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NCBI C++ ToolKit: src/algo/sequence/unit_test/unit_test_orf.cpp Source File

arg_desc->AddKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

comment = desc.

().front()->GetComment();

vector<string> allowable_starts;

longest_orfs =

;

longest = find(allowable_starts.begin(), allowable_starts.end(),

);

(longest != allowable_starts.end()) {

longest_orfs =

;

allowable_starts.erase(longest);

min_length = 300;

max_seq_gap = 30;

(sv, loc_vec, min_length, gcode, allowable_starts, longest_orfs, max_seq_gap);

my_annot->

().Assign(desc);

BOOST_CHECK(my_annot->

(*ref_annot));

;

vector<string> allowable_starts = {{

}};

BOOST_CHECK_NO_THROW(

BOOST_CHECK_EQUAL(loc_vec.size(), 2);

;

vector<string> allowable_starts;

BOOST_CHECK_NO_THROW(

(seq, loc_vec, 60, 11, allowable_starts,

(

& loc: loc_vec) {

BOOST_CHECK(loc_vec.size() > 0);

vector<string> allowable_starts = {

};

BOOST_CHECK_NO_THROW(

(seq, loc_vec, 3, 11, allowable_starts,

(

& loc: loc_vec) {

BOOST_CHECK_EQUAL(count_if(loc_vec.begin(),loc_vec.end(),

return !a->IsPartialStop(eExtreme_Biological);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

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

static CNcbiApplication * Instance(void)

Singleton method.

vector< CRef< objects::CSeq_loc > > TLocVec

static CRef< objects::CSeq_annot > MakeCDSAnnot(const TLocVec &orfs, int genetic_code=1, objects::CSeq_id *id=NULL)

/ This version returns an annot full of CDS features.

static void FindOrfs(const string &seq, TLocVec &results, unsigned int min_length_bp=3, int genetic_code=1, const vector< string > &allowable_starts=vector< string >(), bool longest_orfs=true, size_t max_seq_gap=k_default_max_seq_gap)

Find ORFs in both orientations.

bool IsSetGcode(void) const

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

const Tdata & Get(void) const

Get the member data.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

const TDesc & GetDesc(void) const

Get the Desc member data.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

CRef< objects::CObjectManager > om

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

BOOST_AUTO_TEST_CASE(TestUsingArg)

NCBITEST_INIT_CMDLINE(arg_desc)

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