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Fix warnings; JIRA:RW-2143
JIRA: RW-1908 Removed redundant method
JIRA:RW-1908 In Basic cleanup, check that Bioseq for a molinfo descriptor is in scope before attempting to edit it
xcleanup: Remove NULLs; JIRA:RW-1283
JIRA: RW-1441 Bug fix. Cleanup should convert muids to pmids in Seq-feat.cit
JIRA:RW-1283 Remove trailing whitespace
JIRA: RW-1353 Bug fix
JIRA: RW-1353 Merge changes into trunk
JIRA: RW-1353 - Removed redundant CAutogeneratedCleanup method and redundant argument in CNewCleanup_imp method
JIRA: RW-1353 Removed nonsensical assertion
JIRA: RW-1317 Merge changes into trunk (second attempt)
JIRA: RW-1317 Reverted merge into trunk
JIRA: RW-1317 Merge changes into trunk
excluded autogenerated code
change to structure of cleanup (do field cleanup in User-object cleanup)
JIRA:SQD-4254 Single-strandedness from non-viral nucleotide sequences is removed now
JIRA:GCOL-6148 need to clean dbtag in source dbxref
JIRA:GCOL-6148 still need to clean dbtags in xrefs
JIRA:SQD-3714 only convert whole to int for seqfeat.location
JIRA:BIOS-995 added BioSample autofixes to BasicCleanup
JIRA:SQD-2360
synchronizing with comment tilde fixes in C Toolkit
JIRA:SQD-2208
JIRA:SQD-2205
JIRA:SQD-2211
JIRA:SQD-2228
JIRA:SQD-2206
JIRA:GB-4001 cleanup of both strand restricted to certain feature types
JIRA:SQD-2228
JIRA:SQD-2228
JIRA:SQD-2228
JIRA:SQD-2228
JIRA:SQD-2224
JIRA:SQD-2224
JIRA:SQD-2224 also segset problem
JIRA:SQD-2228
JIRA:SQD-2228
JIRA:SQD-2219
JIRA:SQD-2219
* do genetic code auto-correction (like "-K c" in C cleanasn ) JIRA SQD-1002
* Do not rescue codon recognized fom the feature comment. JIRA SQD-1052 * BioSource seq-feat comments turned into subsources of type "other" * All BioSource seq-feats of type other are merged together with "; " JIRA SQD-990
- Split EC numbers to match new C toolkit functionality
- added some rRNA name fixes. - using improved autogenerator output (relevant autogenerator changes will be committed soon) JIRA SQD-240
- Normalize nested Seq-loc-mixes and normalize location NULLs.
- Throw out UniversalStringClean and use DecodeXML instead - Also, DecodeXML has been expanded to do all the XML codes that C does JIRA SQD-53
- Decode XML ("<" -> "<", etc.) for Seq-feat.comment and Seqdesc.comment
- Fix "'" to apostrophe ' in all strings everywhere - x_UniversalStringClean is the function that cleans every string. - Also, added "antisense" BSEC test (although "antisense" cleaning was already committed ) - Note that the change in autogenerated_cleanup.txt requires a change to datatool, which I will commit soon. JIRA SQD-53
- don't use deprecated CVariation_ref fields - Fix class "antisense" to "antisense_RNA" for ncRNA JIRA SQD-48
Stop-gap solution to the change in Variation_ref.hpp that make this code not compile. A real solution would be to change the autogenerator instead of hand-editing the auto-generated code. I plan to do so soon.
- cleanup now also fixes partial protein
- added removal of flanking quotes to BasicCleanup
- check in the automatic test cases for cleanup (about 300 test cases) - rename some functions to better reflect their purpose - Removed some TODO comments (either fixing the underlying issue or determining that the issue has already been fixed ) JIRA CXX-2186
- More changes to fix some smaller errors. - Now passes all of my checks and Colleen Bollin's checks. - Handle versions fixed up - Including: Almost all const_casts removed - Removing most commented-out code. JIRA CXX-2186
- many changes to string cleanup to fix subtle discrepancies between C and C++ such as tilde handling and when to compress strings or not. - Other small changes such as remembering to clean "origin". - pmid and pubmed mutually fill each other in. - When we create a new object that won't be automatically traversed, we create a sub-CAutogeneratedCleanup that will make sure it's properly handled. (ImpFeatBC) - Fix prefix-handling to realize where there's an "=" or whatever in a string. - Extracting RNA class from product - Use CleanVisString instead of CleanString, since it better matches C. - Working on making the code pass Colleen Bollin's tests JIRA CXX-2186
For BasicCleanup: - C functionality should now all be in C++ (except for implicit behavior I may have failed to see, such as when enum fields become implicitly reset when they're zero ). - Many bugs fixed. This commit passes all my tests (Still needs work because fails on some of the tests provided by Colleen Bollin ). - Added ChangeMade() calls in the places it was missing. JIRA CXX-2186
- Many changes to move C functionality to C++. We're somewhat nearing
the end of the move, BUT there is still more debugging and testing to do.
- This part adds the x_PostProcessing function for work that must
be done after we traverse.
- removed some old commented-out code
- added SET_FIELD_IF_UNSET macro
- fixed UNIQUE_WITHOUT_SORT macro to check if set
JIRA CXX-2186
- continuing to move C functionality to C++ JIRA CXX-2186
More changes to put C functionality into C++ JIRA CXX-2186
- Point to new cleanup code instead of Robert's old cleanup code. - auto-generated code is now MUCH smaller, thanks to improvements in the auto-generator. - CNewCleanup_imp added several new BasicCleanup* entrances to allow us to have the functionality that Robert's old code did. - Several new changes to get C functionality into C++ (e.g. compressing strings, as well as more complex fixes) - external API change: only non-const objects accepted for cleanup now - Code itself is cleaned up a bit. For example, the header file that was just copy-pasted into a .cpp file is now its own .hpp file. JIRA CXX-2186
- Some more base macros, as well as XREF_ON_SEQFEAT macros
- More changes to bring C cleanup functionality to C++ (x_CleanupAndRepairInference, x_MendSatelliteQualifier, etc.)
- This includes changes to auto-generated code.
- CBioseq_Context now keeps track of whether there are multi-interval genes (needed for compatibility with C. Possibly can be removed in the
future)
- Fixed bug in code autogenerator where comment wasn't closed
- ReadLocFromText improved to work with accessions
- asn2flat improvements
- when cleaning a location for gene search, don't add "far" parts. Also, do NOT trim out empty parts of locations. For some reason, this seems
to also give a large speed boost, as much as 4X speedup for asn2flat as a whole (!).
- some functionality works less well for segmented sequences, but better for non-segmented sequences. Since segmented sequences are being phased
out, I consider this acceptable.
- Determine when a SeqLoc's parts are out-of-order using C-style logic (in the future, we may use C++'s location order checker)
JIRA GP-1267
- autogenerated code changes: - Now includes roots Seq-submit and Seq-annot - Non-autogenerated code now uses the autogenerated code in all 3 cases (Seq-entry, Seq-submit and Seq-annot). - ExtendedCleanup now uses BasicCleanup first - Removed some code that was replaced with autogen code - A few changes to better match C code
Note: Large commit.
- Added auto-generated code (the autogenerator inside datatool is not committed yet)
- Added NON_CONST_SET_ITERATE since NON_CONST_ITERATE doesn't actually allow non-const iteration for sets.
- test_basic_cleanup now allows multiple input and output files
- move declaration of CNewCleanup_imp into the new file newcleanup.hpp
- Due to code auto-generation, a lot of hand-made traversal code was able to be removed.
- Commit includes autogenerated_cleanup.txt, which is used by datatool to generate the autogenerated_cleanup.[ch]pp files
- The description language is specified in a file which will be committed in the future into serial/datatool:
traversal_spec_file_parser.cpp
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