[Bioperl-guts-l] [bioperl/bioperl-live] 52e52e: within_element works better

[noreply at github.com]

Branch: refs/heads/release-1-6-2
Home:   https://github.com/bioperl/bioperl-live

Commit: 52e52e6634d2ebfd8e884e5a227702d99c67cd9f
    https://github.com/bioperl/bioperl-live/commit/52e52e6634d2ebfd8e884e5a227702d99c67cd9f
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-12 (Sat, 12 Mar 2011)

Changed paths:
  M Bio/SeqIO/seqxml.pm

Log Message:
-----------
within_element works better


Commit: 117af47b74c1af820a1ab99b71d2a8f45fbae75b
    https://github.com/bioperl/bioperl-live/commit/117af47b74c1af820a1ab99b71d2a8f45fbae75b
Author: hyphaltip <jason at bioperl.org>
Date:   2011-03-14 (Mon, 14 Mar 2011)

Changed paths:
  M Bio/SearchIO/exonerate.pm

Log Message:
-----------
bug reported by sebastien.theil at clermont.inra.fr -- white space before Query now


Commit: 8a5c827e4fb636de73ac5d6d59e0e5893929fd0a
    https://github.com/bioperl/bioperl-live/commit/8a5c827e4fb636de73ac5d6d59e0e5893929fd0a
Author: hyphaltip <jason at bioperl.org>
Date:   2011-03-14 (Mon, 14 Mar 2011)

Changed paths:
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/sam.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/Root/Root.pm
  M Bio/SeqIO/seqxml.pm
  M Bio/Tree/TreeFunctionsI.pm
  M README
  M t/Map/Map.t
  M t/RemoteDB/CUTG.t
  M t/Root/RootI.t

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


Commit: ef979d29bb52b0f0272f894d853bb60342d675da
    https://github.com/bioperl/bioperl-live/commit/ef979d29bb52b0f0272f894d853bb60342d675da
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-16 (Wed, 16 Mar 2011)

Changed paths:
  M Bio/Root/RootI.pm

Log Message:
-----------
improved _rearrange performance by 30%


Commit: 108312d817e06bfa501322df974049564b5c9186
    https://github.com/bioperl/bioperl-live/commit/108312d817e06bfa501322df974049564b5c9186
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-16 (Wed, 16 Mar 2011)

Changed paths:
  M Bio/SeqFeature/Generic.pm

Log Message:
-----------
improved Bio::SeqFeature::Generic::has_tag performance by about 30%


Commit: 68a5215cd25a20c14d2e5fa5e65838958fb8fc73
    https://github.com/bioperl/bioperl-live/commit/68a5215cd25a20c14d2e5fa5e65838958fb8fc73
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-16 (Wed, 16 Mar 2011)

Changed paths:
  M Bio/Location/Atomic.pm

Log Message:
-----------
fix big performance regression in which _load_module was getting called every time(!) a new Bio::Location::Atomic (and subclasses) was created


Commit: e40cfe6c2c3296eb33db1abf8564329208d8b18a
    https://github.com/bioperl/bioperl-live/commit/e40cfe6c2c3296eb33db1abf8564329208d8b18a
Author: Robert Buels <rmb32 at cornell.edu>
Date:   2011-03-16 (Wed, 16 Mar 2011)

Changed paths:
  M Bio/SearchIO/exonerate.pm
  M t/SearchIO/exonerate.t
  A t/data/exonerate.whitespace_before_query.works

Log Message:
-----------
add test for leading whitespace before exonerate query, fix to work with old exonerate format (you should run the tests hyphaltip!)


Commit: 97074c7844a9e9aec48c2a5c7fca31a5bdb89e54
    https://github.com/bioperl/bioperl-live/commit/97074c7844a9e9aec48c2a5c7fca31a5bdb89e54
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-17 (Thu, 17 Mar 2011)

Changed paths:
  M MANIFEST

Log Message:
-----------
update manifest


Commit: 54fb1e79accad148fec0da4b777b654da4e25a57
    https://github.com/bioperl/bioperl-live/commit/54fb1e79accad148fec0da4b777b654da4e25a57
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-17 (Thu, 17 Mar 2011)

Changed paths:
  M t/Map/Map.t

Log Message:
-----------
Revert "volatile data broke test".  Remote database changed data back.

This reverts commit 4b69c5e4333990821def4a3a5db2b8645da71b6c.


Commit: a037bef80334d2387b32148879ddd7f2bfaaa310
    https://github.com/bioperl/bioperl-live/commit/a037bef80334d2387b32148879ddd7f2bfaaa310
Author: Chris Fields <cjfields at bioperl.org>
Date:   2011-03-17 (Thu, 17 Mar 2011)

Log Message:
-----------
Merge branch 'release-1-6-2' of github.com:bioperl/bioperl-live into release-1-6-2


Compare: https://github.com/bioperl/bioperl-live/compare/b67875a...a037bef