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seq_edits processed on seq_regions. A cache of regions are made on creation of the adaptor, this hash is then used for fast testing to see if any seq_edit are needed for a given seq_region

Formatting of SYNOPSIS code.

Passes unit tests.

Using this code on databases not patched up to the v51 schema will fail.

A pre-merge tag was put in place just before this merge:

  pre-multispecies-merge (in ensembl/modules/Bio/EnsEMBL)

registry and not get_XXXAdaptor() explicitly.

modified execute calls to make compatible with other databases. Need to use bind_param first, with the type of the parameter, and execute later

Sequence retrieved from the database is now uppercased.  This is so that softmasking can still be performed correctly when mixed/lower case sequence is stored in the database.

added a caching algorithm to somewhat improve efficiency of certain usage patterns (such as transcript/prediction transcript dumps

modifications so that toplevel is now a pseudo coordinate system representing the highest real coordinate system in a given region

Updates so slices can handle negative strand, not finished yet, and not tested

Modified Clone store method so that it functions correctly.
Changed RawContig and Clone so that they can be instantiated w/o db connection.

    fetch_by_contig_id(int) -> fetch_by_Contig(RawContig)
  store(int, list of Features) -> store(list of Features with attached contigs)

So it get sequence for sanger/estgenes (in theory)

The sequence returned by fetch_by_contig_id_start_end_strand contained \s characters.  Now it does a s/\s//g on it before returning anything.

adding and debugging the get_all_Genes method on Slice.pm

Fixes to handle strandedness of slices and requested sequences in the fetch_by_Slice_start_end_strand method.