[Bioperl-guts-l] [bioperl/bioperl-live] b24365: Minor clarifications

[noreply at github.com]

Branch: refs/heads/master
Home:   https://github.com/bioperl/bioperl-live

Commit: b243657c2535b72506b52c9976723f1cfbaa66e3
    https://github.com/bioperl/bioperl-live/commit/b243657c2535b72506b52c9976723f1cfbaa66e3
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm

Log Message:
-----------
Minor clarifications


Commit: 47d40eb698b9ba65c1602524a0ca2b9745541b38
    https://github.com/bioperl/bioperl-live/commit/47d40eb698b9ba65c1602524a0ca2b9745541b38
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Changed fetch_seqfeatures() so that it uses direct lookup instead of grep()
Added test cases for adding and retrieving subfeatures


Commit: 8eef131ebd4b7b14d9997b503f4e90bb46a990fd
    https://github.com/bioperl/bioperl-live/commit/8eef131ebd4b7b14d9997b503f4e90bb46a990fd
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Little fix for fetch_SeqFeature and more tests


Commit: a2e6ea56015df8264b536ded1e06d2313f8df84d
    https://github.com/bioperl/bioperl-live/commit/a2e6ea56015df8264b536ded1e06d2313f8df84d
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Little fix for fetch_SeqFeature and more tests


Commit: fef99a49b4feb022a5bb6a4a2243ac3c093ebe24
    https://github.com/bioperl/bioperl-live/commit/fef99a49b4feb022a5bb6a4a2243ac3c093ebe24
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M t/Assembly/core.t

Log Message:
-----------
Migrated SeqFeatures in assemblies to Bio::DB::SeqFeature::Store::memory
This finishes the migration of all Bio::Assembly code to Bio::DB::SeqFeature::Store facility!
As a consequence, assembly-related operations are much faster, have a computation time proportional to the number of reads in contigs (instead of exponential), and are thus more adapted to process high-throughput assemblies


Commit: b77433064ca70873f5330a59366cb70e1ab5c191
    https://github.com/bioperl/bioperl-live/commit/b77433064ca70873f5330a59366cb70e1ab5c191
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/maq.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Assembly/Tools/ContigSpectrum.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M t/Assembly/core.t
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Merge branch 'assembly_seqfeature_store'


Commit: 7407a262fe98bf241ec932bfbcb2aced432abe93
    https://github.com/bioperl/bioperl-live/commit/7407a262fe98bf241ec932bfbcb2aced432abe93
Author: Florent Angly <florent.angly at gmail.com>
Date:   2011-03-04 (Fri, 04 Mar 2011)

Changed paths:
  M Bio/AlignIO/stockholm.pm
  M Bio/Restriction/Analysis.pm
  M t/Restriction/Analysis.t

Log Message:
-----------
Merge branch 'master' of github.com:bioperl/bioperl-live


Compare: https://github.com/bioperl/bioperl-live/compare/6a79bde...7407a26