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NCBI C++ ToolKit: src/algo/seqqa/seqtest.cpp Source File

->SetOutput_data().SetType().SetStr(

);

->SetOutput_data().SetClass(

);

TCdregionTester cdregion_tester)

( !

|| !

) {

( ; feat_iter; ++feat_iter) {

(*cdregion_tester)(*id,

, feat_iter, *

);

(feat_iter.GetSize() > 1) {

asn_text.reserve(

.size());

asn_text.push_back(*ch);

->SetOutput_data().AddField(

, asn_text);

(

->IsSetOutput_data() &&

->GetOutput_data().IsSetData() ) {

(

it = eq_range.first; it != eq_range.second;) {

& ref = *it->second;

pair<TTests::iterator, TTests::iterator> iter_pair =

( ; iter_pair.first != iter_pair.second; ++iter_pair.first) {

(!(*iter->second).CanTest(obj,

)) {

ref->

().begin(), ref->

().end());

( ; iter; ++iter) {

(ref && ref->

().size()) {

->SetResults(*ref);

User-defined methods of the data storage class.

Class holding information about root of non-modifiable object hierarchy Do not use it directly.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CSeqTestContext defines any contextual information that a derived class might need.

void RegisterTest(const CTypeInfo *info, CSeqTest *test)

Register a test to be run for a given object sub-type.

void UnRegisterTest(const CTypeInfo *info, CSeqTest *test)

"Un-register" a test for a given object sub-type.

list< CRef< objects::CSeqTestResults > > TResults

virtual void RegisterStandardTests()

Provide a standard battery of quality checks that should always be run.

virtual CRef< objects::CSeq_test_result_set > RunTests(const CSerialObject &obj, const CSeqTestContext *ctx=NULL)

Run tests for a given serial object.

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

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,...

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.

CSeq_test_result_set –.

Base class for all serializable objects.

Check coding regions for "partial", "pseudo", and "except" flags.

Check to see if the sequence contains a CDS feature that has a start codon.

Check to see if the sequence contains a CDS feature that has a stop codon.

Count code-breaks on CDS.

Measure the coding propensity of the CDS feature annotated on a CDS feature.

Compare the annotated protein product of a CDS in the database to actual translation of that CDS.

Count ambiguous residues in transcript and CDS.

Count the number of annotated coding regions.

Check to see if the sequence contains a CDS feature that has an in-frame upstream start codon.

Check to see if the sequence contains a CDS feature that has an in-frame upstream stop codon.

See how far the annotated CDS can be extended 5' to an ATG without hitting a stop.

Categorize ORFs in this transcript sequence.

Count the number of As at the end of the sequence.

Check CDS features for premature stop codons.

Measure the length of an CDS feature on a transcript sequence.

Measure the length of an mRNA sequence.

Compare the annotated protein product of a CDS in the database to actual translation of that CDS.

Base class for all iterators over modifiable object.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

const_iterator_pair equal_range(const key_type &key) const

iterator insert(const value_type &val)

container_type::iterator iterator

container_type::value_type value_type

#define test(a, b, c, d, e)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

static char test_name[128]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

#define MSerial_AsnText

I/O stream manipulators –.

TObjectInfo & Get(void)

Get information about current object.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

@ eCurrent

Use current time. See also CCurrentTime.

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

Defines: CTimeFormat - storage class for time format.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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