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Fix warnings; JIRA:RW-2163
Validator: Some reformatting; JIRA:RW-2163
rename, undeprecate ValidateStructuredComment(); JIRA:RW-2155
JIRA:RW-1971 If Alternative (SRS) BioSample format, lower severity to warning, use distinctive text
JIRA: RW-1759 Modified structured-comment check. The validator now complains in the suffix does not match the prefix
JIRA: RW-1759 Added x_ValidateStructuredCommentUsingRule()
JIRA: RW-1759 Some refactoring. Added x_ValidateStructuredCommentPrefix() and x_ValidateStructuredCommentSuffix() methods
JIRA: RW-1759 Further improvement to suffix check. Make sure that 'report' is properly taken into account
JIRA: RW-1759 Improved logic in structured-comment-suffix check
JIRA: RW-1759 Eliminated try/catch block used to control flow
JIRA: RW-1759 If reporting is turned off in CValidError_desc::ValidateStructuredComment(), exit on first failure
JIRA: RW-1759 Only report messages if 'report' is true
JIRA: RW-1759 x_ValidateStructuredComment() should not return is_valid true when an error message is posted
JIRA: RW-1759 Use the report variable specified by the user when invoking ValidateStructureCommentGeneric() inside ValidateStructuredComment()
JIRA: RW-1759 Perform same checks regardless of whether 'report' is true or false
JIRA: RW-1753 Replaced CValidator::ValidateStructuredComment(const CSeqdesc&, CValidError&) with CValidator::IsValidStructuredComment(const CSeqdesc&)
JIRA: RW-1707 Merged development branch into trunk
JIRA: RW-1637 Update for new information on HumanSTRv2 mandatory fields.
JIRA: RW-1637 Add support for new form of the HumanSTR structured comment.
JIRA:RW-1474 Added s_AsciiString to avoid printing non-ascii characters in error message
JIRA:RW-1490 Check Trace Assembly Archive gives REJECT if accession does not start with TI
xvalidate: Remove (void) signature; JIRA:RW-1283
xvalidate: remove trailing whitespace; JIRA:RW-1283
Removed try-catch blocks around FindCommentRuleEx calls
ValidateStructuredComment calls ValidateStructuredCommentGeneric if empty rule, equivalent to previous catch
Added FindCommentRuleEx
JIRA:VR-886 post separate errors for non-ASCII characters in features and descriptors in addition to the general error for the entire object
JIRA:VR-880 added new valid structured comment prefixes
JIRA:VR-874 "Evidence-For-Name-Assignment" is a valid structured comment prefix.
changes recommended by PVSStudio for performance
JIRA:VR-794 updates to validator codes and messages
JIRA:SQD-4470 added new structured comment type
JIRA:MSS-677 use new User-object class methods for RefGeneTracking
JIRA:SQD-4324 improve performance/memory consumption for large files
JIRA:VR-727 raise field out of order message to error for WGS masters
JIRA:VR-709 Assembly Name should not start with 'NCBI' or 'GenBank'
JIRA:SQD-4266 added new structured comment HumanSTR
JIRA:VR-684 added SIVDataBaseData to list of recognized structured comment prefixes
JIRA:VR-612 suppress RefSeqInText if record is RefSeq
JIRA:VR-612 look for RefSeq in protein name and definition line
JIRA:VR-507
JIRA:VR-504
JIRA:SQD-3518
JIRA:VR-502
JIRA:VR-500 JIRA:VR-501
JIRA:VR-569 JIRA:VR-502
JIRA:VR-504
JIRA:VR-496
JIRA:VR-253 validator was reporting missing structured comment field with wrong code
JIRA:VR-185 add new structured comment type BWP:1.0
JIRA: VR-50: Added cross-check for MolInfo.tech=tsa vs. MolInfo.biomol value. TSA records are expected to have one of these biomol values: transcribed-RNA, mRNA, rRNA, ncRNA. All the others will trigger the ERROR message SEQ_DESCR_WrongBiomolForRechnique.
JIRA:SQD-1550 added MIXS structured comments version 4.0
JIRA:SQD-1636 EBI BioSample accession format can contain an extra letter
JIRA:SQD-1499 fixed bug in CValidError_desc::ValidateStructuredComment
JIRA: SQD-1499 changed ValidateStructuredComment to use CComment_rule static function for finding and normalizing prefix, also removed unused function s_IsGenomeAssembly
JIRA:SQD-1309 added check for CDSonMinusStrandTranscribedRNA
JIRA:SQD-1042 moved function for validating a structured comment user object using a given comment rule to the CComment_rule class, so that it can be used by editing functions that need to know whether a structured comment is or is not valid.
use default structured comment rules if file not found, structured comment rule loading moved to CComment_set class
fixes to compiler warnings
suppress NULL pointer messages
JIRA:SQD-1391 added separate function CheckBioseqEndsForNAndGap to utilities for validator
JIRA:SQD-1366 Bad DBLink capitalization reported as SEV_REJECT
JIRA:SQD-1106 Report at ERROR if IsValidSexValue fails, other problems with /sex qualifier are ERROR for gpipe, WARNING otherwise
StructuredCommentPrefixOrSuffixMissing reports at Warning instead of Info
JIRA:SQD-1244 Raised severity of missing Finishing Goal and Current Finishing Status of Genome-Assembly-Data to ERROR
Added check for existence of StructuredCommentPrefix before trying to get field (requested)
JIRA:SQD-1078 added support for Evidence-Data structured comment to validator
Use typedef type for User-field.data.strs. JIRA: CXX-3421
NOJIRA: Fixed validator test problems
moving validator include files
JIRA:SQD-943 fix segfault
Added prefix list for StructuredComment, BAD_VALIDATOR on Test_Descr_BadStructuredCommentFormat and Test_Descr_MissingKeyword
JIRA:SQD-789 Do not report user object with no type if IsId as well as IsStr
JIRA:SQD-596 Allow empty Unverified user object
JIRA:SQD-596 Report ERR_SEQ_DESCR_UserObjectProblem for empty or unnamed user object - will add removal to SSEC
JIRA:CXX-2918 show actual identifier in DBLinkProblem message
JIRA:SQD-247 added processing for new "invert-match" option for dependent rules.
JIRA:SQD-249 added x_IsBadAltBioSampleFormat to temporarily allow SRS numbers in BioSample
JIRA:CXX-2918 x_IsBadSRAFormat allows D and E as well as S
JIRA:CXX-2918 ValidateDblink bad formats raised to error level
JIRA:CXX-2918 added ValidateDblink
replaced deprecated NStr::IntToString with NStr::SizetToString
Synchronization with C Toolkit
Change to lat-lon validation to use g_FindDataFile and include tables from external files, also added new error ImproperlyNestedSets and adjusted unit test to include this.
Synchronization with C Toolkit. Added tests for structured comments, fake structured comments.
Bug fixes for validator acting on Seq-annot, synchronization with C Toolkit for structured comment format, added more tests to unit test for validator.
Synchronization with C Toolkit, bug fixes for validator.
Synchronization with C Toolkit, added unit test for validator to build
Added validation of individual fields in structured comments (synchronization with recent change in C Toolkit)
Synchronization with C Toolkit
Removed GBQual legal/mandatory association from CGb_qual class because same-purpose code exists in CSeqFeatData and is already in use by other projects. Also made bug fixes to validator code (synchronization with C Toolkit).
Synchronization of validator with C Toolkit.
Temporarily commenting out taxonomy references that are breaking the build.
synchronization with C Toolkit
Synchronization with C Toolkit
Synchronization with C Toolkit.
Synchronization with C Toolkit
Synchronization with the C Toolkit, also resolved some bugs with exceptions being thrown.
Fixed bugs in validator, including problems with iterating for descriptor sets, incorrect implementation of tests, and other changes.
Fixed svn properties in trunk/c++.
CVS $Log$ keyword clean-up: everything except "internal".
Errors from Seqdesc must contain a context
Added PCH ncbi_pch.hpp
Check that RefGenTrackking object has Status field
Use the comment variable
$id: -> $id$
Implemented checks for obsolete, comment and molinfo descriptors
Added check IsTPA
Changes to include directives
Initial submission after splitting former implementation
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