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JIRA: RW-2075 Added git patch
xobjread: remove trailing whitespace; JIRA:RW-1283
Replaced throw() with noexcept. JIRA CXX-11571
In line_error, suppress line number display if there is no line number to report.
JIRA: RW-621 If a GO term cannot be parsed then throw out the GO term but retain everything else in the feature. For the feature table reader, generate a warning for every GO term thrown out. In cleanup, faulty GO terms are thrown out silently, by workflow design. In the GFF3 reader, faulty GO terms are thrown out silently due to current error reporting limitations.
Use the override qualifier consistently in CLineErrorEx to prevent Clang from complaining
added `override` to method to fix compiler warning.
JIRA: RW-807 ILineError now displays non-zero error codes
JIRA: RW-807 Added the CLineErrorEx class. Modifier errors and warnings now have an associated code and subcode
JIRA: MSS-714 ILineError is now derived from IObjtoolsMessage and ILineErrorListener is derived from IObjtoolsListener. ILineErrorListener will now accept any message class derived from IObjtoolsMessage
JIRA: MSS-714 Reverting previous changes until I've fixed bug
JIRA: MSS-714 First attempt at generalising objtools error reporting
JIRA: RW-626 Add check for empty Reference feature
JIRA: GB-7784 Added check for duplicate transcript and protein ids
JIRA: RW-451 Bug fixes
JIRA: GB-7160 Added warning for invalid qualifier
Added IMessage and ncbi::IMessageListener interfaces. JIRA CXX-4254
line_error XML dump was giving invalid XML. JIRA WGS-773
give feat table reader ability to report discouraged feats and quals. JIRA BI-1270
THIS BREAKS BACKWARD COMPATIBILITY, but it looks to me like all files that use this are ready for the change. Deprecated constructors moved from public to protected and then undeprecated. but possibly related to QA-17483
multireader now has an option to show errors as XML. JIRA SPCORE-210
CObjReaderLineException::Message falls back on ILineError::Message if GetMsg is blank. JIRA QA-17483
For backward compatibility, default the last seven arguments in the CObjReaderLineException constructor.
ILineError cannot inherit from object because it breaks the CObject heap code. Also, creation funcs now take the "other lines" field into account. JIRA QA-17483
put funcs with warnings in .cpp instead of .hpp to avoid having warnings in huge numbers of files. JIRA QA-17483
CMessageListenerBase now stores the actual ILineError instead of converting it to a CLineError, so that extra information in child classes can be retrieved. Also, ILineError inherits from CObject now. JIRA QA-17483
* Give CFastaReader a flag for ignoring hyphens but warning. * Remove CFastaReader's getter and setter for completely unknown gap length * Force gaps of unknown length to have size 100 JIRA BI-105
workaround for compiler bug. JIRA BI-105
CFastaReader: some previously-thrown exceptions that are actually recoverable become mere warnings so that BankIt can accumulate them. JIRA BI-105
added few more ILineError problems. JIRA BI-105
JIRA: MSS-214 Add support for custom error messages to CLineError.
Add PutProgress func to IMessageListener. JIRA SPCORE-210
Rename IErrorContainer to IMessageListener. JIRA SPCORE-210
JIRA: MSS-194 Convert VCF reader to use error containers for error processing.
make Dump virtual in case descendents want to override it.
added eProblem_ProgressInfo (not used yet), and moved Dump up from CLineError to ILineError. Dump is also a little more efficient now.
* Make CFastaReader conform to the reader standards. (That is, inherit from CReaderBase and accept IErrorContainers) * Removed the CWarning inner class * Many, many more functions take "IErrorContainer *" now * FASTA errors give more control to IErrorContainer to decide whether to just store or to throw. (there are places where throwing is forced, though) JIRA MSS-194
Support [offset=...] keyword in feature table. JIRA BI-826
* ILineError now supports "OtherLines" (e.g. to show the line number of referenced features, not just the feat where the error occurred) * added flag CFeature_table_reader::fCreateGenesFromCDSs so that a CDS with a non-existent gene can be auto-created with the same intervals as the CDS. * Also checks if multiple CDSs try to create a gene with the same locus or locus-tag * added flag CFeature_table_reader::fCDSsMustBeInTheirGenes to check that all CDSs are within the genes that they xref * Don't add CGene_ref to protein sequences * Parse title after reading sequence so we know the molecule type JIRA BI-801 JIRA BI-826
Add internal partials check to C++ feature table reader. JIRA CXX-3806
CHANGED: objtools/readers/line_error.hpp Eliminate gcc compiler warnings regarding variable initialization out of order.
CHANGED: objtools/readers/line_error.hpp
objtools/readers/bed_reader.cpp
JIRA: GB-1689
FIX: Track line recognition and handling: Any line starting with the
letters "track" will no be recognized as a track line unless it has
at least three columns, and the second and third columns are both
integers. If a line is found to be a track line but does not parse
as one, emit a warning and continue reading anyway.
FIX: Error reporting: Initialize CLineError's eProblem member so that
meaningful error messages get reported down the road.
FIX: Feature assembly: Avoid memory corruption when an expected interval
location turns out to be a point location.
FIX: Annot assembly: Do not generate duplicate conversion info if a
Seq-annot is finalized due to a new track line in the input file.
- CSourceModParser now stores a list of "bad mods", which are mods with bad
qualifier values. This is NOT for storing unused or unknown mods.
- User also has the option of how to handle these "bad mods". They can be
ignored, an error thrown, or an error printed to cerr.
- CFastaReader now has these flags added:
- fBadModThrow: an exception is thrown if there's a bad mod. See above
for definition of "bad".
- fUnknModThrow: an exception is thrown if any mods are unused, which
would likely indicate an invalid mod such as "organims"[sic].
- If user specifies fValidate, the error message that occurs in case
of validation failure now includes the locations of the failure.
- CFeature_table_reader_imp: fixed bug where an issue with parsing a qual's
value could erroneously say that it's an unknown qual type.
- Also, when a qual's val is in double-quotes, remove those double-quotes
JIRA BI-558
CHANGED: objtools/readers/line_error.hpp
objtools/readers/wiggle_data.[hc]pp
objtools/readers/wiggle_reader.cpp
JIRA: MSS-92
(1) Bug fix: Low level wig parsing code would throw the wrong type of error object,
resulting in premature program termination.
(2) Consider data lines with negative position values as valid input whose values
fall outside of recorded range.
CHANGED: objtools/readers/line_error.hpp
objtools/readers/reader_base.[ch]pp
objtools/readers/wiggle_reader.cpp
JIRA: MSS-92
(1) Fix error reporting during the parsing phase in the wiggle reader.
(2) On parsing error in the wiggle reader, do not discard any data read
successfully of to this point.
(3) On parsing error in the wiggle reader, attempt to recover additional
data by advancing to the closest track line or data directive.
(4) Fix a couple of nearby deprediation warnings.
- Make "bad intervals" a different error than the "could not convert string to integer" errors. JIRA BI-444
- refactor ILineError, etc. so that, instead of having an error message, we break the error into components consisting of: - Problem (enum) - Severity - SeqId - Line - FeatureName (might be empty string) - QualifierName(might be empty string) - QualifierValue(might be empty string) - CObjReaderLineException tries to maintain backwards compatibility in at least some of its constructors. - ITableFilter and CSimpleTableFilter are a little cleaner and more customizable. JIRA BI-439
- Show qual and feat name when unrecognized qual - Show feat name when unrecognized feat. - fix a couple minor compiler warnings JIRA BI-437
- error container should now hold line number (which is actually filled in now) and sequence. - Added ITableFilter so we can have a warning/error for certain tags when necessary. JIRA BI-433
Large overhaul of the ID mapper: - Introduce CSeq_loc_Mapper-based mapping for loc-to-loc mappings - Update config file representation to be broader, use standard .ini syntax - Add a unit test - Update interfaces to make sure that virtual dtors are present - Add includes where needed
CHANGED: objtools/readers/error_container interface JIRA MSS-3 Properly separate interface and implementations of error_container and line_error. Provide implementations of IErrorContainer that provide for policies for strict/lenient file parsing. Provide IErrorContainer implementations that allow either a certain number of errors or errors up to a given severity level.
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