region_end, that return something if hslice is defined

Added group_id, level_id methods as well as hslice. Modified in consequence the invert method to set hslice

Added identical_matches and positive_matches methods mainly for use in homologous gene pairing pipeline, but may be useful for others

database used for transform is _always_ taken from slice/contig (i.e. not feature or exon)
tidied up a bit in SeqFeature and BaseAlignFeature

Applied a uniform format to gffstrings between SeqFeature and FeaturePair - the first seven columns will be conserved and any extra information for a FeaturePair gffstring is appended after this.  FeaturePair now calls the superclass gffstring method from SeqFeature and then appends extra columns.