GitLab

vega-49-dev'.

Sprout from master 2008-03-26 14:07:36 UTC Steve Trevanion <st3@sanger.ac.uk> 'merge from vega-48-dev'
Delete:
    misc-scripts/density_feature/vega_repeat_coverage_calc.pl
    misc-scripts/protein_match/process_pmach.pl
    modules/Bio/EnsEMBL/DBSQL/Clone.pm

fetchrow_arrayref() to speed up DB fetching by approx. 100 rows/sec.

'__END__'...

  Change SQL from 'code like "toplevel"' to 'code = "toplevel"'.

  Formatting

In all the feature adaptors, use either _create_feature() or
_create_feature_fast() from BaseFeatureAdaptor in _objs_from_sth() to
create features.

In get_available_adaptors(), add GeneCollection, TranscriptCollection,
ExonCollection, and RepeatFeatureCollection so that one may say, e.g.

  my $rfc = $registry->get_adaptor( 'Human', 'Core',
                                    'RepeatFeatureCollection' );

Add the methods _create_feature() and _create_feature_fast() that will
be called from _objs_from_sth() in the feature adaptors to create
features.

Turn _remap() into a proper method so that we're able to specialize it.

Beautify.

a string that can be 0 (zero).

Similarly use "if (exists( some hash compartment ))" for the same reason.

A couple of changes from "@{ function_returning_array_ref() }($index)"
to "function_returning_array_ref()->[$index]";

General cleanup in comments and code.

Passes the unit tests.

Proper new() for most classes:
  * $class = ref($proto) || $proto;
  * Setting attributes the same way.

Format the getter and setters the same way, especially in
Mapper/Coordinate.pm, getting rid of unneccesary shifts.

sprintf() formatting including '%1$s'.

Minor formatting.