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Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 27 23:00:18 2018 UTC (19 months ago) by olson
Branch: MAIN
CVS Tags: HEAD
Changes since 1.45: +9 -0 lines
Diff to previous 1.45
Merge bob version

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 21 20:54:19 2018 UTC (19 months, 1 week ago) by parrello
Branch: MAIN
Changes since 1.44: +36 -0 lines
Diff to previous 1.44
Changes copied from SEEDtk project.

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 28 03:11:40 2018 UTC (2 years ago) by olson
Branch: MAIN
Changes since 1.43: +41 -9 lines
Diff to previous 1.43
Fixes

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 15 19:38:26 2017 UTC (2 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.42: +4 -25 lines
Diff to previous 1.42
Changes copied from SEEDtk project.

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 21 21:05:57 2017 UTC (3 years, 1 month ago) by parrello
Branch: MAIN
Changes since 1.41: +181 -28 lines
Diff to previous 1.41
Changes copied from SEEDtk project.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 16 02:55:56 2016 UTC (3 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.40: +4 -4 lines
Diff to previous 1.40
Changes copied from SEEDtk project.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 22 19:17:07 2016 UTC (4 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.39: +25 -1 lines
Diff to previous 1.39
Fix for incorrectly initialized genome objects.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 15 20:44:30 2015 UTC (4 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.38: +33 -18 lines
Diff to previous 1.38
Expose sorted_features method. make renumber_features use that, and don't make the renumber dependent on sorting by feature type first.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 15 19:23:08 2015 UTC (4 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.37: +50 -0 lines
Diff to previous 1.37
add bounds() and flattened_feature_aliases()

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 9 21:12:37 2015 UTC (4 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.36: +22 -8 lines
Diff to previous 1.36
When renumbering use the type in the identifier, not the type field.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 9 20:09:44 2015 UTC (4 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.35: +5 -5 lines
Diff to previous 1.35
Change hostname cached value key to start with _ so cleared before writing.
Fix error message for mismatched feature counts.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 31 23:13:33 2015 UTC (4 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.34: +143 -70 lines
Diff to previous 1.34
Break out the id generation from the rest of the add feature code
(there are multiple comments in the code as to why).
Improve condistency of time resolution on time stamps (use Time::HiRes).

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 25 17:55:21 2015 UTC (4 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.33: +18 -18 lines
Diff to previous 1.33
Changes copied from SEEDtk project.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 7 18:52:06 2015 UTC (4 years, 7 months ago) by golsen
Branch: MAIN
Changes since 1.32: +2 -11 lines
Diff to previous 1.32
Slight clean-up on add_contig.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 7 17:55:23 2015 UTC (4 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
another fix

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 7 17:52:50 2015 UTC (4 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.30: +0 -4 lines
Diff to previous 1.30
Fix contig indexing bug

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 10 17:12:01 2015 UTC (4 years, 8 months ago) by golsen
Branch: MAIN
Changes since 1.29: +797 -58 lines
Diff to previous 1.29
More sanity checks and access functions for GenomeTypeObjects.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 9 17:55:42 2015 UTC (4 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.28: +2 -2 lines
Diff to previous 1.28
Fix min bug.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 29 21:10:13 2015 UTC (4 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.27: +3 -2 lines
Diff to previous 1.27
add -id_type to add_feature

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 28 14:54:39 2015 UTC (4 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.26: +2 -1 lines
Diff to previous 1.26
Add owner field.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 20:57:15 2015 UTC (4 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.25: +11 -0 lines
Diff to previous 1.25
Add fig| prefix to naked genome IDs.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 24 20:31:44 2015 UTC (4 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.24: +26 -0 lines
Diff to previous 1.24
Changes copied from SEEDtk project.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 10 15:30:46 2015 UTC (4 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.23: +245 -243 lines
Diff to previous 1.23
Changes copied from SEEDtk project.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 25 04:58:26 2015 UTC (5 years ago) by parrello
Branch: MAIN
Changes since 1.22: +46 -32 lines
Diff to previous 1.22
Added destroy_to_file. Fixed error in analysis_event_id.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 25 20:24:20 2015 UTC (5 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.21: +3 -1 lines
Diff to previous 1.21
Update fields for genome metadata.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 28 17:31:30 2014 UTC (5 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.20: +123 -2 lines
Diff to previous 1.20
Add renumber

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 18 16:14:36 2014 UTC (5 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.19: +8 -0 lines
Diff to previous 1.19
Fixes for IS.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 20:41:28 2014 UTC (5 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0912
Changes since 1.18: +22 -0 lines
Diff to previous 1.18
Add gc computation.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 29 16:49:08 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0729
Changes since 1.17: +5 -2 lines
Diff to previous 1.17
write to alternate assigned_functions file if presented in options

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 28 20:48:10 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.16: +18 -1 lines
Diff to previous 1.16
add filtering on writing of sequence data

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 14 20:29:40 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.15: +29 -1 lines
Diff to previous 1.15
Genome object read/write to seed dir changes.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 11 21:47:48 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.14: +13 -0 lines
Diff to previous 1.14
Add annotations.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 11 21:23:43 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.13: +84 -43 lines
Diff to previous 1.13
Expand the funtionality of write_seed_dir.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 21:09:45 2014 UTC (5 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.12: +2 -1 lines
Diff to previous 1.12
another bug fix

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 20:44:16 2014 UTC (5 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.11: +7 -5 lines
Diff to previous 1.11
Fix bug in add_features_from_list

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 8 21:29:59 2014 UTC (5 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.10: +14 -4 lines
Diff to previous 1.10
Fix bug in the case where GenomeTypeObject::prepare_For_Return is called as a sub not a method

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 7 19:11:51 2014 UTC (5 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
fix nasty little typo

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 7 19:11:14 2014 UTC (5 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +39 -0 lines
Diff to previous 1.8
Add methods.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 6 20:01:13 2014 UTC (5 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.7: +17 -2 lines
Diff to previous 1.7
Remove requirement for Data::Structure::Util.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 1 19:00:46 2014 UTC (5 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.6: +209 -12 lines
Diff to previous 1.6
Modifications for new RAST2 services.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 24 15:27:57 2014 UTC (6 years ago) by olson
Branch: MAIN
Changes since 1.5: +31 -4 lines
Diff to previous 1.5
Use either UUID or Data::UUID.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 20 22:50:57 2014 UTC (6 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.4: +140 -0 lines
Diff to previous 1.4
Add contig index.
Add get_feature_dna
Add write_temp_seed_dir
Add create_from_file constructor.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 7 19:21:59 2014 UTC (6 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.3: +24 -15 lines
Diff to previous 1.3
Add support to add_feature for passing in a precomputed id - so we can do batch assignment of ids before
we get here.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 6 21:11:56 2014 UTC (6 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.2: +121 -2 lines
Diff to previous 1.2
modifications for new rast2 code

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 3 20:35:06 2013 UTC (6 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.1: +22 -10 lines
Diff to previous 1.1
Added translation and ID-server support.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 5 22:56:12 2013 UTC (6 years, 7 months ago) by gdpusch
Branch: MAIN
Initial checkin

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