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NCBI C++ ToolKit: src/objtools/writers/unit_test/unit_test_gff3writer.cpp Source File

( ! dirEntry.

() ) {

name =

.GetName();

sFileName =

.GetName();

vector<string> vecFileNamePieces;

( sFileName,

, vecFileNamePieces );

BOOST_REQUIRE(vecFileNamePieces.size() == 3);

sTestName = vecFileNamePieces[0];

BOOST_REQUIRE(!sTestName.empty());

sObjType = vecFileNamePieces[1];

BOOST_REQUIRE(!sObjType.empty());

sFileType = vecFileNamePieces[2];

BOOST_REQUIRE(!sFileType.empty());

(*m_pTestNameToInfoMap)[vecFileNamePieces[0]];

list<string> supportedObjectTypes{

,

,

,

,

,

};

typeIt = std::find(supportedObjectTypes.begin(), supportedObjectTypes.end(), sObjType);

(typeIt == supportedObjectTypes.end()) {

BOOST_FAIL(

<< sObjType <<

);

test_info_to_load.

= sObjType;

BOOST_FAIL(

<< sFileName <<

);

BOOST_FAIL(

<<

<<

);

cerr <<

<<

<<

<< endl;

(!pI->EndOfData()) {

(

& alignIt: pAlignSet->

()) {

pEntry->

(*pBioseq_set);

cerr <<

<<

<<

<< endl;

cerr <<

<< endl;

vector<string> kEmptyStringVec;

& sName = name_to_info_it->first +

+ name_to_info_it->second.mObjType;

cerr <<

<< testInfo.

.

() <<

<<

(testInfo.

==

) {

(testInfo.

==

) {

(testInfo.

==

) {

(!pI->EndOfData()) {

(testInfo.

==

) {

(

& alignIt: pAlignSet->

()) {

(testInfo.

==

) {

BOOST_ERROR(

<< sTestName <<

);

(!success && keep) {

BOOST_ERROR(

<< sTestName <<

);

arg_descrs->AddDefaultKey(

,

,

,

arg_descrs->AddDefaultKey(

,

,

,

arg_descrs->AddFlag(

,

,

arg_descrs->AddFlag(

,

,

test_cases_dir( args[

].AsDirectory() );

BOOST_REQUIRE_MESSAGE( test_cases_dir.

(),

<< test_cases_dir.

() );

update_all = args[

].AsBoolean();

update_case = args[

].AsString();

(!update_case.empty()) {

vector<string> kEmptyStringVec;

& sName = name_to_info_it->first;

& testInfo = name_to_info_it->second;

cout <<

<< sName << endl;

& sName = name_to_info_it->first;

& testInfo = name_to_info_it->second;

cout <<

<< sName << endl;

BOOST_CHECK_NO_THROW(

(sName, testInfo, args[

]));

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

bool WriteAnnot(const CSeq_annot &annot, const string &asmblyName="", const string &asmblyAccession="") override

Write a trailer marking the end of a parsing context.

bool WriteBioseqHandle(CBioseq_Handle bsh, const string &asmblyName="", const string &asmblyAccession="") override

Write Bioseq contained in given handle Essentially, will write all features that live on the given Bi...

bool WriteSeqEntryHandle(CSeq_entry_Handle seh, const string &asmblyName="", const string &asmblyAccession="") override

Write Seq-entry contained in a given handle.

bool WriteAlign(const CSeq_align &, const string &asmblyName="", const string &asmblyAccession="") override

Write a raw Seq-align to the internal output stream.

bool WriteFooter() override

Write a file trailer.

bool WriteHeader() override

Write a file header.

static CNcbiApplication * Instance(void)

Singleton method.

TTestNameToInfoMap * m_pTestNameToInfoMap

void operator()(const CDirEntry &dirEntry)

CTestNameToInfoMapLoader(TTestNameToInfoMap *pTestNameToInfoMap, const string &extInput, const string &extOutput, const string &extErrors)

static void test_type(TDSSOCKET *tds, TDSCOLUMN *col)

static SQLCHAR output[256]

static int RunTests(void)

Code to iterate through all tests to run.

static char test_name[128]

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eString

An arbitrary string.

@ eDirectory

Name of file directory.

void FindFilesInDir(const CDir &dir, const vector< string > &masks, const vector< string > &masks_subdir, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Find files in the specified directory.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

bool CompareTextContents(const string &file, ECompareText mode, size_t buf_size=0) const

Compare files contents in text form.

bool IsFile(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a file.

static string GetTmpName(ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

string GetName(void) const

Get the base entry name with extension (if any).

const string & GetPath(void) const

Get entry path.

virtual bool Copy(const string &new_path, TCopyFlags flags=fCF_Default, size_t buf_size=0) const

Copy the entry to a location specified by "new_path".

virtual bool Exists(void) const

Check existence of file.

@ fCF_Overwrite

The following flags define what to do when the destination entry already exists:

@ fFF_Recursive

descend into sub-dirs

@ fFF_Default

default behavior

@ eSerial_AsnText

ASN.1 text.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

TLoader * GetLoader(void) const

Get pointer to the loader.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

const Tdata & Get(void) const

Get the member data.

TSet & SetSet(void)

Select the variant.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

Utility stuff for more convenient using of Boost.Test library.

BOOST_AUTO_TEST_CASE(RunTests)

const string extErrors("errors")

void sUpdateAll(CDir &test_cases_dir)

map< TTestName, STestInfo > TTestNameToInfoMap

const string dirTestFiles("gff3writer_test_cases")

CGff3Writer * sGetWriter(CScope &scope, CNcbiOstream &ostr)

const string extOutput("gff3")

void sUpdateCase(CDir &test_cases_dir, const string &test_name)

const string extInput("asn")

const string extKeep("new")

void sRunTest(const string &sTestName, const STestInfo &testInfo, bool keep)

NCBITEST_INIT_CMDLINE(arg_descrs)

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