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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastp__tests_8cpp_source.html below:

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

73 const

vector<CRef<CDbtag> >& db

76 if

((*dbtag)->GetDb() ==

"taxon"

) {

77 return

(*dbtag)->GetTag().GetId();

92 if

( !annot || !

ctx

) {

102 if

(alns.size() == 0) {

105

.AddField(

"has_blastp_match"

false

);

114

= *alns.front()->GetSegs().GetDenseg().GetIds()[0];

118 if

(prod_taxid == 0) {

121

.AddField(

"has_blastp_match"

false

);

129 int

length_top_match;

130 double

e_value_top_match;

133 const CSeq_id

& match_id = *(*aln)->GetSegs().GetDenseg().GetIds()[1];

134 if

(!(*aln)->GetNamedScore(

"score"

, score)) {

136 throw

runtime_error(

"No BLAST score found"

);

138 if

(score > top_score) {

140 if

(hit_taxid == prod_taxid || hit_taxid == 0) {

153

.AddField(

"has_blastp_match"

false

);

158

.AddField(

"has_blastp_match"

true

);

163 if

(!top_match->

GetNamedScore

(

"e_value"

, e_value_top_match)) {

164 throw

runtime_error(

"No e-value found"

);

167 result

->SetOutput_data().AddField(

"best_score"

, top_score);

168 result

->SetOutput_data().AddField(

"e_value_top_match"

, e_value_top_match);

170

.AddField(

"length_top_match"

, length_top_match);

171 result

->SetOutput_data().AddField(

"id_top_match"

174

.AddField(

"title_top_match"

175

sequence::CDeflineGenerator().GenerateDefline(hand));

static CObject_id::TId s_GetTaxid(const CSeq_id &id, CScope &scope)

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

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,...

bool GetNamedScore(const string &id, int &score) const

Get score.

CSeq_test_result_set â.

Base class for all serializable objects.

CRef< objects::CSeq_test_result_set > RunTest(const CSerialObject &obj, const CSeqTestContext *ctx)

RunTest() is called for each registered object.

bool CanTest(const CSerialObject &obj, const CSeqTestContext *ctx) const

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

API (CDeflineGenerator) for computing sequences' titles ("definitions").

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const string AsFastaString(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TOrg & GetOrg(void) const

Get the Org member data.

const TDb & GetDb(void) const

Get the Db member data.

Tdata & Set(void)

Assign a value to data member.

const TDenseg & GetDenseg(void) const

Get the variant data.

const TIds & GetIds(void) const

Get the Ids member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsAlign(void) const

Check if variant Align is selected.

const TSource & GetSource(void) const

Get the variant data.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

@ e_Source

source of materials, includes Org-ref

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