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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestalnreader_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/unit_test/unit_test_alnreader.cpp Source File

61 const string

& filename) {

62 mStream

.open(filename.c_str());

89 if

(!err.

SeqId

().empty()) {

93 if

(err.

Line

() == 0) {

95

"None (Encountered during pre or post processing)"

<< endl;

103 mStream

"Problem : "

<< codeStr <<

"."

<< subCodeStr << endl;

106

vector<string> messageLines;

108 if

(!messageLines.empty()) {

109 mStream

"Message : "

<< messageLines.front() << endl;

110 for

(

auto i

=1;

< messageLines.size(); ++

) {

111 mStream

" "

<< messageLines[

] << endl;

116 if

(!qualName.empty()) {

117 mStream

"Mod Name : "

<< qualName << endl;

121 if

(!qualValue.empty()) {

122 mStream

"Mod Value : "

<< qualValue << endl;

170 if

(!dirEntry.

IsFile

()) {

175 string

name =

file

.GetName();

183 const string

sFileName =

file

.GetName();

184

vector<CTempString> vecFileNamePieces;

186

BOOST_REQUIRE(vecFileNamePieces.size() == 2);

189

BOOST_REQUIRE(!tsTestName.

empty

());

191

BOOST_REQUIRE(!tsFileType.

empty

());

194

(*m_pTestNameToInfoMap)[vecFileNamePieces[0]];

211

BOOST_FAIL(

"Unknown file type "

<< sFileName <<

"."

);

225 const string

& testName,

233

pReader->SetUseNexusInfo(

false

);

240 const string

& testName)

252

BOOST_FAIL(

"input file "

input

" does not exist."

);

254

cerr <<

"Creating new test case from "

input

" ..."

<< endl;

267

pReader->Read(

flags

, &logger);

270 catch

(std::exception&) {

273

cerr <<

" Produced new error listing "

output

"."

<< endl;

280

cerr <<

" Produced new ASN1 file "

output

"."

<< endl;

281

cerr <<

" ... Done."

<< endl;

287 const

vector<string> kEmptyStringVec;

299 const string

& sName = name_to_info_it->first;

307

cerr <<

"Testing "

<< testInfo.

mInFile

GetName

() <<

" against "

317

unique_ptr<CAlnReader> pReader(

sGetReader

(sTestName, ifstr));

326

pReader->Read(

flags

, &logger);

327

pEntry = pReader->GetSeqEntry(

sGetFastaFlags

(sTestName), &logger);

344 if

(!successOutput) {

350 if

(!successErrors) {

356 if

(!successOutput || !successErrors) {

357

BOOST_ERROR(

"Error: "

<< sTestName <<

" failed due to post processing diffs."

);

370

arg_descrs->AddDefaultKey(

"test-dir"

"TEST_FILE_DIRECTORY"

371 "Set the root directory under which all test files can be found."

375

arg_descrs->AddDefaultKey(

"update-case"

"UPDATE_CASE"

376 "Produce .asn and .error files from given name for new or updated test case."

380

arg_descrs->AddFlag(

"update-all"

381 "Update all test cases to current reader code (dangerous)."

384

arg_descrs->AddFlag(

"keep-diffs"

385 "Keep output files that are different from the expected."

387

arg_descrs->AddDefaultKey(

"single-case"

389 "Run specified case only"

403 CDir

test_cases_dir( args[

"test-dir"

].AsDirectory() );

404

BOOST_REQUIRE_MESSAGE( test_cases_dir.

IsDir

(),

405 "Cannot find dir: "

<< test_cases_dir.

GetPath

() );

407 bool

update_all = args[

"update-all"

].AsBoolean();

413 string

update_case = args[

"update-case"

].AsString();

414 if

(!update_case.empty()) {

419 string

single_case = args[

"single-case"

].AsString();

420 if

(!single_case.empty()) {

428

BOOST_CHECK_NO_THROW(

429 sRunTest

(single_case, testInfo, args[

"keep-diffs"

]));

433 const

vector<string> kEmptyStringVec;

443 const string

& sName = name_to_info_it->first;

444 const STestInfo

& testInfo = name_to_info_it->second;

445

cout <<

"Verifying: "

<< sName << endl;

455 const string

& sName = name_to_info_it->first;

456 const STestInfo

& testInfo = name_to_info_it->second;

457

cout <<

"Running test: "

<< sName << endl;

459

BOOST_CHECK_NO_THROW(

sRunTest

(sName, testInfo, args[

"keep-diffs"

]));

class CAlnReader supports importing a large variety of text-based alignment formats into standard dat...

int TReadFlags

binary OR of EReadFlags

objects::CFastaDeflineReader::TFastaFlags TFastaFlags

bool PutError(const ILineError &err)

Store error in the container, and return true if error was stored fine, and return false if the calle...

CErrorLogger(const string &filename)

size_t Count() const override

void StoreError(const ILineError &err)

static CNcbiApplication * Instance(void)

Singleton method.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

TTestNameToInfoMap * m_pTestNameToInfoMap

void operator()(const CDirEntry &dirEntry)

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

virtual const string & QualifierName(void) const =0

virtual EDiagSev Severity(void) const

virtual string Message() const

virtual int GetCode(void) const

virtual int GetSubCode(void) const

string SeverityStr() const

virtual const string & SeqId(void) const =0

virtual unsigned int Line(void) const =0

virtual const string & QualifierValue(void) const =0

Operators to edit gaps in sequences.

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.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

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.

@ fFF_Recursive

descend into sub-dirs

@ fFF_Default

default behavior

#define ENUM_METHOD_NAME(EnumName)

#define MSerial_AsnText

I/O stream manipulators â.

@ fAddMods

Parse defline mods and add to SeqEntry.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Check if a string ends with a specified suffix value.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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

Check if a string starts with a specified prefix value.

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 dirTestFiles("alnreader_test_cases")

const string extErrors("errors")

CAlnReader * sGetReader(const string &testName, ifstream &ifstr)

CAlnReader::TFastaFlags sGetFastaFlags(const string &testName)

void sUpdateAll(CDir &test_cases_dir)

const string extInput("aln")

const string extOutput("asn")

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

const string extKeep("new")

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

NCBITEST_INIT_CMDLINE(arg_descrs)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unit__test__alnreader_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/unit_test/unit_test_alnreader.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/unittestalnreader_8cpp_source.html below: