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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/prot__prod__tests_8cpp_source.html below:

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

66  for

( ; iter; ++iter) {

83  if

( !

id

|| !

ctx

) {

93

.GetBioseqHandle(

dynamic_cast<const CSeq_id

&

>

(obj)).GetInst_Length();

95

.AddField(

"length"

,

len

);

106  if

( !

id

|| !

ctx

) {

118  bool

has_partial =

false

;

121  const

list<CRef<CSeq_feat> >&

ftable 125  if

((*it)->IsSetPartial() && (*it)->GetPartial()) {

137

.AddField(

"annotated_cdd_hits"

, hits);

139

.AddField(

"has_partial_cdd_hit"

, has_partial);

173  catch

(std::exception&) {

186  if

( !

id

|| !

ctx

) {

199  throw

runtime_error(

"CTestProtProd_EntrezNeighbors::RunTest: " 206

vector<TGi> sp_neigh;

207

vector<TGi> neigh_subset;

209  for

(

unsigned int

start = 0; start < neigh.size(); start +=

kChunkSize

) {

210

neigh_subset.clear();

212  if

(start +

i

== neigh.size()) {

215

neigh_subset.push_back(neigh[start +

i

]);

217

e2c.

FilterIds

(neigh_subset,

"protein"

,

"srcdb_swiss-prot[PROP] NOT txid" 219  if

(!sp_neigh.empty()) {

223  result

->SetOutput_data().AddField(

"has_swissprot_neighbor_different_taxid"

,

225  if

(!sp_neigh.empty()) {

229  for

(

unsigned int i

= 0;

i

< neigh_subset.size(); ++

i

) {

230

index[neigh_subset[

i

]] =

i

;

232  unsigned int

lowest_index = neigh_subset.size();

234  for

(

unsigned int i

= 0;

i

< sp_neigh.size(); ++

i

) {

235  if

(index[sp_neigh[

i

]] < lowest_index) {

236

lowest_index = index[sp_neigh[

i

]];

237

first_gi = sp_neigh[

i

];

241

neigh_id.

SetGi

(first_gi);

243

.AddField(

"top_match_seq_id"

, neigh_id.

GetSeqIdString

(

true

));

244  int

length_top_match =

245  ctx

->GetScope().GetBioseqHandle(neigh_id).GetBioseqLength();

247

.AddField(

"length_top_match"

, length_top_match);

User-defined methods of the data storage class.

void FilterIds(const vector< TUid > &query_uids, const string &db, const string &query_string, vector< TUid > &result_uids)

Given some uids, a database, and an entrez query string, determine which of these uids match the quer...

void GetNeighbors(TUid query_uid, const string &db_from, const string &db_to, vector< TUid > &neighbor_uids)

A simplified interface for getting neighbors (links)

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,...

CSeq_test_result_set –.

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.

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

RunTest() is called for each registered object.

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_ForceGi

return only a gi-based seq-id

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

const string & GetName(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TOrg & GetOrg(void) const

Get the Org member data.

Tdata & Set(void)

Assign a value to data member.

TGi GetGi(void) const

Get the variant data.

TGi & SetGi(void)

Select the variant.

const TSource & GetSource(void) const

Get the variant data.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

Defines: CTimeFormat - storage class for time format.

TTaxId s_GetTaxId(const CBioseq_Handle &hand)

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