CSeqTest Class Reference

Search Toolkit Book for CSeqTest

Class CSeqTest provides a general API for performing a given test on. More...

#include <seqtest.hpp>

Inheritance diagram for CSeqTest:

Collaboration diagram for CSeqTest:

List of all members.

Public Member Functions
virtual bool	CanTest (const CSerialObject &obj, const CSeqTestContext *ctx) const =0
	Test to see whether the given object *can* be used in this test.
virtual CRef < objects::CSeq_test_result_set >	RunTest (const CSerialObject &obj, const CSeqTestContext *ctx)=0
	RunTest() is called for each registered object.
Protected Types
typedef void(*	TCdregionTester )(const objects::CSeq_id &, const CSeqTestContext *ctx, objects::CFeat_CI, objects::CSeq_test_result &)
	A fuction type that analyzes coding regions.
Protected Member Functions
CRef< objects::CSeq_test_result >	x_SkeletalTestResult (const string &test_name)
	Create a Seq-test-result with some fields filled in, including a name for this test, which must be supplied as an argument.
CRef < objects::CSeq_test_result_set >	x_TestAllCdregions (const CSerialObject &obj, const CSeqTestContext *ctx, const string &test_name, TCdregionTester cdregion_tester)
	Given a Seq-id and a context, analyze all coding regions by calling a supplied function.

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Detailed Description

Class CSeqTest provides a general API for performing a given test on.

Definition at line 95 of file seqtest.hpp.

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Member Typedef Documentation

typedef void(* CSeqTest::TCdregionTester)(const objects::CSeq_id &, const CSeqTestContext *ctx, objects::CFeat_CI, objects::CSeq_test_result &) [protected]

A fuction type that analyzes coding regions.

Definition at line 113 of file seqtest.hpp.

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Member Function Documentation

virtual bool CSeqTest::CanTest	(	const CSerialObject &	obj,
		const CSeqTestContext *	ctx
	)		const [pure virtual]

Test to see whether the given object *can* be used in this test.

Implemented in CTestProtProd_EntrezNeighbors, CTestBlastp, CTestSeqId, CTestSingleAln, CTestTranscript, and CTestProtProd.

virtual CRef<objects::CSeq_test_result_set> CSeqTest::RunTest	(	const CSerialObject &	obj,
		const CSeqTestContext *	ctx
	)		[pure virtual]

RunTest() is called for each registered object.

Derived code has the guarantee that the CSerialObject can be down-cast to the bound registered type. Derived code should also assume that the context object may be NULL.

Implemented in CTestTranscript_CountAmbiguities, CTestTranscript_OrfExtension, CTestTranscript_Code_break, CTestTranscript_Orfs, CTestTranscript_PolyA, CTestTranscript_Utrs, CTestTranscript_CompareProtProdToTrans, CTestTranscript_PrematureStopCodon, CTestTranscript_CdsStopCodon, CTestTranscript_CdsStartCodon, CTestTranscript_TranscriptCdsLength, CTestTranscript_TranscriptLength, CTestTranscript_CodingPropensity, CTestTranscript_InframeUpstreamStop, CTestTranscript_InframeUpstreamStart, CTestProtProd_EntrezNeighbors, CTestTranscript_CdsFlags, CTestSingleAln_All, CTestTranscript_CountCdregions, CTestBlastp_All, CTestProtProd_Cdd, CTestProtProd_ProteinLength, and CTestSeqId_Biomol.

CRef< CSeq_test_result > CSeqTest::x_SkeletalTestResult

(

const string &

test_name

)

[protected]

Create a Seq-test-result with some fields filled in, including a name for this test, which must be supplied as an argument.

Definition at line 54 of file seqtest.cpp.

References CTime::eCurrent.

Referenced by CTestSeqId_Biomol::RunTest(), CTestProtProd_ProteinLength::RunTest(), CTestProtProd_Cdd::RunTest(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), CTestTranscript_CountCdregions::RunTest(), CTestProtProd_EntrezNeighbors::RunTest(), CTestTranscript_TranscriptLength::RunTest(), CTestTranscript_PolyA::RunTest(), CTestTranscript_Orfs::RunTest(), CTestTranscript_CountAmbiguities::RunTest(), and x_TestAllCdregions().

CRef< CSeq_test_result_set > CSeqTest::x_TestAllCdregions	(	const CSerialObject &	obj,
		const CSeqTestContext *	ctx,
		const string &	test_name,
		TCdregionTester	cdregion_tester
	)		[protected]

Given a Seq-id and a context, analyze all coding regions by calling a supplied function.

If the serial object passed in is not a Seq-id, the result is null.

Definition at line 69 of file seqtest.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqTestContext::GetScope(), ITERATE, MSerial_AsnText, CRef< C, Locker >::Reset(), SAnnotSelector::SetResolveDepth(), CSeq_loc::SetWhole(), and x_SkeletalTestResult().

Referenced by CTestTranscript_CdsFlags::RunTest(), CTestTranscript_InframeUpstreamStart::RunTest(), CTestTranscript_InframeUpstreamStop::RunTest(), CTestTranscript_CodingPropensity::RunTest(), CTestTranscript_TranscriptCdsLength::RunTest(), CTestTranscript_CdsStartCodon::RunTest(), CTestTranscript_CdsStopCodon::RunTest(), CTestTranscript_PrematureStopCodon::RunTest(), CTestTranscript_CompareProtProdToTrans::RunTest(), CTestTranscript_Utrs::RunTest(), CTestTranscript_Code_break::RunTest(), CTestTranscript_OrfExtension::RunTest(), and CTestTranscript_CountAmbiguities::RunTest().

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The documentation for this class was generated from the following files:

• include/algo/seqqa/seqtest.hpp
• src/algo/seqqa/seqtest.cpp