Improved process communication. Implemented parsing.

Temporary utility to dump xref sequences to a FASTA file. Needed for development/debugging of xref mapping system.

Temporary utility to dump Ensembl transcript sequences to a FASTA file. Needed for development/debugging of xref mapping system.

Added storing of dependent xref label and linkage annotation (mainly for GO dependent xrefs so far).

Added seq_region_id index to density_feature (speeds up some queries, particularly those used in the DensityFeatures healthcheck)

much code duplication removed by adding load_adaptors which other load methods call. load_adaptors is now also called if an unknown DBAdaptor is passed (which could happen with registry autoloading. Added a test for variation adaptor

Laura detected subtle repeat_masked sequence bug. On reverse strand sequence, masking happened after reverse complementing, putting it into wrong spot

all objs_from_sth have a small buglet, fixed for this one. Features overhanging the slice and not overlapping were not filtered out

Added get_available_adaptors to get the pairs of name / adaptor modules. This should make it easier to read etc