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NCBI C++ ToolKit: src/objects/seq/unit_test/seq_loc_unit_test.cpp Source File

33 #define NCBI_TEST_APPLICATION 43 #include <boost/test/parameterized_test.hpp> 76 MakeLoc

(

"int { from 10, to 20, id gi 2 }"

);

107 " int { from 10, to 20, strand plus, id gi 2 }," 108 " pnt { point 30, strand minus, id gi 3}" 126 "Seq-loc ::= int {\n" 146 "Seq-loc ::= pnt {\n" 161 " int { from 10, to 20, strand plus, id gi 2 }," 163 " int { from 25, to 27, strand plus, id gi 2 }," 165 " int { from 25, to 26, strand plus, id gi 2 }," 166 " int { from 27, to 27, strand minus, id gi 2 }" 169 " pnt { point 30, strand minus, id gi 3}" 187 "Seq-loc ::= int {\n" 212 "Seq-loc ::= int {\n" 237 "Seq-loc ::= int {\n" 262 "Seq-loc ::= int {\n" 282 "Seq-loc ::= pnt {\n" 297 " int { from 10, to 20, strand plus, id gi 2 }," 298 " pnt { point 30, strand minus, id gi 3}" 316 "Seq-loc ::= int {\n" 324 "Seq-loc ::= int {\n" 344 "Seq-loc ::= pnt {\n" 352 "Seq-loc ::= pnt {\n" 362

BOOST_CHECK_EQUAL(loc2,

363 "Seq-loc ::= packed-pnt {\n" 378 " int { from 10, to 20, strand plus, id gi 2 }," 379 " pnt { point 30, strand minus, id gi 3}" 397 "Seq-loc ::= int {\n" 405 "Seq-loc ::= pnt {\n" 424 "Seq-loc ::= pnt {\n" 431 "Seq-loc ::= pnt {\n" 441

BOOST_CHECK_EQUAL(loc2,

442 "Seq-loc ::= packed-int {\n" 463 " int { from 10, to 20, strand plus, id gi 2 }," 464 " pnt { point 30, strand minus, id gi 3}" 482 "Seq-loc ::= int {\n" 490 "Seq-loc ::= int {\n" 510 "Seq-loc ::= pnt {\n" 517 "Seq-loc ::= pnt {\n" 527

BOOST_CHECK_EQUAL(loc2,

528 "Seq-loc ::= mix {\n" 548 " a { point 10, strand plus, id gi 2 }," 549 " b { point 30, strand minus, id gi 3}" 568 "Seq-loc ::= pnt {\n" 588 "Seq-loc ::= pnt {\n" 598

BOOST_CHECK_EQUAL(loc2,

599 "Seq-loc ::= bond {\n" 618 " pnt { point 10, strand plus, id gi 2 }," 619 " pnt { point 30, strand minus, id gi 3}," 620 " pnt { point 40, id gi 4}" 638 "Seq-loc ::= pnt {\n" 657 "Seq-loc ::= pnt {\n" 675 "Seq-loc ::= pnt {\n" 697 "Seq-loc ::= pnt {\n" 716 "Seq-loc ::= pnt {\n" 734 "Seq-loc ::= pnt {\n" 743

BOOST_CHECK_EQUAL(loc2,

744 "Seq-loc ::= mix {\n" 777 "Seq-loc ::= pnt {\n" 796 "Seq-loc ::= pnt {\n" 814 "Seq-loc ::= pnt {\n" 823

BOOST_CHECK_EQUAL(loc2,

824 "Seq-loc ::= mix {\n" 847 " int { from 10, to 20, strand plus, id gi 2 }," 849 " int { from 25, to 27, strand plus, id gi 2 }," 851 " int { from 25, to 26, strand plus, id gi 2 }," 852 " int { from 27, to 27, strand minus, id gi 2 }" 855 " pnt { point 30, strand minus, id gi 3}" 873 "Seq-loc ::= int {\n" 898 "Seq-loc ::= int {\n" 923 "Seq-loc ::= int {\n" 948 "Seq-loc ::= int {\n" 968 "Seq-loc ::= pnt {\n" 978

BOOST_CHECK_EQUAL(loc2,

979 "Seq-loc ::= mix {\n" 1015

BOOST_CHECK_EQUAL(loc2,

1016 "Seq-loc ::= mix {\n" 1059 " int { from 25, to 27, strand plus, id gi 2 }," 1061 " int { from 25, to 26, strand plus, id gi 2 }," 1062 " int { from 27, to 27, strand minus, id gi 2 }" 1087 "Seq-loc ::= int {\n" 1112 "Seq-loc ::= int {\n" 1137 "Seq-loc ::= int {\n" 1148

BOOST_CHECK_EQUAL(loc2,

1149 "Seq-loc ::= equiv {\n" 1191

BOOST_CHECK_EQUAL(loc2,

1192 "Seq-loc ::= mix {\n" 1214

BOOST_CHECK_EQUAL(loc2,

1215 "Seq-loc ::= mix {\n" 1239

BOOST_CHECK_EQUAL(loc2,

1240 "Seq-loc ::= mix {\n" 1264

BOOST_CHECK_EQUAL(loc2,

1265 "Seq-loc ::= mix {\n" 1289

BOOST_CHECK_EQUAL(loc2,

1290 "Seq-loc ::= mix {\n" 1300

BOOST_CHECK_EQUAL(loc2,

1301 "Seq-loc ::= equiv {\n" 1326

BOOST_CHECK_EQUAL(loc2,

1327 "Seq-loc ::= mix {\n" 1374 if

( range.

GetFrom

() != point || range.

GetTo

() != point ) {

1387 const size_t

LCOUNT =

m_Locs

.size();

1404 const int

LCOUNT = 1000000;

1405 const int

TCOUNT = 4;

1410 for

(

int i

= 0;

< LCOUNT; ++

) {

1412 if

(

rnd

.GetRand(0, 2) > 0 ) {

1413

loc->

SetPnt

().SetPoint(

);

1419

loc->

SetId

id

);

1424

start_counter.

Set

(TCOUNT);

1426

vector< CRef<CThread> > tt(TCOUNT);

1427 for

(

int i

= 0;

< TCOUNT; ++

) {

1431 for

(

int i

= 0;

< TCOUNT; ++

) {

1433

tt[

]->Join(&exit_data);

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Seq-loc iterator class â iterates all intervals from a seq-loc in the correct order.

CTotalRangeThread(const TSeqLocs &locs, CAtomicCounter &start_counter)

CAtomicCounter & m_StartCounter

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

static void x_CheckPoint(CSeq_loc::TRange range, TSeqPos point)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

void Set(TValue new_value) THROWS_NONE

Set atomic counter value.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

TValue Get(void) const THROWS_NONE

Get atomic counter value.

#define MSerial_AsnText

I/O stream manipulators â.

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

bool IsBondA(void) const

Return true if current position is A part of a bond.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

size_t GetEquivSetsCount(void) const

Return number of recursuve equiv parts current position in.

void SetTo(TSeqPos to)

Set the range to position.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

bool IsInEquivSet(void) const

Return true if current position is in some equiv part.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

void SetStrand(ENa_strand strand)

Set the range strand.

void MakeBondAB(void)

Make bond at current position with the next position (A and B) The current and next parts must be poi...

bool HasEquivSets(void) const

Return true if location has equiv parts.

bool IsSetStrand(void) const

Get strand.

CSeq_id_Handle GetSeq_id_Handle(void) const

bool IsWhole(void) const

True if the current location is a whole sequence.

void SetSeq_id_Handle(const CSeq_id_Handle &id)

Set seq_id of the current location.

bool IsInBond(void) const

Location of type equiv define set of equivalent locations.

void SetPoint(TSeqPos pos)

Set the range from and to positions.

CSeq_loc_I InsertInterval(const CSeq_id_Handle &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

bool IsEmpty(void) const

True if the current location is empty.

pair< CSeq_loc_CI, CSeq_loc_CI > GetEquivSetRange(size_t level=0) const

Return iterators that cover equiv set of current position result.first is the first segment in the eq...

void SetPos(size_t pos)

Set iterator's position.

pair< CSeq_loc_I, CSeq_loc_I > GetEquivPartRange(size_t level=0) const

Return iterators that cover equiv part of current position result.first is the first segment in the e...

TRange GetRange(void) const

Get the range.

bool IsBondB(void) const

Return true if current position is B part of a bond.

pair< CSeq_loc_CI, CSeq_loc_CI > GetEquivPartRange(size_t level=0) const

Return iterators that cover equiv part of current position result.first is the first segment in the e...

void RemoveBond(void)

Remove bond at current position - it may be either A or B part.

ENa_strand GetStrand(void) const

pair< CSeq_loc_I, CSeq_loc_I > GetEquivSetRange(size_t level=0) const

Return iterators that cover equiv set of current position result.first is the first segment in the eq...

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void SetEquivMode(EEquivMode mode)

Change equiv modification mode.

bool IsPoint(void) const

True if the current location is a single point.

@ eMake_PreserveType

use most compact Seq-loc type (default)

@ eEquiv_new_part

New equiv part will be started with the inserted element.

@ eEquiv_new_equiv

A new equiv set will be created, even if the insertion point is already inside of an existing equiv,...

@ eEquiv_none

By default no equiv sets are created or expanded except if insertion point is completely inside of an...

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsGi(void) const

Check if variant Gi is selected.

static void text(MDB_val *v)

static size_t rnd(size_t minimal, size_t maximal)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Multi-threading â classes, functions, and features.

vector< CRef< CSeq_loc > > TSeqLocs

string MakeASN(const Obj &loc)

DEFINE_STATIC_MUTEX(s_BoostMutex)

CRef< CSeq_loc > MakeLoc(const char *text)

BOOST_AUTO_TEST_CASE(TestSingle)

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

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__loc__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seq/unit_test/seq_loc_unit_test.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqlocunit__test_8cpp_source.html below: