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Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 25 21:01:46 2009 UTC (10 years ago) by parrello
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.24: +21 -0 lines
Diff to previous 1.24
Added a method to compute the total location length.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 17 20:42:53 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_release_2008_09_29
Changes since 1.23: +13 -2 lines
Diff to previous 1.23
Fix translation gunk.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 14 09:07:39 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_06_16
Changes since 1.22: +5 -6 lines
Diff to previous 1.22
Changed the name of the Constrain function to avoid a naming conflict. Fixed a comment.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 29 05:32:10 2008 UTC (11 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.21: +2 -3 lines
Diff to previous 1.21
Fixed the pod docs.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 5 01:51:44 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.20: +255 -235 lines
Diff to previous 1.20
Added new support for gene boundary methods.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 25 20:19:50 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.19: +8 -2 lines
Diff to previous 1.19
Fixed so that the location is not changed if  pick-gene-boundaries call fails.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 25 18:53:35 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.18: +21 -12 lines
Diff to previous 1.18
Changed PickGeneBoundaries to use option-style parameters. Added tracing for search failures at level 3.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 24 04:19:14 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.17: +39 -28 lines
Diff to previous 1.17
Changed PickGeneBoundaries to allow specification of a location as a search limit and to fail if one of the searches fails.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 19 06:03:34 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
Fixed an even stupider bug.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 19 05:57:22 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
Fixed a stupid error.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 19 05:54:47 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.14: +28 -34 lines
Diff to previous 1.14
Fixed PickGeneBoundaries to recover more gracefully when unable to find a stop codon.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 19 03:46:33 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.13: +332 -99 lines
Diff to previous 1.13
Revamped DNA searching to be more compatible with the requirements of picking gene boundaries. Extended to allow for specifying translation codes in the constructor.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 18 23:11:02 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.12: +152 -175 lines
Diff to previous 1.12
Replaced Search so that it does what the documentation says, which is to stop searching at the specified limit. Added the ability to omit the limit and simply search to the end of the location.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 6 13:59:34 2007 UTC (12 years ago) by parrello
Branch: MAIN
Changes since 1.11: +20 -20 lines
Diff to previous 1.11
Changed POD format for better compatability with Wiki.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 11 17:27:54 2007 UTC (12 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Removed a FIG dependency that was causing duplicate-method warnings.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.9: +17 -0 lines
Diff to previous 1.9
Added license words.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 10 07:38:44 2005 UTC (14 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.8: +183 -92 lines
Diff to previous 1.8
Fixed the Search method to handle cases where it must search more than 9000 base pairs.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 17:24:27 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.7: +7 -6 lines
Diff to previous 1.7
Fixed a bug in the section of "ExtremeCodon" that adjusts to the trailing edge of a codon.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 03:59:19 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.6: +11 -4 lines
Diff to previous 1.6
Fixed an error in "Search" that goofed things up if the desired codon pattern was not found.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 5 17:43:53 2005 UTC (14 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fix bad bug in calling starts

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 31 16:29:33 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.4: +44 -16 lines
Diff to previous 1.4
Updated the Extend method to allow extending inward.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jul 31 00:40:24 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.3: +33 -4 lines
Diff to previous 1.3
Fixed a bug in the handling of ExtremeCodon when the direction is to the right.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 30 23:53:16 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.2: +49 -0 lines
Diff to previous 1.2
Added new ExtremeCodon method.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 27 19:43:33 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.1: +216 -26 lines
Diff to previous 1.1
Added new methods for extracting codon DNA and accessing points near each end of a location.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 26 20:07:58 2005 UTC (14 years, 4 months ago) by parrello
Branch: MAIN
Added new FullLocation object for manipulation sequences of locations.

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