GitLab

Removed contig_list definition from clone constructor. Ctgs were not retrieved if list was defined

Sped up general feature creation a bit more

was assuming a straight array.

Superfamily SeqFeatures were created with analysis=>analysisid instead of analysis=>analysis, which made SeqFeature choke.  Fix0red.

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.

-Sped up general feature retrieval a little bit

functional but needs more work

Added GeneWrapper and SliceWrappers so embl dump works with new main trunk

These were causing infinite recursion due to new superclass implementation of entire_seq, attach_seq, and contig methods

- RawContigAdaptor->store and CloneAdaptor->store adjusted to set both dbID and adaptor of stored objects

for raw_contig <-> slice and slice <-> slice
(transform() and _transfrom_XXX())

added is_splittable() (default 0)

cleaned up contig(), entire_seq() and attach_seq()

(this isn't being set). if someone can find a better way, please do