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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/suspect__feat_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/suspect_feat.cpp Source File

56

CFixSuspectProductName::CFixSuspectProductName()

60

CFixSuspectProductName::~CFixSuspectProductName()

64 void

CFixSuspectProductName::SetRulesFilename(

const string

& filename)

66

m_filename = filename;

69 void

CFixSuspectProductName::SetupOutput(std::function<std::ostream&()>

)

76 if

(m_rules.NotEmpty() && !m_rules->Get().empty())

79 for

(

const auto

& rule : m_rules->Get()) {

80 if

(rule->CanGetReplace() && rule->StringMatchesSuspectProductRule(product_name))

88 void

CFixSuspectProductName::ReportFixedProduct(

const string

& oldproduct,

const string

& newproduct,

const CSeq_loc

& loc,

const string

& locustag)

const 93

std::ostream& report_ostream = m_output();

97

report_ostream <<

"Changed "

<< oldproduct <<

" to "

<< newproduct <<

" "

label

" "

<< locustag <<

"\n\n"

;

102 static

constexpr string_view hypotetic_protein_name =

"hypothetical protein"

;

104

std::lock_guard<COnceMutex>

{m_mutex};

106 if

(m_mutex.IsFirstRun() && m_rules.Empty())

109 if

(filename.empty()) {

113

filename = rules_env;

119 bool

modified =

false

;

126 auto

& prot_name = feature.

SetData

().SetProt().SetName().front();

128 if

(0 !=

NStr::Compare

(prot_name, hypotetic_protein_name)) {

130 while

(

auto

rule = x_FixSuspectProductName(prot_name)) {

133

rule, *scope, prot_name,

134

[&mapped, &feattree] {

143

[&mapped, &feattree] {

169 auto

feattree =

Ref

(

new

feature::CFeatTree(seh));

172

[](

const CBioseq

& bioseq){

return

bioseq.

IsAa

(); },

174

this->FixSuspectProductNames(feature, scope, feattree);

User-defined methods of the data storage class.

static CNcbiApplication * Instance(void)

Singleton method.

namespace ncbi::objects::

CConstRef< objects::CSuspect_rule_set > GetProductRules(const string &name="")

string FixProductName(const objects::CSuspect_rule *rule, objects::CScope &scope, string &prot_name, GetFeatureFunc get_mrna, GetFeatureFunc get_cds)

const CNcbiEnvironment & GetEnvironment(void) const

Get the application's cached environment.

const string & Get(const string &name, bool *found=NULL) const

Get environment value by name.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

CMappedFeat GetBestParentForFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype parent_subtype, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Compare of a substring with another string.

static const char label[]

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

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

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TProt & GetProt(void) const

Get the variant data.

void VisitAllFeatures(objects::CSeq_entry_EditHandle &entry_h, _M m)

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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