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NCBI C++ ToolKit: include/objtools/unit_test_util/unit_test_util.hpp Source File

(

& sTestNAme,

(

& sErrorText) = 0;

dirWithTestCases,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

map< string, CFile > TMapSuffixToFile

virtual void RunTest(const string &sTestNAme, const TMapSuffixToFile &mapSuffixToFile)=0

This function is called for each test.

virtual void OnError(const string &sErrorText)=0

This is called when an error occurs, and if ITestRunner is using boost it should indicate that using,...

virtual ~ITestRunner(void)

Include a standard set of the NCBI C++ Toolkit most basic headers.

TLoader * GetLoader(void) const

Get pointer to the loader.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool RevokeDataLoader(CDataLoader &loader)

Revoke previously registered data loader.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_UNIT_TEST_UTIL_EXPORT

const struct ncbi::grid::netcache::search::fields::KEY key

Defines NCBI C++ diagnostic APIs, classes, and macros.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static const GLdouble origin[]

void SetSynthetic_construct(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGenProdSetNucProtSet(CRef< objects::CSeq_id > nuc_id, CRef< objects::CSeq_id > prot_id)

CRef< objects::CPub > BuildGoodCitGenPub(CRef< objects::CAuthor > author, int serial_number)

void ReverseAlignmentStrand(objects::CDense_seg &denseg, size_t pos, size_t seq_len)

CRef< objects::CSeq_feat > MakeGeneForFeature(CRef< objects::CSeq_feat > feat)

CRef< objects::CSeq_feat > MakeMiscFeature(CRef< objects::CSeq_id > id, size_t right_end=10, size_t left_end=0)

CRef< objects::CAuthor > BuildGoodAuthor()

void SetDrosophila_melanogaster(CRef< objects::CSeq_entry > entry)

void SetTaxon(objects::CBioSource &src, size_t taxon)

void SetSubSource(objects::CBioSource &src, objects::CSubSource::TSubtype subtype, string val)

CRef< objects::CSeq_annot > BuildGoodGraphAnnot(string id)

void SetChromosome(objects::CBioSource &src, string chromosome)

void SetTech(CRef< objects::CSeq_entry > entry, objects::CMolInfo::TTech tech)

CRef< objects::CSeq_entry > BuildGoodEcoSetWithAlign(size_t front_insert=5)

void ChangeNucId(CRef< objects::CSeq_entry > np_set, CRef< objects::CSeq_id > id)

CRef< objects::CSeq_feat > AddProtFeat(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_id > BuildRefSeqId(void)

CRef< objects::CPub > BuildGoodArticlePub()

CRef< objects::CSeq_feat > AddGoodImpFeat(CRef< objects::CSeq_entry > entry, string key)

void SetFocus(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > GetNucProtSetFromGenProdSet(CRef< objects::CSeq_entry > entry)

void SetGenome(CRef< objects::CSeq_entry > entry, objects::CBioSource::TGenome genome)

void AddToDeltaSeq(CRef< objects::CSeq_entry > entry, string seq)

void SetDiv(CRef< objects::CSeq_entry > entry, string div)

void ChangeProtId(CRef< objects::CSeq_entry > np_set, CRef< objects::CSeq_id > id)

CRef< objects::CSeq_entry > MakeProteinForGoodNucProtSet(string id)

void ChangeProductId(CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_id > id)

CRef< objects::CSeq_feat > GetCDSFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_align > BuildGoodAlign()

void SetSebaea_microphylla(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeqdesc > BuildGoodPubSeqdesc()

CRef< objects::CPub > BuildGoodCitSubPub()

CRef< CSeq_feat > BuildGoodFeat()

CRef< objects::CSeq_entry > BuildGoodProtSeq(void)

void ResetOrgname(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_feat > GetCDSFromGenProdSet(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_annot > AddFeat(CRef< objects::CSeq_feat > feat, CRef< objects::CSeq_entry > entry)

void SetTaxname(CRef< objects::CSeq_entry > entry, string taxname)

CRef< objects::CSeq_feat > GetmRNAFromGenProdSet(CRef< objects::CSeq_entry > entry)

ETraverseAndRunTestCasesFlags

Flags that control TraverseAndRunTestCases, if needed.

@ fTraverseAndRunTestCasesFlags_DoNOTIgnoreREADMEFiles

Overrides default behavior (which is to disregard files whose prefix is "README")

void RetranslateCdsForNucProtSet(CRef< objects::CSeq_entry > entry, objects::CScope &scope)

void ChangeNucProtSetProteinId(CRef< objects::CSeq_entry > entry, CRef< objects::CSeq_id > id)

void TraverseAndRunTestCases(ITestRunner *pTestRunner, CDir dirWithTestCases, const set< string > &setOfRequiredSuffixes, const set< string > &setOfOptionalSuffixes=set< string >(), const set< string > &setOfIgnoredSuffixes=set< string >(), TTraverseAndRunTestCasesFlags fFlags=0)

This is for running data-driven test cases below the given top-level test directory.

void SetCompleteness(CRef< objects::CSeq_entry > entry, objects::CMolInfo::TCompleteness completeness)

CRef< objects::CSeq_entry > BuildSegSetPart(string id_str)

void SetNucProtSetPartials(CRef< objects::CSeq_entry > entry, bool partial5, bool partial3)

void SetOrigin(CRef< objects::CSeq_entry > entry, objects::CBioSource::TOrigin origin)

int TTraverseAndRunTestCasesFlags

CRef< objects::CSeq_entry > BuildGoodSeq(void)

CRef< objects::CSeq_feat > MakeIntronForMixLoc(CRef< objects::CSeq_id > id)

void SetSpliceForMixLoc(objects::CBioseq &seq)

CRef< objects::CSeq_feat > AddMiscFeature(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGoodEcoSet()

void SetTransgenic(objects::CBioSource &src, bool do_set)

CRef< objects::CSeq_id > IdFromEntry(CRef< objects::CSeq_entry > entry)

void ChangeId(CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_id > id)

void MakeNucProtSet3Partial(CRef< objects::CSeq_entry > entry)

void SetMGcode(CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode mgcode)

CRef< objects::CSeq_feat > GetProtFeatFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > GetProteinSequenceFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

void SetPGcode(CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode pgcode)

void RemoveDescriptorType(CRef< objects::CSeq_entry > entry, objects::CSeqdesc::E_Choice desc_choice)

void SetProteinPartial(CRef< objects::CSeq_entry > pentry, bool partial5, bool partial3)

void SetBiomol(CRef< objects::CSeq_entry > entry, objects::CMolInfo::TBiomol biomol)

CRef< objects::CSeq_entry > BuildGoodNucProtSet(void)

CRef< objects::CSeq_feat > MakemRNAForCDS(CRef< objects::CSeq_feat > feat)

CRef< objects::CSeq_entry > BuildGoodSegSet(void)

void SetOrgMod(objects::CBioSource &src, objects::COrgMod::TSubtype subtype, string val)

CRef< objects::CSeq_entry > GetNucleotideSequenceFromGoodNucProtSet(CRef< objects::CSeq_entry > entry)

void ClearFocus(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_loc > MakeMixLoc(CRef< objects::CSeq_id > id)

void SetNucProtSetProductName(CRef< objects::CSeq_entry > entry, string new_name)

void AddGoodPub(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_feat > MakeCDSForGoodNucProtSet(const string &nuc_id, const string &prot_id)

void AddGoodSource(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_feat > BuildtRNA(CRef< objects::CSeq_id > id)

void SetCommon(CRef< objects::CSeq_entry > entry, string common)

void RevComp(objects::CBioseq &bioseq)

void SetGcode(CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode gcode)

CRef< objects::CSeq_feat > BuildGoodtRNA(CRef< objects::CSeq_id > id)

void ChangeNucProtSetNucId(CRef< objects::CSeq_entry > entry, CRef< objects::CSeq_id > id)

void AdjustProtFeatForNucProtSet(CRef< objects::CSeq_entry > entry)

void RemoveDeltaSeqGaps(CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > BuildGoodDeltaSeq(void)

CRef< objects::CSeq_feat > AddGoodSourceFeature(CRef< objects::CSeq_entry > entry)

void AddFeatAnnotToSeqEntry(CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_entry > entry)

CRef< objects::CSeq_entry > GetGenomicFromGenProdSet(CRef< objects::CSeq_entry > entry)

void SetDbxref(objects::CBioSource &src, string db, objects::CObject_id::TId id)

void MakeSeqLong(objects::CBioseq &seq)

CRef< objects::CSeq_entry > BuildGoodGenProdSet()

void SetLineage(CRef< objects::CSeq_entry > entry, string lineage)

void RemoveDbxref(objects::CBioSource &src, string db, objects::CObject_id::TId id)

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