/[v1]/trunk/c++/src/app/asn_cleanup/huge_file_cleanup.cpp
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Log of /trunk/c++/src/app/asn_cleanup/huge_file_cleanup.cpp

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Revision 101210 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 16 14:19:11 2023 UTC (5 months, 2 weeks ago) by gotvyans
File length: 24907 byte(s)
Copied from: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp revision 101209
Diff to previous 99315 
JIRA: RW-2144
Moved huge_file_cleanup.cpp to asn_cleanup
May be temporarly until other parts of huge mode processing
are ready for a dedicated folder
Revision 99315 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 8 20:23:24 2023 UTC (13 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 24910 byte(s)
Diff to previous 99308 
JIRA: RW-1942 Some final tweaks. Only fix colliding feature ids in extended cleanup. Do not call CFixFeatureId::s_ApplyToSeqInSet() in huge-file mode
Revision 99308 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 8 16:58:36 2023 UTC (13 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 24538 byte(s)
Diff to previous 99288 
JIRA: RW-1942 Some cleanup. Added CCleanupHugeAsnReader::TFeatIdInfo
Revision 99288 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 7 15:11:18 2023 UTC (13 months, 4 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 24045 byte(s)
Diff to previous 99251 
JIRA: RW-1942 Fix colliding feature ids when small-genome sets are enabled
Revision 99251 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 2 18:52:42 2023 UTC (14 months ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 23829 byte(s)
Diff to previous 99238 
JIRA: RW-1942 Added code for updating colliding feature ids. Still need to test this, and it doesn't yet work for small-genome sets.
Revision 99238 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 1 16:53:54 2023 UTC (14 months ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 21297 byte(s)
Diff to previous 99221 
JIRA: RW-1942 Use CSeq_feat hooks to record feature-id information. This change allows us to skip over the feature ids appearing in Xrefs.
Revision 99221 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 28 18:53:36 2023 UTC (14 months ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 21822 byte(s)
Diff to previous 99212 
JIRA: RW-1942 Reworked code for recording colliding feature ids in huge-fule mode. This is still a work in progress and is not yet working as intended
Revision 99212 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 27 16:35:26 2023 UTC (14 months ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 19419 byte(s)
Diff to previous 99171 
JIRA: RW-1942 Some hacky prototype code.
Revision 99171 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 22 15:25:24 2023 UTC (14 months, 1 week ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 15893 byte(s)
Diff to previous 98857 
JIRA: RW-1942 Some preparatory work. Moved code that sets feature-id hooks into its own method
Revision 98857 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 13 18:43:15 2023 UTC (15 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 15358 byte(s)
Diff to previous 98856 
JIRA: RW-1830 Reverted the changes in logic introduced in r661575 and r661574. I'm not so sure the original logic was incorrect.
Revision 98856 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 13 18:05:49 2023 UTC (15 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 15590 byte(s)
Diff to previous 98844 
JIRA: RW-1830 Modified behaviour in huge-file mode to match the latest change to CInfluenzaSet.
Revision 98844 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 12 19:14:34 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 15330 byte(s)
Diff to previous 98835 
JIRA: RW-1830 Minor housekeeping. Changed the names of some variables and functions
Revision 98835 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 11 19:48:55 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 15189 byte(s)
Diff to previous 98825 
JIRA: RW-1830 Some housekeeping
Revision 98825 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 10 19:54:37 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 14845 byte(s)
Diff to previous 98817 
JIRA: RW-1830 Use flu labels to order small-genome sets
Revision 98817 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 10 17:20:09 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 14782 byte(s)
Diff to previous 98816 
JIRA: RW-1830 modified the code so that small-genome sets appear after other sets and sequences. This is what happens in regular mode
Revision 98816 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 10 15:56:13 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 14576 byte(s)
Diff to previous 98810 
JIRA: RW-1830 Bug fixes
Revision 98810 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 9 18:43:01 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 14792 byte(s)
Diff to previous 98806 
JIRA: RW-1830 Relax id checks to make the accession versions optional
Revision 98806 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 9 15:44:28 2023 UTC (15 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 14052 byte(s)
Diff to previous 98781 
JIRA: RW-1830 Added check for partial features. Also, some bug fixes and tweaks.
Revision 98781 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 5 16:38:02 2023 UTC (15 months, 4 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 11598 byte(s)
Diff to previous 98658 
JIRA: RW-1830 Partial implementation of the new functionality. The new code is incomplete because it doesn't check for partial feature locations. Sequences with incomplete genes or coding regions are not wrapped in small-genome sets.
Revision 98658 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Dec 16 15:11:31 2022 UTC (16 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 6217 byte(s)
Diff to previous 98650 
JIRA: RW-1857 Overrode LoadSeqEntry(const TBioseqSetInfo&, eAddTopEntry) in CCleanupHugeAsnReader
Revision 98650 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 15 19:13:48 2022 UTC (16 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 6856 byte(s)
Diff to previous 98647 
JIRA: RW-1857 Hold off on overriding LoadSeqEntry() in CCleanupHugeAsnReader until I understand asn_cleanup a little better
Revision 98647 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 15 17:02:14 2022 UTC (16 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 7083 byte(s)
Diff to previous 98640 
JIRA: RW-1857 added code for sorting top-level descriptors. Added some skeleton code for CCleanupHugeAsnReader::LoadSeqEntry()
Revision 98640 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 14 19:38:26 2022 UTC (16 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 5799 byte(s)
Diff to previous 98636 
JIRA: RW-1857 Implemented code for adding NCBI user objects in huge-file mode. It appears to be working, but needs a bit more refinement and testing.
Revision 98636 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 14 16:28:35 2022 UTC (16 months, 2 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 5549 byte(s)
Diff to previous 98630 
JIRA: RW-1857 CCleanupHugeAsnReader::m_Changes is no longer a reference to another instance of CCleanupChangeCore. Added a CCleanupHugeAsnReader::GetChanges() method.
Revision 98630 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 13 20:17:41 2022 UTC (16 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 5502 byte(s)
Diff to previous 98628 
JIRA: RW-1857 Added code for logging changes
Revision 98628 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 13 18:15:50 2022 UTC (16 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 5053 byte(s)
Diff to previous 98610 
JIRA: RW-1857 Added code for moving top-level descriptors.
Revision 98610 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 12 16:35:27 2022 UTC (16 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 3853 byte(s)
Diff to previous 98605 
JIRA: RW-1857 Added CCleanupHugeAsnReader::x_CleanupTopLevelDescriptors().
Revision 98605 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 12 13:05:34 2022 UTC (16 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 2896 byte(s)
Diff to previous 98598 
JIRA: RW-1857 Cleaned up handling of genbank-set descriptors in regular mode.
Revision 98598 - (view) (download) (as text) (annotate) - [select for diffs]
Added Fri Dec 9 15:21:08 2022 UTC (16 months, 3 weeks ago) by foleyjp
Original Path: trunk/c++/src/objtools/cleanup/huge_file_cleanup.cpp
File length: 2895 byte(s) 
JIRA: RW-1857 Created CCleanupHugeAsnReader. Overrode the FlattenGenbankSet() method to handle eClass_not_set conversions in cleanup.

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