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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdesc__per__bioseq_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/discrepancy/seqdesc_per_bioseq.cpp Source File

m_Objs[

].Add(*

.SeqdescObjRef(*biosrc, biosrc));

m_Objs[

].Add(*

.SeqdescObjRef(*biosrc));

m_Objs[

].Add(*

.SeqdescObjRef(*biosrc));

(biosrc && molinfo && !bioseq.

()) {

m_Objs[

].Add(*

.SeqdescObjRef(*biosrc));

(

& field : user.

()) {

(field_rule.

()) {

(rules.

()) {

(

& rule : rules.

()) {

(ret ==

) {

(

& desc :

.GetSeqdesc()) {

(!prefix.empty()) {

(!errors.empty()) {

m_Objs[

].Add(*

.SeqdescObjRef(desc, &desc,

*

(new_rule)));

prefix_tail =

;

suffix_tail =

;

suffix = prefix.substr(0, prefix.size() - prefix_tail.size()) + suffix_tail;

(

& field : user.

()) {

field->SetData().SetStr(prefix);

field->SetData().SetStr(suffix);

(bioseq.

()) {

(

& desc :

.GetAllSeqdesc()) {

(desc.IsComment() && !desc.GetComment().empty()) {

& comment = desc.GetComment();

(comment.find(

) == string::npos) {

m_Objs[comment].Add(*

.SeqdescObjRef(desc, &desc));

&

= m_Objs.GetMap();

(

.size() > 1) {

(

& it :

) {

subitem =

+ it.first;

(

obj : it.second->GetObjects()) {

obj->SetMoreInfo(

*

(&*

));

rep[

][subitem].

().

(*obj);

(

& desc :

.GetSeqdesc()) {

m_Objs[

].Add(*

.SeqdescObjRef(desc));

(bioseq.

()) {

(

& desc :

.GetAllSeqdesc()) {

m_Objs[

].Add(*

.BioseqObjRef());

(

> 1) {

m_Objs[

].Add(*

.BioseqObjRef());

const string & GetLineage(void) const

bool IsSetLineage(void) const

virtual vector< CRef< CReportItem > > GetSubitems() const =0

static void Add(TReportObjectList &list, TReportObjectSet &hash, CReportObj &obj, bool unique=true)

CReportNode & Ext(bool b=true)

CRef< CReportItem > Export(CDiscrepancyCore &test, bool unique=true) const

@ eObjectType_StructuredComment

@ eObjectType_AutodefOptions

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

#define DISCREPANCY_SUMMARIZE(name)

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

TGenome GetGenome(void) const

Get the Genome member data.

bool IsSetSubtype(void) const

Check if a value has been assigned to Subtype data member.

void SetGenome(TGenome value)

Assign a value to Genome data member.

bool IsSetGenome(void) const

Check if a value has been assigned to Genome data member.

bool IsSetData(void) const

the object itself Check if a value has been assigned to Data data member.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetMol(void) const

Check if a value has been assigned to Mol data member.

const TSource & GetSource(void) const

Get the variant data.

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TMol GetMol(void) const

Get the Mol member data.

TComment & SetComment(void)

Select the variant.

TSource & SetSource(void)

Select the variant.

TBiomol GetBiomol(void) const

Get the Biomol member data.

TUser & SetUser(void)

Select the variant.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eBiomol_genomic_mRNA

reported a mix of genomic and cdna sequence

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

static const char * kStructuredCommentPrefix

const CComment_rule * FindAppropriateRule(const CComment_set &rules, const CUser_object &user)

static const char * kStructuredCommentSuffix

static EPrefixOrSuffixType GetPrefixOrSuffixType(const CUser_field &field)

static bool IsAppropriateRule(const CComment_rule &rule, const CUser_object &user)

static CS_CONTEXT * context

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