release document:  Make sure that the regular expression doesn't match
too much.

inefficiently implemented.

added _register_chained_special for projection to the same coord system. Only accessed vis project_to_slice

  Returns an array of bins, each bin containing the fraction of the bin
  that is coverage by any feature.

The current implementation is correct but inefficient.

  Returns an array of bins, each bin containing the sum of the fractions
  of features overlapping that bin.  A feature fully inside a bin will
  contribute 1 to the sum while a feature spanning exactly three bins
  (from the very start of the first to the very end of the third) will
  contribute 1/3 to the sum of each bin.

register_chained - has new optional argument of to_slice, the slice to register, ignoring others. SQL changed to only get those in the slcie requird if argument is passsed.

object creation time:

  Rename method lightweight() as is_lightweight().

  Remove -light argument from method populate().

Add example to SYNOPSIS of how to restrict by analysis.logic_name.

Further small modifications of POD.

analysis.logic_name by using -analysis in the constructor, e.g.
"-analysis => 'Dust'" (for a feature collection of repeat features).

Each Collection sub-class needs to specialize the _has_analysis() method
so that it returns true if there is an analysis_id in the main feature
table for that feature type.

the feature specific part.

implem'ted.

Do some argument checking in get_bins().

Move some code around.

and ProteinAlignFeature.  Currently gets all data from the
{dna,protein}_align_feature tables without no join to any other table.

  Flushes (deletes) all cached data not associated with the current
  slice.

Also store the projection segments and the mapping from seq_region_ids
to the projection segments in the class.

Added external_db_id and hcoverage, for the 2 new columns in dna_align_feature and protein_align_feature.

lines shorter.