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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vectorscreen__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/align_format/unit_test/vectorscreen_unit_test.cpp Source File

34 #define NCBI_BOOST_NO_AUTO_TEST_MAIN 50 using namespace ncbi

;

52 using namespace

ncbi::align_format;

65  TSeqPos

from[] = {0, 11, 33, 34, 1008};

66  TSeqPos

to[] = {10, 32, 33, 1007, 1056};

67  int type

[] = {3, 1, 2, 4, 0};

70

BOOST_REQUIRE((*iter)->range.GetFrom() == from[

i

]);

71

BOOST_REQUIRE((*iter)->range.GetTo() == to[

i

]);

72

BOOST_REQUIRE((*iter)->type ==

type

[

i

]);

81  TSeqPos

from[] = {1008, 11, 18};

84

BOOST_REQUIRE((*iter)->GetSeqRange(0).GetFrom() == from[

i

]);

85

BOOST_REQUIRE((*iter)->GetSeqRange(0).GetTo() == to[

i

]);

99

seqalign->

Set

() = align;

107

x_TestRangeList(vec);

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

static void ExtractSeqalignSetFromDiscSegs(objects::CSeq_align_set &target, const objects::CSeq_align_set &source)

If a Seq-align-set contains Seq-aligns with discontinuous type segments, extract the underlying Seq-a...

void x_MergeSeqalign(objects::CSeq_align_set &seqalign)

merge overlapping seqalign

list< AlnInfo * > m_AlnInfoList

internal match list

CConstRef< objects::CSeq_align_set > m_SeqalignSetRef

the current seqalign

CRef< objects::CSeq_align_set > m_FinalSeqalign

the processed seqalign

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ 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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

list< CRef< CSeq_align > > TAlign

const TData & GetData(void) const

Get the Data member data.

Magic spell ;-) needed for some weird compilers... very empiric.

Defines NCBI C++ exception handling.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

static void x_TestRangeList(CVecscreenTest &vec)

static void VecscreenDisplay(void)

static void x_TestSeqalign(CVecscreenTest &vec)

CVecscreenTest(const CSeq_align_set &seqalign, TSeqPos master_length)

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

BOOST_AUTO_TEST_CASE(VecscreenDisplay)

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