1 /* $Id: ValidErrItem.hpp 621199 2020-12-07 20:57:00Z ivanov $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 */
27
28 /// @file ValidErrItem.hpp
29 /// User-defined methods of the data storage class.
30 ///
31 /// This file was originally generated by application DATATOOL
32 /// using the following specifications:
33 /// 'valerr.asn'.
34 ///
35 /// New methods or data members can be added to it if needed.
36 /// See also: ValidErrItem_.hpp
37
38
39 #ifndef OBJECTS_VALERR_VALIDERRITEM_HPP
40 #define OBJECTS_VALERR_VALIDERRITEM_HPP
41
42 #include <corelib/ncbistd.hpp>
43 #include <corelib/ncbidiag.hpp>
44 #include <objects/seqset/Seq_entry.hpp>
45
46 // generated includes
47 #include <objects/valerr/ValidErrItem_.hpp>
48
49 // generated classes
50
51 BEGIN_NCBI_SCOPE
52
53 BEGIN_objects_SCOPE // namespace ncbi::objects::
54
55 // =========================== Internal error types ==========================
56
57 #define ERR_CODE_BEGIN(x) x##BEGIN
58 #define ERR_CODE_END(x) x##END
59
60 /*
61 Validation errors can be saved as data objects. So we must
62 take care that these error code numbers do not change.
63 Only add new codes at the ends of groups. (right before ERR_CODE_END(...)).
64 Only add new groups of error codes at the end of enums, (right before eErr_Max).
65 Do not change the initialization constants (e.g. = 1000 )
66 eErr_Max must always be the last.
67 */
68 enum EErrType {
69 eErr_ALL = 0,
70 eErr_UNKNOWN,
71
72 ERR_CODE_BEGIN(SEQ_INST),
73 eErr_SEQ_INST_ExtNotAllowed,
74 eErr_SEQ_INST_ExtBadOrMissing,
75 eErr_SEQ_INST_SeqDataNotFound,
76 eErr_SEQ_INST_SeqDataNotAllowed,
77 eErr_SEQ_INST_ReprInvalid,
78 eErr_SEQ_INST_CircularProtein,
79 eErr_SEQ_INST_BadProteinMoltype,
80 eErr_SEQ_INST_MolNotSet,
81 eErr_SEQ_INST_MolinfoOther,
82 eErr_SEQ_INST_FuzzyLen,
83 eErr_SEQ_INST_InvalidLen,
84 eErr_SEQ_INST_InvalidAlphabet,
85 eErr_SEQ_INST_SeqDataLenWrong,
86 eErr_SEQ_INST_SeqPortFail,
87 eErr_SEQ_INST_InvalidResidue,
88 eErr_SEQ_INST_StopInProtein,
89 eErr_SEQ_INST_PartialInconsistent,
90 eErr_SEQ_INST_ShortSeq,
91 eErr_SEQ_INST_NoIdOnBioseq,
92 eErr_SEQ_INST_BadDeltaSeq,
93 eErr_SEQ_INST_LongHtgsSequence,
94 eErr_SEQ_INST_LongLiteralSequence,
95 eErr_SEQ_INST_ConflictingIdsOnBioseq,
96 eErr_SEQ_INST_MolNuclAcid,
97 eErr_SEQ_INST_ConflictingBiomolTech,
98 eErr_SEQ_INST_SeqIdNameHasSpace,
99 eErr_SEQ_INST_IdOnMultipleBioseqs,
100 eErr_SEQ_INST_DuplicateSegmentReferences,
101 eErr_SEQ_INST_TrailingX,
102 eErr_SEQ_INST_BadSeqIdFormat,
103 eErr_SEQ_INST_PartsOutOfOrder,
104 eErr_SEQ_INST_BadSecondaryAccn,
105 eErr_SEQ_INST_ZeroGiNumber,
106 eErr_SEQ_INST_RnaDnaConflict,
107 eErr_SEQ_INST_HistoryGiCollision,
108 eErr_SEQ_INST_GiWithoutAccession,
109 eErr_SEQ_INST_MultipleAccessions,
110 eErr_SEQ_INST_HistAssemblyMissing,
111 eErr_SEQ_INST_TerminalNs,
112 eErr_SEQ_INST_UnexpectedIdentifierChange,
113 eErr_SEQ_INST_InternalNsInSeqLit,
114 eErr_SEQ_INST_SeqLitGapLength0,
115 eErr_SEQ_INST_TpaAssemblyProblem,
116 eErr_SEQ_INST_SeqLocLength,
117 eErr_SEQ_INST_MissingGaps,
118 eErr_SEQ_INST_CompleteTitleProblem,
119 eErr_SEQ_INST_CompleteCircleProblem,
120 eErr_SEQ_INST_BadHTGSeq,
121 eErr_SEQ_INST_GapInProtein,
122 eErr_SEQ_INST_BadProteinStart,
123 eErr_SEQ_INST_TerminalGap,
124 eErr_SEQ_INST_OverlappingDeltaRange,
125 eErr_SEQ_INST_LeadingX,
126 eErr_SEQ_INST_InternalNsInSeqRaw,
127 eErr_SEQ_INST_InternalNsAdjacentToGap,
128 eErr_SEQ_INST_CaseDifferenceInSeqID,
129 eErr_SEQ_INST_DeltaComponentIsGi0,
130 eErr_SEQ_INST_FarFetchFailure,
131 eErr_SEQ_INST_InternalGapsInSeqRaw,
132 eErr_SEQ_INST_SelfReferentialSequence,
133 eErr_SEQ_INST_WholeComponent,
134 eErr_SEQ_INST_TSAHistAssemblyMissing,
135 eErr_SEQ_INST_ProteinsHaveGeneralID,
136 eErr_SEQ_INST_HighNContent,
137 eErr_SEQ_INST_SeqLitDataLength0,
138 eErr_SEQ_INST_HighNContentStretch,
139 eErr_SEQ_INST_HighNContentPercent,
140 eErr_SEQ_INST_UnknownLengthGapNot100,
141 eErr_SEQ_INST_SeqGapProblem,
142 eErr_SEQ_INST_WGSMasterLacksStrucComm,
143 eErr_SEQ_INST_TSAMasterLacksStrucComm,
144 eErr_SEQ_INST_AllNs,
145 eErr_SEQ_INST_FarLocationExcludesFeatures,
146 eErr_SEQ_INST_ProteinShouldNotHaveGaps,
147 eErr_SEQ_INST_MitoMetazoanTooLong,
148 eErr_SEQ_INST_ESTshouldBemRNA,
149 eErr_SEQ_INST_HTGS_STS_GSS_WGSshouldBeGenomic,
150 eErr_SEQ_INST_HTGS_STS_GSS_WGSshouldNotBeRNA,
151 eErr_SEQ_INST_mRNAshouldBeSingleStranded,
152 eErr_SEQ_INST_TSAshouldBNotBeDNA,
153 eErr_SEQ_INST_GenomeSeqGapProblem,
154 eErr_SEQ_INST_SeqGapBadLinkage,
155 eErr_SEQ_INST_TSAseqGapProblem,
156 eErr_SEQ_INST_WGSseqGapProblem,
157 eErr_SEQ_INST_CompleteGenomeHasGaps,
158 eErr_SEQ_INST_HighNcontent5Prime,
159 eErr_SEQ_INST_HighNcontent3Prime,
160 eErr_SEQ_INST_HighNpercent5Prime,
161 eErr_SEQ_INST_HighNpercent3Prime,
162 eErr_SEQ_INST_CircBactGenomeProblem,
163 ERR_CODE_END(SEQ_INST),
164
165 ERR_CODE_BEGIN(SEQ_DESCR) = 1000,
166 eErr_SEQ_DESCR_BioSourceMissing,
167 eErr_SEQ_DESCR_InvalidForType,
168 eErr_SEQ_DESCR_FileOpenCollision,
169 eErr_SEQ_DESCR_Unknown,
170 eErr_SEQ_DESCR_NoPubFound,
171 eErr_SEQ_DESCR_NoOrgFound,
172 eErr_SEQ_DESCR_MultipleBioSources,
173 eErr_SEQ_DESCR_NoMolInfoFound,
174 eErr_SEQ_DESCR_BadCountryCode,
175 eErr_SEQ_DESCR_NoTaxonID,
176 eErr_SEQ_DESCR_InconsistentBioSources,
177 eErr_SEQ_DESCR_MissingLineage,
178 eErr_SEQ_DESCR_SerialInComment,
179 eErr_SEQ_DESCR_BioSourceNeedsFocus,
180 eErr_SEQ_DESCR_BadOrganelleLocation,
181 eErr_SEQ_DESCR_MultipleChromosomes,
182 eErr_SEQ_DESCR_BadSubSource,
183 eErr_SEQ_DESCR_BadOrgMod,
184 eErr_SEQ_DESCR_InconsistentProteinTitle,
185 eErr_SEQ_DESCR_Inconsistent,
186 eErr_SEQ_DESCR_ObsoleteSourceLocation,
187 eErr_SEQ_DESCR_ObsoleteSourceQual,
188 eErr_SEQ_DESCR_StructuredSourceNote,
189 eErr_SEQ_DESCR_UnnecessaryBioSourceFocus,
190 eErr_SEQ_DESCR_RefGeneTrackingWithoutStatus,
191 eErr_SEQ_DESCR_UnwantedCompleteFlag,
192 eErr_SEQ_DESCR_CollidingPublications,
193 eErr_SEQ_DESCR_TransgenicProblem,
194 eErr_SEQ_DESCR_TaxonomyLookupProblem,
195 eErr_SEQ_DESCR_MultipleTitles,
196 eErr_SEQ_DESCR_RefGeneTrackingOnNonRefSeq,
197 eErr_SEQ_DESCR_BioSourceInconsistency,
198 eErr_SEQ_DESCR_FastaBracketTitle,
199 eErr_SEQ_DESCR_MissingText,
200 eErr_SEQ_DESCR_BadCollectionDate,
201 eErr_SEQ_DESCR_BadPCRPrimerSequence,
202 eErr_SEQ_DESCR_BadPunctuation,
203 eErr_SEQ_DESCR_BadPCRPrimerName,
204 eErr_SEQ_DESCR_BioSourceOnProtein,
205 eErr_SEQ_DESCR_BioSourceDbTagConflict,
206 eErr_SEQ_DESCR_DuplicatePCRPrimerSequence,
207 eErr_SEQ_DESCR_MultipleNames,
208 eErr_SEQ_DESCR_MultipleComments,
209 eErr_SEQ_DESCR_LatLonFormat,
210 eErr_SEQ_DESCR_LatLonRange,
211 eErr_SEQ_DESCR_LatLonValue,
212 eErr_SEQ_DESCR_LatLonCountry,
213 eErr_SEQ_DESCR_LatLonState,
214 eErr_SEQ_DESCR_BadSpecificHost,
215 eErr_SEQ_DESCR_RefGeneTrackingIllegalStatus,
216 eErr_SEQ_DESCR_ReplacedCountryCode,
217 eErr_SEQ_DESCR_BadInstitutionCode,
218 eErr_SEQ_DESCR_BadCollectionCode,
219 eErr_SEQ_DESCR_IncorrectlyFormattedVoucherID,
220 eErr_SEQ_DESCR_UnstructuredVoucher,
221 eErr_SEQ_DESCR_ChromosomeLocation,
222 eErr_SEQ_DESCR_MultipleSourceQualifiers,
223 eErr_SEQ_DESCR_UnbalancedParentheses,
224 eErr_SEQ_DESCR_IdenticalInstitutionCode,
225 eErr_SEQ_DESCR_BadCountryCapitalization,
226 eErr_SEQ_DESCR_WrongVoucherType,
227 eErr_SEQ_DESCR_TitleHasPMID,
228 eErr_SEQ_DESCR_BadKeyword,
229 eErr_SEQ_DESCR_NoOrganismInTitle,
230 eErr_SEQ_DESCR_MissingChromosome,
231 eErr_SEQ_DESCR_LatLonAdjacent,
232 eErr_SEQ_DESCR_BadStrucCommInvalidFieldName,
233 eErr_SEQ_DESCR_BadStrucCommInvalidFieldValue,
234 eErr_SEQ_DESCR_BadStrucCommMissingField,
235 eErr_SEQ_DESCR_BadStrucCommFieldOutOfOrder,
236 eErr_SEQ_DESCR_BadStrucCommMultipleFields,
237 eErr_SEQ_DESCR_BioSourceNeedsChromosome,
238 eErr_SEQ_DESCR_MolInfoConflictsWithBioSource,
239 eErr_SEQ_DESCR_FakeStructuredComment,
240 eErr_SEQ_DESCR_StructuredCommentPrefixOrSuffixMissing,
241 eErr_SEQ_DESCR_LatLonWater,
242 eErr_SEQ_DESCR_LatLonOffshore,
243 eErr_SEQ_DESCR_MissingPersonalCollectionName,
244 eErr_SEQ_DESCR_LatLonPrecision,
245 eErr_SEQ_DESCR_DBLinkProblem,
246 eErr_SEQ_DESCR_FinishedStatusForWGS,
247 eErr_SEQ_DESCR_BadTentativeName,
248 eErr_SEQ_DESCR_OrganismNotFound,
249 eErr_SEQ_DESCR_TaxonomyIsSpeciesProblem,
250 eErr_SEQ_DESCR_TaxonomyConsultRequired,
251 eErr_SEQ_DESCR_TaxonomyNucleomorphProblem,
252 eErr_SEQ_DESCR_InconsistentMolTypeBiomol,
253 eErr_SEQ_DESCR_BadInstitutionCountry,
254 eErr_SEQ_DESCR_AmbiguousSpecificHost,
255 eErr_SEQ_DESCR_BadAltitude,
256 eErr_SEQ_DESCR_RefGeneTrackingOnNucProtSet,
257 eErr_SEQ_DESCR_InconsistentDates,
258 eErr_SEQ_DESCR_MultipleTaxonIDs,
259 eErr_SEQ_DESCR_ScaffoldLacksBioProject,
260 eErr_SEQ_DESCR_CompleteGenomeLacksBioProject,
261 eErr_SEQ_DESCR_TaxonomyPlastidsProblem,
262 eErr_SEQ_DESCR_OrganismIsUndefinedSpecies,
263 eErr_SEQ_DESCR_SuspectedContaminatedCellLine,
264 eErr_SEQ_DESCR_WrongOrganismFor16SrRNA,
265 eErr_SEQ_DESCR_InconsistentWGSFlags,
266 eErr_SEQ_DESCR_TitleNotAppropriateForSet,
267 eErr_SEQ_DESCR_StrainContainsTaxInfo,
268 eErr_SEQ_DESCR_InconsistentBioSources_ConLocation,
269 eErr_SEQ_DESCR_InconsistentRefSeqMoltype,
270 eErr_SEQ_DESCR_InconsistentMolInfo,
271 eErr_SEQ_DESCR_InconsistentMolInfoTechnique,
272 eErr_SEQ_DESCR_InconsistentTaxName,
273 eErr_SEQ_DESCR_InconsistentMolType,
274 eErr_SEQ_DESCR_InconsistentGenBankblocks,
275 eErr_SEQ_DESCR_InconsistentTaxNameSet,
276 eErr_SEQ_DESCR_InconsistentTPA,
277 eErr_SEQ_DESCR_BacteriaMissingSourceQualifier,
278 eErr_SEQ_DESCR_BadBioSourceFrequencyValue,
279 eErr_SEQ_DESCR_BadPlasmidChromosomeLinkageName,
280 eErr_SEQ_DESCR_BadPlastidName,
281 eErr_SEQ_DESCR_EnvironSampleMissingQualifier,
282 eErr_SEQ_DESCR_InconsistentVirusMoltype,
283 eErr_SEQ_DESCR_InvalidMatingType,
284 eErr_SEQ_DESCR_InvalidSexQualifier,
285 eErr_SEQ_DESCR_InvalidTissueType,
286 eErr_SEQ_DESCR_MissingEnvironmentalSample,
287 eErr_SEQ_DESCR_MissingMetagenomicQualifier,
288 eErr_SEQ_DESCR_MissingPlasmidLocation,
289 eErr_SEQ_DESCR_MissingPlasmidName,
290 eErr_SEQ_DESCR_OrgModValueInvalid,
291 eErr_SEQ_DESCR_StrainWithEnvironSample,
292 eErr_SEQ_DESCR_UnculturedNeedsEnvSample,
293 eErr_SEQ_DESCR_BadTextInSourceQualifier,
294 eErr_SEQ_DESCR_OrgModMissingValue,
295 eErr_SEQ_DESCR_BadAssemblyName,
296 eErr_SEQ_DESCR_BadKeywordForStrucComm,
297 eErr_SEQ_DESCR_BadKeywordNoTechnique,
298 eErr_SEQ_DESCR_BadKeywordUnverified,
299 eErr_SEQ_DESCR_BadStrucCommInvalidPrefix,
300 eErr_SEQ_DESCR_BadStrucCommInvalidSuffix,
301 eErr_SEQ_DESCR_BINDoesNotMatch,
302 eErr_SEQ_DESCR_CollidingPubMedID,
303 eErr_SEQ_DESCR_CommentMissingText,
304 eErr_SEQ_DESCR_DBLinkBadAssembly,
305 eErr_SEQ_DESCR_DBLinkBadBioProject,
306 eErr_SEQ_DESCR_DBLinkBadBioSample,
307 eErr_SEQ_DESCR_DBLinkBadCapitalization,
308 eErr_SEQ_DESCR_DBLinkBadFormat,
309 eErr_SEQ_DESCR_DBLinkBadSRAaccession,
310 eErr_SEQ_DESCR_DBLinkMissingUserObject,
311 eErr_SEQ_DESCR_DBLinkOnSet,
312 eErr_SEQ_DESCR_InvalidForTypeGIBB,
313 eErr_SEQ_DESCR_InvalidMolInfo,
314 eErr_SEQ_DESCR_MoltypeOther,
315 eErr_SEQ_DESCR_MoltypeOtherGenetic,
316 eErr_SEQ_DESCR_MoltypeUnknown,
317 eErr_SEQ_DESCR_MultipleDBLinkObjects,
318 eErr_SEQ_DESCR_MultipleStrucComms,
319 eErr_SEQ_DESCR_NoKeywordHasTechnique,
320 eErr_SEQ_DESCR_NoSourceDescriptor,
321 eErr_SEQ_DESCR_NucleotideTechniqueOnProtein,
322 eErr_SEQ_DESCR_ProteinTechniqueOnNucleotide,
323 eErr_SEQ_DESCR_RegionMissingText,
324 eErr_SEQ_DESCR_StrucCommMissingPrefixOrSuffix,
325 eErr_SEQ_DESCR_StrucCommMissingUserObject,
326 eErr_SEQ_DESCR_SyntheticConstructNeedsArtificial,
327 eErr_SEQ_DESCR_SyntheticConstructWrongMolType,
328 eErr_SEQ_DESCR_TaxonomyAmbiguousName,
329 eErr_SEQ_DESCR_TaxonomyServiceProblem,
330 eErr_SEQ_DESCR_TitleMissingText,
331 eErr_SEQ_DESCR_TPAassemblyWithoutTPAKeyword,
332 eErr_SEQ_DESCR_UserObjectNoData,
333 eErr_SEQ_DESCR_UserObjectNoType,
334 eErr_SEQ_DESCR_WGSmasterLacksBioProject,
335 eErr_SEQ_DESCR_WGSmasterLacksBioSample,
336 eErr_SEQ_DESCR_WGSMasterLacksBothBioSampleBioProject,
337 eErr_SEQ_DESCR_WrongBiomolForTSA,
338 eErr_SEQ_DESCR_AmbiguousName,
339 eErr_SEQ_DESCR_ModifierTypeConflict,
340 eErr_SEQ_DESCR_AmbiguousModForward,
341 eErr_SEQ_DESCR_AmbiguousTypeMaterial,
342 eErr_SEQ_DESCR_EmptyOrgInput,
343 eErr_SEQ_DESCR_HostIdenticalToOrganism,
344 eErr_SEQ_DESCR_MultipleStrains,
345 eErr_SEQ_DESCR_BadVariety,
346 eErr_SEQ_DESCR_BadTypeMaterial,
347 eErr_SEQ_DESCR_TaxonomyNoCommonAncestor,
348 eErr_SEQ_DESCR_TaxonomyNoValidTaxids,
349 eErr_SEQ_DESCR_TaxonomyEmptyInput,
350 eErr_SEQ_DESCR_ChromosomeWithoutLocation,
351 eErr_SEQ_DESCR_TaxonomyBlankSample,
352 eErr_SEQ_DESCR_NonViralSegment,
353 ERR_CODE_END(SEQ_DESCR),
354
355
356 ERR_CODE_BEGIN(GENERIC) = 2000,
357 eErr_GENERIC_NonAsciiAsn,
358 eErr_GENERIC_Spell,
359 eErr_GENERIC_AuthorListHasEtAl,
360 eErr_GENERIC_MissingPubInfo,
361 eErr_GENERIC_UnnecessaryPubEquiv,
362 eErr_GENERIC_BadPageNumbering,
363 eErr_GENERIC_MedlineEntryPub,
364 eErr_GENERIC_BadDate,
365 eErr_GENERIC_StructuredCitGenCit,
366 eErr_GENERIC_CollidingSerialNumbers,
367 eErr_GENERIC_EmbeddedScript,
368 eErr_GENERIC_PublicationInconsistency,
369 eErr_GENERIC_SgmlPresentInText,
370 eErr_GENERIC_UnexpectedPubStatusComment,
371 eErr_GENERIC_PastReleaseDate,
372 eErr_GENERIC_MissingISOJTA,
373 eErr_GENERIC_MissingVolume,
374 eErr_GENERIC_MissingVolumeEpub,
375 eErr_GENERIC_MissingPages,
376 eErr_GENERIC_MissingPagesEpub,
377 eErr_GENERIC_BarcodeTooShort,
378 eErr_GENERIC_BarcodeMissingPrimers,
379 eErr_GENERIC_BarcodeMissingCountry,
380 eErr_GENERIC_BarcodeMissingVoucher,
381 eErr_GENERIC_BarcodeTooManyNs,
382 eErr_GENERIC_BarcodeBadCollectionDate,
383 eErr_GENERIC_BarcodeMissingOrderAssignment,
384 eErr_GENERIC_BarcodeLowTrace,
385 eErr_GENERIC_BarcodeFrameShift,
386 eErr_GENERIC_BarcodeStructuredVoucher,
387 eErr_GENERIC_BarcodeTestFails,
388 eErr_GENERIC_BarcodeTestPasses,
389 eErr_GENERIC_InvalidAsn,
390 eErr_GENERIC_DeltaSeqError,
391 eErr_GENERIC_DuplicateIDs,
392 eErr_GENERIC_MissingPubRequirement,
393 ERR_CODE_END(GENERIC),
394
395 ERR_CODE_BEGIN(SEQ_PKG) = 3000,
396 eErr_SEQ_PKG_NoCdRegionPtr,
397 eErr_SEQ_PKG_NucProtProblem,
398 eErr_SEQ_PKG_SegSetProblem,
399 eErr_SEQ_PKG_EmptySet,
400 eErr_SEQ_PKG_NucProtNotSegSet,
401 eErr_SEQ_PKG_SegSetNotParts,
402 eErr_SEQ_PKG_SegSetMixedBioseqs,
403 eErr_SEQ_PKG_PartsSetMixedBioseqs,
404 eErr_SEQ_PKG_PartsSetHasSets,
405 eErr_SEQ_PKG_FeaturePackagingProblem,
406 eErr_SEQ_PKG_GenomicProductPackagingProblem,
407 eErr_SEQ_PKG_InconsistentMolInfoBiomols,
408 eErr_SEQ_PKG_ArchaicFeatureLocation,
409 eErr_SEQ_PKG_ArchaicFeatureProduct,
410 eErr_SEQ_PKG_GraphPackagingProblem,
411 eErr_SEQ_PKG_InternalGenBankSet,
412 eErr_SEQ_PKG_ConSetProblem,
413 eErr_SEQ_PKG_NoBioseqFound,
414 eErr_SEQ_PKG_INSDRefSeqPackaging,
415 eErr_SEQ_PKG_GPSnonGPSPackaging,
416 eErr_SEQ_PKG_RefSeqPopSet,
417 eErr_SEQ_PKG_BioseqSetClassNotSet,
418 eErr_SEQ_PKG_OrphanedProtein,
419 eErr_SEQ_PKG_MissingSetTitle,
420 eErr_SEQ_PKG_NucProtSetHasTitle,
421 eErr_SEQ_PKG_ComponentMissingTitle,
422 eErr_SEQ_PKG_SingleItemSet,
423 eErr_SEQ_PKG_MisplacedMolInfo,
424 eErr_SEQ_PKG_ImproperlyNestedSets,
425 eErr_SEQ_PKG_SeqSubmitWithWgsSet,
426 eErr_SEQ_PKG_InconsistentMoltypeSet,
427 ERR_CODE_END(SEQ_PKG),
428
429 ERR_CODE_BEGIN(SEQ_FEAT) = 4000,
430 eErr_SEQ_FEAT_InvalidForType,
431 eErr_SEQ_FEAT_PartialProblem,
432 eErr_SEQ_FEAT_InvalidType,
433 eErr_SEQ_FEAT_Range,
434 eErr_SEQ_FEAT_MixedStrand,
435 eErr_SEQ_FEAT_AnticodonMixedStrand,
436 eErr_SEQ_FEAT_GenomeSetMixedStrand,
437 eErr_SEQ_FEAT_SeqLocOrder,
438 eErr_SEQ_FEAT_CdTransFail,
439 eErr_SEQ_FEAT_StartCodon,
440 eErr_SEQ_FEAT_InternalStop,
441 eErr_SEQ_FEAT_NoProtein,
442 eErr_SEQ_FEAT_MisMatchAA,
443 eErr_SEQ_FEAT_TransLen,
444 eErr_SEQ_FEAT_NoStop,
445 eErr_SEQ_FEAT_TranslExcept,
446 eErr_SEQ_FEAT_MissingProteinName,
447 eErr_SEQ_FEAT_NotSpliceConsensus,
448 eErr_SEQ_FEAT_OrfCdsHasProduct,
449 eErr_SEQ_FEAT_GeneRefHasNoData,
450 eErr_SEQ_FEAT_ExceptInconsistent,
451 eErr_SEQ_FEAT_ProtRefHasNoData,
452 eErr_SEQ_FEAT_GenCodeMismatch,
453 eErr_SEQ_FEAT_RNAtype0,
454 eErr_SEQ_FEAT_UnknownImpFeatKey,
455 eErr_SEQ_FEAT_UnknownImpFeatQual,
456 eErr_SEQ_FEAT_WrongQualOnImpFeat,
457 eErr_SEQ_FEAT_MissingQualOnImpFeat,
458 eErr_SEQ_FEAT_PseudoCdsHasProduct,
459 eErr_SEQ_FEAT_IllegalDbXref,
460 eErr_SEQ_FEAT_FarLocation,
461 eErr_SEQ_FEAT_DuplicateFeat,
462 eErr_SEQ_FEAT_UnnecessaryGeneXref,
463 eErr_SEQ_FEAT_TranslExceptPhase,
464 eErr_SEQ_FEAT_TrnaCodonWrong,
465 eErr_SEQ_FEAT_BothStrands,
466 eErr_SEQ_FEAT_CDSgeneRange,
467 eErr_SEQ_FEAT_CDSmRNArange,
468 eErr_SEQ_FEAT_OverlappingPeptideFeat,
469 eErr_SEQ_FEAT_SerialInComment,
470 eErr_SEQ_FEAT_MultipleCDSproducts,
471 eErr_SEQ_FEAT_FocusOnBioSourceFeature,
472 eErr_SEQ_FEAT_PeptideFeatOutOfFrame,
473 eErr_SEQ_FEAT_InvalidQualifierValue,
474 eErr_SEQ_FEAT_mRNAgeneRange,
475 eErr_SEQ_FEAT_TranscriptLen,
476 eErr_SEQ_FEAT_TranscriptMismatches,
477 eErr_SEQ_FEAT_CDSproductPackagingProblem,
478 eErr_SEQ_FEAT_DuplicateExonInterval,
479 eErr_SEQ_FEAT_DuplicateAnticodonInterval,
480 eErr_SEQ_FEAT_PolyAsiteNotPoint,
481 eErr_SEQ_FEAT_ImpFeatBadLoc,
482 eErr_SEQ_FEAT_LocOnSegmentedBioseq,
483 eErr_SEQ_FEAT_UnnecessaryCitPubEquiv,
484 eErr_SEQ_FEAT_ImpCDShasTranslation,
485 eErr_SEQ_FEAT_ImpCDSnotPseudo,
486 eErr_SEQ_FEAT_MissingMRNAproduct,
487 eErr_SEQ_FEAT_AbuttingIntervals,
488 eErr_SEQ_FEAT_MultiIntervalGene,
489 eErr_SEQ_FEAT_FeatContentDup,
490 eErr_SEQ_FEAT_BadProductSeqId,
491 eErr_SEQ_FEAT_RnaProductMismatch,
492 eErr_SEQ_FEAT_MissingCDSproduct,
493 eErr_SEQ_FEAT_BadTrnaCodon,
494 eErr_SEQ_FEAT_BadTrnaAA,
495 eErr_SEQ_FEAT_OnlyGeneXrefs,
496 eErr_SEQ_FEAT_UTRdoesNotAbutCDS,
497 eErr_SEQ_FEAT_BadConflictFlag,
498 eErr_SEQ_FEAT_ConflictFlagSet,
499 eErr_SEQ_FEAT_LocusTagProblem,
500 eErr_SEQ_FEAT_CollidingLocusTags,
501 eErr_SEQ_FEAT_AltStartCodonException,
502 eErr_SEQ_FEAT_PartialsInconsistent,
503 eErr_SEQ_FEAT_GenesInconsistent,
504 eErr_SEQ_FEAT_DuplicateTranslExcept,
505 eErr_SEQ_FEAT_TranslExceptAndRnaEditing,
506 eErr_SEQ_FEAT_NoNameForProtein,
507 eErr_SEQ_FEAT_TaxonDbxrefOnFeature,
508 eErr_SEQ_FEAT_UnindexedFeature,
509 eErr_SEQ_FEAT_CDSmRNAmismatch,
510 eErr_SEQ_FEAT_UnnecessaryException,
511 eErr_SEQ_FEAT_LocusTagProductMismatch,
512 eErr_SEQ_FEAT_MrnaTransFail,
513 eErr_SEQ_FEAT_PseudoCdsViaGeneHasProduct,
514 eErr_SEQ_FEAT_MissingGeneXref,
515 eErr_SEQ_FEAT_FeatureCitationProblem,
516 eErr_SEQ_FEAT_NestedSeqLocMix,
517 eErr_SEQ_FEAT_WrongQualOnFeature,
518 eErr_SEQ_FEAT_MissingQualOnFeature,
519 eErr_SEQ_FEAT_CodonQualifierUsed,
520 eErr_SEQ_FEAT_UnknownFeatureQual,
521 eErr_SEQ_FEAT_BadCharInAuthorName,
522 eErr_SEQ_FEAT_PolyATail,
523 eErr_SEQ_FEAT_ProteinNameEndsInBracket,
524 eErr_SEQ_FEAT_CDSwithMultipleMRNAs,
525 eErr_SEQ_FEAT_MultipleEquivBioSources,
526 eErr_SEQ_FEAT_MultipleEquivPublications,
527 eErr_SEQ_FEAT_BadFullLengthFeature,
528 eErr_SEQ_FEAT_RedundantFields,
529 eErr_SEQ_FEAT_CDSwithNoMRNAOverlap,
530 eErr_SEQ_FEAT_CDSwithNoMRNA,
531 eErr_SEQ_FEAT_FeatureProductInconsistency,
532 eErr_SEQ_FEAT_ImproperBondLocation,
533 eErr_SEQ_FEAT_GeneXrefWithoutGene,
534 eErr_SEQ_FEAT_SeqFeatXrefProblem,
535 eErr_SEQ_FEAT_ProductFetchFailure,
536 eErr_SEQ_FEAT_SuspiciousGeneXref,
537 eErr_SEQ_FEAT_MissingTrnaAA,
538 eErr_SEQ_FEAT_CollidingFeatureIDs,
539 eErr_SEQ_FEAT_ExceptionProblem,
540 eErr_SEQ_FEAT_PolyAsignalNotRange,
541 eErr_SEQ_FEAT_OldLocusTagMismtach,
542 eErr_SEQ_FEAT_DuplicateGeneOntologyTerm,
543 eErr_SEQ_FEAT_InvalidInferenceValue,
544 eErr_SEQ_FEAT_HypotheticalProteinMismatch,
545 eErr_SEQ_FEAT_FeatureRefersToAccession,
546 eErr_SEQ_FEAT_SelfReferentialProduct,
547 eErr_SEQ_FEAT_ITSdoesNotAbutRRNA,
548 eErr_SEQ_FEAT_FeatureSeqIDCaseDifference,
549 eErr_SEQ_FEAT_FeatureLocationIsGi0,
550 eErr_SEQ_FEAT_GapFeatureProblem,
551 eErr_SEQ_FEAT_PseudoCdsHasProtXref,
552 eErr_SEQ_FEAT_ErroneousException,
553 eErr_SEQ_FEAT_SegmentedGeneProblem,
554 eErr_SEQ_FEAT_WholeLocation,
555 eErr_SEQ_FEAT_BadEcNumberFormat,
556 eErr_SEQ_FEAT_BadEcNumberValue,
557 eErr_SEQ_FEAT_EcNumberProblem,
558 eErr_SEQ_FEAT_VectorContamination,
559 eErr_SEQ_FEAT_MinusStrandProtein,
560 eErr_SEQ_FEAT_BadProteinName,
561 eErr_SEQ_FEAT_GeneXrefWithoutLocus,
562 eErr_SEQ_FEAT_UTRdoesNotExtendToEnd,
563 eErr_SEQ_FEAT_CDShasTooManyXs,
564 eErr_SEQ_FEAT_SuspiciousFrame,
565 eErr_SEQ_FEAT_TerminalXDiscrepancy,
566 eErr_SEQ_FEAT_UnnecessaryTranslExcept,
567 eErr_SEQ_FEAT_SuspiciousQualifierValue,
568 eErr_SEQ_FEAT_NotSpliceConsensusDonor,
569 eErr_SEQ_FEAT_NotSpliceConsensusAcceptor,
570 eErr_SEQ_FEAT_RareSpliceConsensusDonor,
571 eErr_SEQ_FEAT_SeqFeatXrefNotReciprocal,
572 eErr_SEQ_FEAT_SeqFeatXrefFeatureMissing,
573 eErr_SEQ_FEAT_FeatureInsideGap,
574 eErr_SEQ_FEAT_FeatureCrossesGap,
575 eErr_SEQ_FEAT_BadAuthorSuffix,
576 eErr_SEQ_FEAT_BadAnticodonAA,
577 eErr_SEQ_FEAT_BadAnticodonCodon,
578 eErr_SEQ_FEAT_AnticodonStrandConflict,
579 eErr_SEQ_FEAT_UndesiredGeneSynonym,
580 eErr_SEQ_FEAT_UndesiredProteinName,
581 eErr_SEQ_FEAT_FeatureBeginsOrEndsInGap,
582 eErr_SEQ_FEAT_GeneOntologyTermMissingGOID,
583 eErr_SEQ_FEAT_PseudoRnaHasProduct,
584 eErr_SEQ_FEAT_PseudoRnaViaGeneHasProduct,
585 eErr_SEQ_FEAT_BadRRNAcomponentOrder,
586 eErr_SEQ_FEAT_BadRRNAcomponentOverlap,
587 eErr_SEQ_FEAT_MissingGeneLocusTag,
588 eErr_SEQ_FEAT_MultipleProtRefs,
589 eErr_SEQ_FEAT_BadInternalCharacter,
590 eErr_SEQ_FEAT_BadTrailingCharacter,
591 eErr_SEQ_FEAT_BadTrailingHyphen,
592 eErr_SEQ_FEAT_MultipleGeneOverlap,
593 eErr_SEQ_FEAT_BadCharInAuthorLastName,
594 eErr_SEQ_FEAT_PseudoCDSmRNArange,
595 eErr_SEQ_FEAT_ExtendablePartialProblem,
596 eErr_SEQ_FEAT_GeneXrefNeeded,
597 eErr_SEQ_FEAT_RubiscoProblem,
598 eErr_SEQ_FEAT_ProteinNameHasPMID,
599 eErr_SEQ_FEAT_BadGeneOntologyFormat,
600 eErr_SEQ_FEAT_InconsistentGeneOntologyTermAndId,
601 eErr_SEQ_FEAT_DuplicateGeneConflictingLocusTag,
602 eErr_SEQ_FEAT_ShortIntron,
603 eErr_SEQ_FEAT_GeneXrefStrandProblem,
604 eErr_SEQ_FEAT_CDSmRNAXrefLocationProblem,
605 eErr_SEQ_FEAT_LocusCollidesWithLocusTag,
606 eErr_SEQ_FEAT_IdenticalGeneSymbolAndSynonym,
607 eErr_SEQ_FEAT_RptUnitRangeProblem,
608 eErr_SEQ_FEAT_TooManyInferenceAccessions,
609 eErr_SEQ_FEAT_SgmlPresentInText,
610 eErr_SEQ_FEAT_MissingLocation,
611 eErr_SEQ_FEAT_MultipleBioseqs,
612 eErr_SEQ_FEAT_DifferntIdTypesInSeqLoc,
613 eErr_SEQ_FEAT_IntervalBeginsOrEndsInGap,
614 eErr_SEQ_FEAT_InconsistentRRNAstrands,
615 eErr_SEQ_FEAT_CDSonMinusStrandMRNA,
616 eErr_SEQ_FEAT_tRNAmRNAmixup,
617 eErr_SEQ_FEAT_ProductLength,
618 eErr_SEQ_FEAT_InconsistentPseudogeneCounts,
619 eErr_SEQ_FEAT_DeletedEcNumber,
620 eErr_SEQ_FEAT_ReplacedEcNumber,
621 eErr_SEQ_FEAT_SplitEcNumber,
622 eErr_SEQ_FEAT_PeptideFeatureLacksCDS,
623 eErr_SEQ_FEAT_EcNumberDataMissing,
624 eErr_SEQ_FEAT_ShortExon,
625 eErr_SEQ_FEAT_ExtraProteinFeature,
626 eErr_SEQ_FEAT_AssemblyGapAdjacentToNs,
627 eErr_SEQ_FEAT_AssemblyGapCoversSequence,
628 eErr_SEQ_FEAT_FeatureBeginsOrEndsWithN,
629 eErr_SEQ_FEAT_FeatureIsMostlyNs,
630 eErr_SEQ_FEAT_CDSonMinusStrandTranscribedRNA,
631 eErr_SEQ_FEAT_MultipleGenCodes,
632 eErr_SEQ_FEAT_InvalidFuzz,
633 eErr_SEQ_FEAT_BadCDScomment,
634 eErr_SEQ_FEAT_IntronIsStopCodon,
635 eErr_SEQ_FEAT_InconsistentPseudogeneValue,
636 eErr_SEQ_FEAT_MultiIntervalIntron,
637 eErr_SEQ_FEAT_SeqLocTypeProblem,
638 eErr_SEQ_FEAT_RefSeqInText,
639 eErr_SEQ_FEAT_ColdShockProteinProblem,
640 eErr_SEQ_FEAT_BadLocation,
641 eErr_SEQ_FEAT_GenCodeInvalid,
642 eErr_SEQ_FEAT_TranslExceptIsPartial,
643 eErr_SEQ_FEAT_GeneIdMismatch,
644 eErr_SEQ_FEAT_ProductShouldBeWhole,
645 eErr_SEQ_FEAT_CDSmRNAMismatchProteinIDs,
646 eErr_SEQ_FEAT_CDSmRNAMissingProteinIDs,
647 eErr_SEQ_FEAT_CDSmRNAMismatchTranscriptIDs,
648 eErr_SEQ_FEAT_CDSmRNAmismatchCount,
649 eErr_SEQ_FEAT_CDSmRNAMismatchLocation,
650 eErr_SEQ_FEAT_CDSmRNANotMatched,
651 eErr_SEQ_FEAT_PartialProblemHasStop,
652 eErr_SEQ_FEAT_PartialProblemMismatch3Prime,
653 eErr_SEQ_FEAT_PartialProblemMismatch5Prime,
654 eErr_SEQ_FEAT_PartialProblemNotSpliceConsensus3Prime,
655 eErr_SEQ_FEAT_PartialProblemNotSpliceConsensus5Prime,
656 eErr_SEQ_FEAT_PartialProblemmRNASequence5Prime,
657 eErr_SEQ_FEAT_PartialProblemmRNASequence3Prime,
658 eErr_SEQ_FEAT_PartialProblemOrganelle5Prime,
659 eErr_SEQ_FEAT_PartialProblemOrganelle3Prime,
660 eErr_SEQ_FEAT_PartialProblem5Prime,
661 eErr_SEQ_FEAT_PartialProblem3Prime,
662 eErr_SEQ_FEAT_PartialsInconsistentCDSProtein,
663 eErr_SEQ_FEAT_InvalidPseudoQualifier,
664 eErr_SEQ_FEAT_InvalidRptUnitRange,
665 eErr_SEQ_FEAT_InvalidRptUnitSeqCharacters,
666 eErr_SEQ_FEAT_InvalidRepeatUnitLength,
667 eErr_SEQ_FEAT_MismatchedAllele,
668 eErr_SEQ_FEAT_InvalidOperonMatchesGene,
669 eErr_SEQ_FEAT_InvalidPunctuation,
670 eErr_SEQ_FEAT_InvalidAlleleDuplicates,
671 eErr_SEQ_FEAT_InvalidCompareRefSeqAccession,
672 eErr_SEQ_FEAT_RepeatSeqDoNotMatch,
673 eErr_SEQ_FEAT_RecombinationClassOtherNeedsNote,
674 eErr_SEQ_FEAT_RegulatoryClassOtherNeedsNote,
675 eErr_SEQ_FEAT_UnparsedtRNAAnticodon,
676 eErr_SEQ_FEAT_UnparsedtRNAProduct,
677 eErr_SEQ_FEAT_rRNADoesNotHaveProduct,
678 eErr_SEQ_FEAT_InvalidCompareMissingVersion,
679 eErr_SEQ_FEAT_InvalidCompareBadAccession,
680 eErr_SEQ_FEAT_MobileElementInvalidQualifier,
681 eErr_SEQ_FEAT_InvalidReplace,
682 eErr_SEQ_FEAT_InvalidVariationReplace,
683 eErr_SEQ_FEAT_InvalidNumberQualifier,
684 eErr_SEQ_FEAT_InvalidProductOnGene,
685 eErr_SEQ_FEAT_InvalidMatchingReplace,
686 eErr_SEQ_FEAT_InvalidCodonStart,
687 eErr_SEQ_FEAT_WrongQualOnCDS,
688 eErr_SEQ_FEAT_EcNumberInCDSComment,
689 eErr_SEQ_FEAT_EcNumberInProteinName,
690 eErr_SEQ_FEAT_EcNumberInProteinComment,
691 eErr_SEQ_FEAT_EcNumberEmpty,
692 eErr_SEQ_FEAT_GeneLocusCollidesWithLocusTag,
693 eErr_SEQ_FEAT_LocusTagGeneLocusMatch,
694 eErr_SEQ_FEAT_LocusTagHasSpace,
695 eErr_SEQ_FEAT_OldLocusTagBadFormat,
696 eErr_SEQ_FEAT_OldLocusTagWithoutLocusTag,
697 eErr_SEQ_FEAT_BadRRNAcomponentOverlapRRNA,
698 eErr_SEQ_FEAT_BadRRNAcomponentOverlapAndOrder,
699 eErr_SEQ_FEAT_BadRRNAcomponentOverlapTRNA,
700 eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron,
701 eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron,
702 eErr_SEQ_FEAT_IdenticalMRNAtranscriptIDs,
703 eErr_SEQ_FEAT_InvalidFeatureForMRNA,
704 eErr_SEQ_FEAT_InvalidFeatureForNucleotide,
705 eErr_SEQ_FEAT_InvalidFeatureForProtein,
706 eErr_SEQ_FEAT_InvalidRNAFeature,
707 eErr_SEQ_FEAT_InvalidTRNAdata,
708 eErr_SEQ_FEAT_mRNAUnnecessaryException,
709 eErr_SEQ_FEAT_AssemblyGapFeatureProblem,
710 eErr_SEQ_FEAT_ExceptionMissingText,
711 eErr_SEQ_FEAT_MiscFeatureNeedsNote,
712 eErr_SEQ_FEAT_MissingExceptionFlag,
713 eErr_SEQ_FEAT_NoCDSbetweenUTRs,
714 eErr_SEQ_FEAT_RepeatRegionNeedsNote,
715 eErr_SEQ_FEAT_CDSrange,
716 eErr_SEQ_FEAT_tRNArange,
717 eErr_SEQ_FEAT_ExceptionRequiresLocusTag,
718 eErr_SEQ_FEAT_BadTranssplicedInterval,
719 eErr_SEQ_FEAT_TRNAinsideTMRNA,
720 eErr_SEQ_FEAT_IncorrectQualifierCapitalization,
721 eErr_SEQ_FEAT_CDSdoesNotMatchVDJC,
722 eErr_SEQ_FEAT_GeneOnNucPositionOfPeptide,
723 ERR_CODE_END(SEQ_FEAT),
724
725 ERR_CODE_BEGIN(SEQ_ALIGN) = 5000,
726 eErr_SEQ_ALIGN_SeqIdProblem,
727 eErr_SEQ_ALIGN_StrandRev,
728 eErr_SEQ_ALIGN_DensegLenStart,
729 eErr_SEQ_ALIGN_StartLessthanZero,
730 eErr_SEQ_ALIGN_StartMorethanBiolen,
731 eErr_SEQ_ALIGN_EndLessthanZero,
732 eErr_SEQ_ALIGN_EndMorethanBiolen,
733 eErr_SEQ_ALIGN_LenLessthanZero,
734 eErr_SEQ_ALIGN_LenMorethanBiolen,
735 eErr_SEQ_ALIGN_SumLenStart,
736 eErr_SEQ_ALIGN_AlignDimSeqIdNotMatch,
737 eErr_SEQ_ALIGN_SegsDimSeqIdNotMatch,
738 eErr_SEQ_ALIGN_FastaLike,
739 eErr_SEQ_ALIGN_NullSegs,
740 eErr_SEQ_ALIGN_SegmentGap,
741 eErr_SEQ_ALIGN_SegsDimOne,
742 eErr_SEQ_ALIGN_AlignDimOne,
743 eErr_SEQ_ALIGN_Segtype,
744 eErr_SEQ_ALIGN_BlastAligns,
745 eErr_SEQ_ALIGN_PercentIdentity,
746 eErr_SEQ_ALIGN_ShortAln,
747 eErr_SEQ_ALIGN_UnexpectedAlignmentType,
748 eErr_SEQ_ALIGN_SegsDimMismatch,
749 eErr_SEQ_ALIGN_SegsNumsegMismatch,
750 eErr_SEQ_ALIGN_SegsStartsMismatch,
751 eErr_SEQ_ALIGN_SegsPresentMismatch,
752 eErr_SEQ_ALIGN_SegsPresentStartsMismatch,
753 eErr_SEQ_ALIGN_SegsPresentStrandsMismatch,
754 eErr_SEQ_ALIGN_NucProtMixture,
755
756 ERR_CODE_END(SEQ_ALIGN),
757
758 ERR_CODE_BEGIN(SEQ_GRAPH) = 6000,
759 eErr_SEQ_GRAPH_GraphMin,
760 eErr_SEQ_GRAPH_GraphMax,
761 eErr_SEQ_GRAPH_GraphBelow,
762 eErr_SEQ_GRAPH_GraphAbove,
763 eErr_SEQ_GRAPH_GraphByteLen,
764 eErr_SEQ_GRAPH_GraphOutOfOrder,
765 eErr_SEQ_GRAPH_GraphBioseqLen,
766 eErr_SEQ_GRAPH_GraphSeqLitLen,
767 eErr_SEQ_GRAPH_GraphSeqLocLen,
768 eErr_SEQ_GRAPH_GraphStartPhase,
769 eErr_SEQ_GRAPH_GraphStopPhase,
770 eErr_SEQ_GRAPH_GraphDiffNumber,
771 eErr_SEQ_GRAPH_GraphACGTScore,
772 eErr_SEQ_GRAPH_GraphNScore,
773 eErr_SEQ_GRAPH_GraphGapScore,
774 eErr_SEQ_GRAPH_GraphOverlap,
775 eErr_SEQ_GRAPH_GraphBioseqId,
776 eErr_SEQ_GRAPH_GraphACGTScoreMany,
777 eErr_SEQ_GRAPH_GraphNScoreMany,
778 eErr_SEQ_GRAPH_GraphLocInvalid,
779 ERR_CODE_END(SEQ_GRAPH),
780
781 ERR_CODE_BEGIN(SEQ_ANNOT) = 7000,
782 eErr_SEQ_ANNOT_AnnotIDs,
783 eErr_SEQ_ANNOT_AnnotLOCs,
784 ERR_CODE_END(SEQ_ANNOT),
785
786 ERR_CODE_BEGIN(INTERNAL) = 8000,
787 eErr_INTERNAL_Exception,
788 ERR_CODE_END(INTERNAL),
789
790 eErr_MAX
791 };
792
793 /////////////////////////////////////////////////////////////////////////////
794 class NCBI_VALERR_EXPORT CValidErrItem : public CValidErrItem_Base
795 {
796 typedef CValidErrItem_Base Tparent;
797 public:
798
799 // destructor
800 CValidErrItem(void);
801 ~CValidErrItem(void);
802
803 // severity with proper type.
804 EDiagSev GetSeverity (void) const;
805 // Error code
806 const string GetErrCode (void) const;
807 static size_t GetErrCount(void);
808 // Error group (SEQ_FEAT, SEQ_INST etc.)
809 const string GetErrGroup (void) const;
810 // Verbose message
811 const string GetVerbose (void) const;
812 // Offending object
813 const CSerialObject& GetObject (void) const;
814 bool IsSetObject (void) const;
815 void SetObject(const CSerialObject& obj);
816
817 // Convert Severity from enum to a string representation
818 static const string ConvertSeverity(EDiagSev sev);
819 static const string ConvertErrCode(unsigned int);
820 static const string ConvertErrGroup(unsigned int);
821
822 // Convert error code from string to unsigned int
823 static unsigned int ConvertToErrCode(const string& str);
824
825 bool IsSetContext(void) const;
826 const CSeq_entry& GetContext(void) const;
SetContext(CConstRef<CSeq_entry> ctx)827 void SetContext(CConstRef<CSeq_entry> ctx) { m_Ctx = ctx; }
828
829 // use previously populated fields to construct the "standard" description
830 void SetFeatureObjDescFromFields();
831
832 private:
833 friend class CValidError;
834
835 // constructor
836 CValidErrItem(EDiagSev sev, // severity
837 unsigned int ec, // error code
838 const string& msg, // message
839 const string& obj_desc, // object description
840 const CSerialObject& obj, // offending object
841 const string& acc, // accession
842 const int ver, // version of object.
843 const int seq_offset = 0); // sequence offset
844
845 CValidErrItem(EDiagSev sev, // severity
846 unsigned int ec, // error code
847 const string& msg, // message
848 const string& obj_desc, // object description
849 const CSerialObject& obj, // offending object
850 const string& acc, // accession
851 const int ver, // version of object.
852 const string& feature_id, // feature ID
853 const int seq_offset = 0); // sequence offset
854
855 // constructor
856 CValidErrItem(EDiagSev sev, // severity
857 unsigned int ec, // error code
858 const string& msg, // message
859 const string& obj_desc, // object description
860 const CSerialObject& obj, // offending object
861 const CSeq_entry& context, // desc's context.
862 const string& acc, // accession
863 const int ver, // version of object.
864 const int seq_offset = 0); // sequence offset
865
866 // Prohibit default & copy constructor and assignment operator
867 CValidErrItem(const CValidErrItem& value);
868 CValidErrItem& operator=(const CValidErrItem& value);
869
870 // member data values that are not serialized.
871 CConstRef<CSerialObject> m_Object; // offending object
872 CConstRef<CSeq_entry> m_Ctx; // currently used for Seqdesc objects only
873
874 static const string sm_Terse[];
875 static const string sm_Verbose[];
876 };
877
878 /////////////////// CValidErrItem inline methods
879
880 // constructor
881 inline
CValidErrItem(void)882 CValidErrItem::CValidErrItem(void)
883 {
884 }
885
886
887 inline
GetSeverity(void) const888 EDiagSev CValidErrItem::GetSeverity(void) const
889 {
890 // convert from internal integer to external enum type.
891 return static_cast<EDiagSev>(GetSev());
892 }
893
894
895 inline
IsSetContext(void) const896 bool CValidErrItem::IsSetContext(void) const
897 {
898 return m_Ctx.NotEmpty();
899 }
900
901 inline
GetContext(void) const902 const CSeq_entry& CValidErrItem::GetContext(void) const
903 {
904 return *m_Ctx;
905 }
906
907
908 /////////////////// end of CValidErrItem inline methods
909
910
911
912 END_objects_SCOPE // namespace ncbi::objects::
913
914 END_NCBI_SCOPE
915
916 #endif // OBJECTS_VALERR_VALIDERRITEM_HPP
917 /* Original file checksum: lines: 94, chars: 2634, CRC32: d01b90f9 */
918