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NCBI C++ ToolKit: src/gui/objutils/snp_gui.cpp Source File

zoomAnnotName = sAnnotName;

(!name.IsNamed()) {

base_name != sAnnotName) {

(zoom_level <= max_zoom_level) {

(zoom_level > best_zoom_level || best_zoom_level > max_zoom_level) {

best_zoom_level = zoom_level;

(zoom_level < best_zoom_level) {

best_zoom_level = zoom_level;

features_estimate(0);

( ; graph_iter; ++graph_iter) {

features_estimate += (*iter_gr *

+

);

features_estimate += (*iter_gr *

+

);

s_SamplingRange(100 * 1000);

features_estimate = (double(start_count + one_third_count + two_third_count + end_count) / double(s_SamplingRange * 4)) * range.

();

features_estimate;

=

;

=

;

=

;

;

;

it == sm_ClinSigMap.

() ?

.Set(0.007f, 0.588f, 0.145f);

.Set(0.011f, 0.784f, 0.192f);

.Set(0.866f, 0.372f, 0.788f);

.Set(0.796f, 0.043f, 0.674f);

.Set(0.282f, 0.309f, 0.796f);

.Set(0.349f, 0.349f, 0.349f);

sig_term = clinsig;

vector<string> tokens;

(

& it : tokens) {

max_index = 0;

(

index = 0; index < tokens.size(); ++index) {

sev_it = sm_Pathogenicity.

(severity);

(sev_it != sm_Pathogenicity.

()) {

max_it = sm_Pathogenicity.

(max_significance);

(max_it == sm_Pathogenicity.

()) {

max_significance = severity;

(sev_it->second > max_it->second) {

max_significance = severity;

tokens[max_index];

sBaseURL(

);

sBaseURL +

+ colorTheme +

;

sBaseURL +

+ colorTheme +

;

sBaseURL +

+ colorTheme +

;

ColorKeys[] = {

v = (

)floor(pvalue);

ColorKeys[v-1];

&colorTheme)

vector<string> tokens;

pFormatter->AddDividerRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

,

(entry->ClinSigID, colorTheme));

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(

+rsid,

+rsid) +

(sClinSig.empty() ?

() :

+ sClinSig +

));

pFormatter->FinishRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->FinishRow();

sPackagedOMIM, sGene;

vector<string> tokens;

(tokens.size() > 0) {

sPackagedOMIM = tokens[0];

(tokens.size() > 1) {

isGoToPresent(

);

pFormatter->AddPubmedLinksRow(entry->pmids, isGoToPresent,

);

pFormatter->AddDividerRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(

+rsid,

+rsid));

pFormatter->FinishRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->FinishRow();

isGoToPresent(

);

pFormatter->AddPubmedLinksRow(entry->pmids, isGoToPresent,

);

pFormatter->AddDividerRow();

(entry->snpid > 0) {

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(

+rsid,

+rsid));

pFormatter->FinishRow();

(entry->geneId > 0) {

geneId = entry->geneStringId;

(!geneId.empty()) {

pFormatter->StartRow();

pFormatter->AddTagCol(

);

(!entry->geneName.empty()) {

geneId +=

+ entry->geneName +

;

pFormatter->AddValueCol(geneId);

pFormatter->FinishRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->FinishRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(entry->trait,

+ entry->trait +

));

pFormatter->FinishRow();

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->FinishRow();

(entry->pvalue > 0) {

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->FinishRow();

(!entry->context.empty()) {

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(entry->context);

pFormatter->FinishRow();

(!entry->population.empty()) {

pFormatter->StartRow();

pFormatter->AddTagCol(

);

pFormatter->AddValueCol(entry->population);

pFormatter->FinishRow();

isGoToPresent(

);

pFormatter->AddPubmedLinksRow(entry->pmids, isGoToPresent,

);

(!iGeneMap->first.empty()) {

));

& isGoToPresent,

isFirstRow(

);

pFormatter->StartRow();

pFormatter->AddTagCol(isFirstRow ?

:

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(iLinkList->first, iLinkList->second));

pFormatter->FinishRow();

& isGoToPresent)

isFirstRow(

);

pFormatter->StartRow();

pFormatter->AddTagCol(isFirstRow ?

:

);

pFormatter->AddValueCol(pFormatter->CreateNcbiLink(iLinkList->first, iLinkList->second));

pFormatter->FinishRow();

(entry->dbgaptext.empty())

TNameValueMap aNameValueMap;

TNameValueMap::const_iterator iNameValue;

((iNameValue = aNameValueMap.find(

)) != aNameValueMap.end() &&

!iNameValue->second.empty()) {

pFormatter->

(

);

((iNameValue = aNameValueMap.find(

)) != aNameValueMap.end() && !iNameValue->second.empty() && iNameValue->second !=

) {

phs(

+

(6 - iNameValue->second.length(),

) + iNameValue->second);

iNameValue = aNameValueMap.find(

);

pFormatter->

(

((iNameValue != aNameValueMap.end() && !iNameValue->second.empty()) ? iNameValue->second :

) +

);

((iNameValue = aNameValueMap.find(

)) != aNameValueMap.end() && !iNameValue->second.empty() && iNameValue->second !=

) {

pha(iNameValue->second);

pha_padded(

+

(6 - iNameValue->second.length(),

) + iNameValue->second);

iNameValue = aNameValueMap.find(

);

pFormatter->

(

((iNameValue != aNameValueMap.end() && !iNameValue->second.empty()) ? iNameValue->second :

) +

);

(bin.

) {

uo = ref.

(

);

= uf->GetString();

(start_pos ==

)

start_pos += attr_name.size() + 1;

attr_value =

.substr (start_pos, end_pos ==

?

: end_pos - start_pos);

!attr_value.empty();

vector<string> alt_alleles;

(

iVariation: var_list) {

(iVariation->IsSetData() && iVariation->GetData().IsInstance()) {

isReference(

);

((*iDelta)->CanGetSeq()) {

(DeltaSeq.

()) {

ref_allele = sAllele;

alt_alleles.push_back(sAllele);

alt_alleles.push_back(

);

maybeAllSnv = (ref_allele.size() == 1);

(

u=0; u < alt_alleles.size(); ++u) {

(alt_alleles[u].

() != 1) {

maybeAllSnv =

;

maybeAllMnv =

;

refSize = ref_allele.size();

(

u=0; u < alt_alleles.size(); ++u) {

(alt_alleles[u].

() != refSize) {

maybeAllMnv =

;

maybeAllIns =

;

(

u=0; u < alt_alleles.size(); ++u) {

(alt_alleles[u].

() <= ref_allele.size()) {

maybeAllIns =

;

(alt_alleles.size() == 1 && alt_alleles[0].empty()) {

);

TRsIdVariationMap RsIdVariationMap;

(

Term: Terms) {

(!sAssemblyAccession.empty()) {

sSNPSearchURL +=

+ sAssemblyAccession;

sSearchResult;

sSearchResult >> SearchByRsIdReply;

(

iPlacements: SearchByRsIdReply.

()) {

rsid(iPlacements->GetRsid());

pVariation->SetData().SetNote(

);

pVariation->SetDescription(

);

pVariation->SetId().SetDb(

);

pVariation->SetId().SetTag().SetStr(rsid);

pId(

(

(iPlacements->GetAcc_ver())));

iPlacements->GetFrom(),

iPlacements->GetFrom() + iPlacements->GetLength() - 1)));

pPlacement->SetLoc(*pLocation);

(iPlacements->CanGetAssembly_acc()) {

pPlacement->SetAssembly().SetDb(

);

pPlacement->SetAssembly().SetTag().SetStr(iPlacements->GetAssembly_acc());

pVariation->SetPlacements().push_back(pPlacement);

iRsIdVariationMap(RsIdVariationMap.find(rsid));

(iRsIdVariationMap == RsIdVariationMap.end()) {

iRsIdVariationMap = InsertResult.first;

iRsIdVariationMap->second.push_back(pVariation);

(

iRsIdVariationMap: RsIdVariationMap) {

(list<string>, iTerms, Terms) {

(!sAssemblyAccession.empty()) {

sSNPSearchURL +=

+ sAssemblyAccession;

sSearchResult;

& ResultRoot(ResultXml.get_root_node());

ParamIdSet(ResultRoot.run_xpath_query(ParamIdExpr));

(ParamIdSet.size() == 1,

);

& ParamIdAttrs(ParamIdSet.begin()->get_attributes());

sClin, sComment, sResultID, sQueryId;

sAttrName(iParamIdAttrs->get_name());

(sAttrName ==

)

sClin = iParamIdAttrs->get_value();

(sAttrName ==

)

sComment = iParamIdAttrs->get_value();

(sAttrName ==

)

sQueryId = iParamIdAttrs->get_value();

(sAttrName ==

)

sResultID = iParamIdAttrs->get_value();

(!sResultID.empty()) {

SNPSearchResult.first = sResultID;

PlacementSet(ResultRoot.run_xpath_query(PlacementExpr));

& PlacementAttrs(iPlacementSet->get_attributes());

sAccession, sFrom, sTo, sAssemblyName, sGeneSymbol, sTopLevel;

sAttrName(iPlacementAttrs->get_name());

(sAttrName ==

)

sTo = iPlacementAttrs->get_value();

(sAttrName ==

)

sFrom = iPlacementAttrs->get_value();

(sAttrName ==

)

sAssemblyName = iPlacementAttrs->get_value();

(sAttrName ==

)

sAccession = iPlacementAttrs->get_value();

(sAttrName ==

)

sGeneSymbol = iPlacementAttrs->get_value();

(sAttrName ==

)

sTopLevel = iPlacementAttrs->get_value();

NStr::StringToNumeric<TSeqPos>(sFrom),

NStr::StringToNumeric<TSeqPos>(sTo)));

pPlacement->SetLoc(*pLocation);

pPlacement->SetAssembly().SetDb(

);

pPlacement->SetAssembly().SetTag().SetStr(sAssemblyName);

pVariation->SetPlacements().push_back(pPlacement);

pVariation->SetData().SetNote(

);

pVariation->SetDescription(

);

pVariation->SetId().SetDb(

);

pVariation->SetId().SetTag().SetStr(sResultID);

(!sComment.empty())

pVariation->SetDescription(sComment);

(!sGeneSymbol.empty() || !sTopLevel.empty() || !sComment.empty() || !sQueryId.empty()) {

(!sGeneSymbol.empty()) {

(!sQueryId.empty()) {

(!sComment.empty()) {

(sTopLevel ==

) {

pVariation->SetExt().push_back(pExt);

SNPSearchResult.second.push_back(pVariation);

ResultList.push_back(SNPSearchResult);

(sTerms,

, CompoundResultList);

ResultList.insert(ResultList.end(), iCompoundResultList->second.begin(), iCompoundResultList->second.end());

*

=

;

TRsIdVariationMap RsIdVariationMap;

(

Term: Terms) {

sSNPSearchURL += Term;

(!sAssemblyAccession.empty()) {

sSNPSearchURL +=

+ sAssemblyAccession;

sSearchResult;

(sSearchResult.empty())

pVariation->SetData().SetNote(

);

pVariation->SetDescription(

);

pVariation->SetId().SetDb(

);

pVariation->SetId().SetTag().SetStr(varid);

pLocation(

(

(*pId, from, from + length - 1)));

pPlacement->SetLoc(*pLocation);

pPlacement->SetAssembly().SetDb(

);

pPlacement->SetAssembly().SetTag().SetStr(assembly_acc);

pVariation->SetPlacements().push_back(pPlacement);

iRsIdVariationMap(RsIdVariationMap.find(varid));

(iRsIdVariationMap == RsIdVariationMap.end()) {

iRsIdVariationMap = InsertResult.first;

iRsIdVariationMap->second.push_back(pVariation);

(

iRsIdVariationMap: RsIdVariationMap) {

& sVariantID,

& ref_allele,

& alt_alleles) :

m_sRefAllele_orig(ref_allele)

(alt_alleles,

, m_AltAlleles_orig);

m_sRefAllele_display = m_sRefAllele_orig.empty() ?

(

) : m_sRefAllele_orig;

(

alt_allele_orig: m_AltAlleles_orig) {

m_AltAlleles_display.push_back(alt_allele_orig.empty() ?

(

) : alt_allele_orig);

m_AltAlleles_display.push_back(

);

m_Len = m_sRefAllele_orig.length() - 1;

m_Len = m_sRefAllele_orig.length() - 1;

our_id->Assign(seq_id);

& sVariantID,

& ref_allele,

& alt_alleles) :

allele_len = -1;

all_alt_alleles_same_len =

;

((alt_allele_display.length() == 5) && (alt_allele_display[0] ==

) && (alt_allele_display[4] ==

))

new_allele_len(

(allele_len, (

)alt_allele_display.length()));

(allele_len != -1 && new_allele_len != allele_len) {

all_alt_alleles_same_len =

;

allele_len = new_allele_len;

= sBriefLine +

+

all_alt_alleles_same_len(

);

(allele_len > 0) {

=

;

=

;

=

;

;

(it_info != end_pos) {

svtype = svtype_map.find(svtype_value);

(svtype != svtype_map.end()) {

(svtype_value ==

)

(svtype_value ==

)

(it_info != end_pos) {

end_str = it_info->second;

(!end_str.empty()) {

(end >

+ 1) {

(

== EVCF_Type::eVCF_ClinVar) {

(it_info != end_pos) {

it = sm_CLNVCSO2Type.

(it_info->second);

(it != sm_CLNVCSO2Type.

()) {

sInfoColumns;

(!sInfoColumns.empty()) {

sInfoColumns +=

;

sInfoColumns += column_value.first +

+ column_value.second;

sInfoColumns;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TAnnotNames & GetAnnotNames(void) const

size_t GetSize(void) const

Random-access iterator to access const JSON array element.

bool IsObject(void) const

CJson_ConstObject GetObject(void) const

Get JSON object contents of the node.

CJson_ConstArray GetArray(void) const

Get JSON array contents of the node.

CJson_ConstValue GetValue(void) const

Get JSON value contents of the node.

Uint8 GetUint8(void) const

TStringType GetString(void) const

bool ParseString(const TStringType &v)

Read JSON data from a UTF8 string.

bool ReadSucceeded(void) const

Test if the most recent read was successful.

static CNcbiApplication * Instance(void)

Singleton method.

class CRgbaColor provides a simple abstraction for managing colors.

namespace ncbi::objects::

CConstRef< CUser_object > FindExt(const string &ext_type) const

Find extension by type in exts container.

URL-decoder for string pairs parser.

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

storage for gene maps as seen in strings in SBinEntry::genes_reported and SBinEntry::genes_mapped

@ eIND

individual tracks (Venter, Watson, etc), data same as in eCLIN

@ eCITED

Cited Variations.

@ eCLIN

Clinical Variations.

@ eGAP

dbGaP analysis files

@ eGCAT

NHGRI GWAS Catalog Track (AKA Association Results)

static string SourceAsString(TSource Source)

get human-readable text for various source types

list< CRef< SBinEntry > > TBinEntryList

@ eLetterCase_ForceLower

always use lower case only

static string ClinSigAsString(const CVariation_ref &var, ELetterCase LetterCase=eLetterCase_Mixed)

get a human-readable text for various clinical significance types

const_iterator end() const

const_iterator find(const key_type &key) const

The xml::attributes class is used to access all the attributes of one xml::node.

The xml::document class is used to hold the XML tree and various bits of information about it.

The xml::node_set class is used to store xpath query result set.

The xml::node class is used to hold information about one XML node.

The xml::xpath_expression class is used to store xpath query string and optional XML namespaces.

static vector< string > arr

This file contains the definition of the xml::event_parser class.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_ASSERT(expr, mess)

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static TAnnotNameType NameTypeStrToValue(const string &type)

static bool IsExtendedNAA(const string &annot, bool isStrict=false)

check if a given annotation is an extended NAA (named accession[.version][number],...

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

@ eAnnot_Unnamed

unnamed annotation

vector< string > m_AltAlleles_orig

virtual void FinishRow()=0

finish the row (i.e. no other contents will be added to it)

static void GetBinLinks(const NSnpBins::SBin &bin, TLinkList &LinkList)

get a list of links associated with a given SNP bin

static const string pmURL

standard NCBI resourse URLs

string GetRefAllele_display() const

static const string snpURL

list< TSNPSearchCompoundResult > TSNPSearchCompoundResultList

results of a search for one or several ids

static const string c_SNPVarExt_TopLevel

list< CRef< CVariation > > TSNPSearchResultList

various placements of a variation

static size_t EstimateSNPCount(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

static NSnp::TClinSigID ClinSigFromString(const string &clinsig)

converts string to clinical significance type (CPhenotype::EClinical_significance)

static const int c_BinWidth

standard width and height of a bin

static string SelectClinSigTerm(const string &clinsig)

returns the term with the highest pathogenicity if the CLNSIG string has multiple parts (terms)

static bool m_isSearchByRsid

virtual void AddValueCol(const string &sContents="", unsigned width=200, bool isNoWrap=false)=0

adds a value column to the row

const list< string > & GetAltAlleles_display() const

static string PValueAsColorKey(double pvalue)

preferred colorings for a given pvalue

string GetInfoColumnsAsString() const

static void Fetch(const string &url, string &result, const STimeout *timeout=kDefaultTimeout, bool is_cache=false)

Fetch a URL from the net using http GET.

static const string c_SNPVarExt_SearchClass

objects::CVariation_inst::EType m_VariationType

static void x_MakeClinVarLink(CConstRef< NSnpBins::SBinEntry > BinEntry, CIRef< ITooltipFormatter > pFormatter, bool &isGoToPresent)

makes a ClinVar link suitable for putting into a tooltip

virtual void AddTagCol(const string &sContents="", const string &sBulletSrc="")=0

adds a tag column to the row

static const string c_SNPVarExt_GeneSymbol

static void x_MakeVarVuLink(CConstRef< NSnpBins::SBinEntry > BinEntry, CIRef< ITooltipFormatter > pFormatter, bool &isGoToPresent, TGi gi)

makes a varVu link suitable for putting into a tooltip

static bool GetClinSigValue(const CSeq_feat &ref, string &attr_value)

returns CLNSIG attribute value from VcfAttribute user object returns false if not found

static void x_ProcessDbgaptext(CConstRef< NSnpBins::SBinEntry > BinEntry, ITooltipFormatter *pFormatter)

processes dbgaptext field and puts its contents into a tooltip

static const string geneRevURL

static void SearchByVarId(const std::string &sTerms, const string &sAssemblyAccession, TSNPSearchCompoundResultList &ResultList)

static bool isFromVcf(const CSeq_feat &variation_ref)

CConstRef< objects::CSeq_loc > m_SeqLoc

static const string VarVuURL

static string ClinSigAsColorKey(NSnp::TClinSigID ClinSigID)

preferred colorings for SNP clinical significances

static const string phenotypeURL

static string ClinSigAsImgURL(NSnp::TClinSigID ClinSigID, const string &colorTheme)

gets a URL to an image representing the given clinical significance

static const string PHAURL

pair< string, TSNPSearchResultList > TSNPSearchCompoundResult

results of a search for a given id (string) TSNPSearchResultList may be empty if the id has been foun...

static const string geneSymURL

static const string GAPStudyURL

static CVariation_inst::EType GetVcfType(const CSeq_feat &variation_ref)

static const string GenomeURL

static CGraph_CI GetGraph_CI(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

static const string ClinVarIdURL

standard NCBI resourse URLs

list< string > m_AltAlleles_display

unique_ptr< objects::CInt_fuzz::ELim > m_LimitValue

static const string omimURL

static const string c_SNPVarExt_QueryId

static string PValueToString(double pvalue)

static const string c_SNPVarExt_Comment

list< TLink > TLinkList

list of URL links

static const string ClinVarURL

static void GetBinTooltip(const NSnpBins::SBin &bin, CIRef< ITooltipFormatter > pFormatter, TGi gi, const std::string &colorTheme)

generate a tooltip for a given bin object and put it into the formatter

int GetLongestAlleleLen(bool &all_alt_alleles_same_len) const

static string m_sSearchHost

void GetLabel(string &label, CLabel::ELabelType type) const

virtual void StartRow()=0

start a new table row

CVcfVariant(const objects::CSeq_id &seq_id, const string &sVariantID, size_t pos, const string &ref_allele, const string &alt_alleles)

alternative alleles separated by /

static CFeat_CI GetFeat_CI(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

string GetAltAlleles_orig() const

static void ClinSigAsColor(NSnp::TClinSigID ClinSigID, CRgbaColor &color)

returns color for clinsig values (SV-4908) returns #767677 for undefined values

virtual string CreateNcbiLink(const string &sText, const string &sUrl) const =0

construct the HTML code for a link from the displayed text label and supplied NCBI URL path

static const int c_BinHeight

static void Search(const std::string &sTerms, const std::string &sAssemblyAccession, TSNPSearchCompoundResultList &ResultList)

search for given SNP ID(s) and get a list of results

static void x_GetSearchHost()

string GetAllAlleles_display() const

string GetVariationTypeAsString() const

unique_ptr< objects::CDelta_item::EAction > m_DeltaItemAction

const TPrim & Get(void) const

TRange GetTotalRange(void) const

TSeqPos GetComp(void) const

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

const CSeq_loc & GetLoc(void) const

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

const CSeq_graph::C_Graph & GetGraph(void) const

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

position_type GetLength(void) const

bool IntersectingWith(const TThisType &r) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

virtual bool GetBool(const string &section, const string &name, bool default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get boolean value of specified parameter name.

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void Parse(const CTempString str, NStr::EMergeDelims merge_argsep=NStr::eMergeDelims)

Parse the string.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static size_t StringToSizet(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to size_t.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fWithCommas

Use commas as thousands separator.

@ eNocase

Case insensitive compare.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TData & GetData(void) const

Get the Data member data.

bool IsVariation(void) const

Check if variant Variation is selected.

const TVariation & GetVariation(void) const

Get the variant data.

const TInt & GetInt(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

const TByte & GetByte(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

bool IsByte(void) const

Check if variant Byte is selected.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ eMol_genomic

"g." coordinates in HGVS

TType GetType(void) const

Get the Type member data.

E_Choice Which(void) const

Which variant is currently selected.

TObservation GetObservation(void) const

Get the Observation member data.

const TSet & GetSet(void) const

Get the variant data.

const TDelta & GetDelta(void) const

Get the Delta member data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetDelta(void) const

Check if it is safe to call GetDelta method.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool CanGetObservation(void) const

Check if it is safe to call GetObservation method.

bool IsSet(void) const

Check if variant Set is selected.

list< CRef< CDelta_item > > TDelta

bool IsSetVariations(void) const

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

EClinical_significance

does this variant have known clinical significance?

const TVariations & GetVariations(void) const

Get the Variations member data.

bool IsSetData(void) const

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

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_inv

delta=[del, ins.seq= RevComp(variation-location)]

@ eType_mnp

delta=[morph of length >1]

@ eType_microsatellite

delta=[del, ins.seq= repeat-unit with fuzzy multiplier] variation-location is the microsat expansion ...

@ eType_delins

delta=[del, ins]

@ eType_cnv

delta=[del, ins= 'this' with fuzzy multiplier]

@ eType_translocation

delta=like delins

@ eResource_link_clinical

Clinical if LSDB, OMIM, TPA, Diagnostic (0x10)

@ eAction_del_at

excise sequence at location if multiplier is specified, delete len(location)*multiplier positions dow...

@ e_This

same location as variation-ref itself

@ eObservation_reference

inst represents the reference base at the position

@ eClinical_significance_drug_response

@ eClinical_significance_probable_pathogenic

@ eClinical_significance_unknown

@ eClinical_significance_untested

@ eClinical_significance_pathogenic

@ eClinical_significance_probable_non_pathogenic

@ eClinical_significance_other

@ eClinical_significance_histocompatibility

@ eClinical_significance_non_pathogenic

bool IsPlacements(void) const

Check if variant Placements is selected.

const TPlacements & GetPlacements(void) const

Get the variant data.

unsigned int

A callback function used to compare two keys in a database.

constexpr bool empty(list< Ts... >) noexcept

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Process information in the NCBI Registry, including working with configuration files.

const int kMaxDoublePrecision

static const char * sSearchByVarIdHost

static void s_GetVcfAttribute(const CSeq_feat &ref, const string &attr_name, string &attr_value)

const int kMaxDoubleStringSize

TBinEntryList m_EntryList

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