123 if ( ext.
HasField(
"orig-var-type" ) ) {
136 mType =
"complex_structural_alteration";
140 mType =
"copy_number_gain";
146 for ( CVariation_ref::TConsequence::const_iterator cit = consequences.begin();
147 cit != consequences.end(); ++cit )
149 if ( (*cit)->IsLoss_of_heterozygosity() ) {
150 mType =
"loss_of_heterozygosity";
155 mType =
"copy_number_loss";
158 if ( var_ref.
IsCNV() ) {
159 mType =
"copy_number_variation";
170 mType =
"single_nucleotide_variation";
222 for ( CUser_object::TData::const_iterator cit =
data.begin();
223 cit !=
data.end(); ++cit )
227 key = (*cit)->GetLabel().GetStr();
228 value = (*cit)->GetData().GetStr();
236 key =
key.substr(
string(
"custom-").length() );
334 if ( ext.
HasField(
"custom-var_type" ) ) {
350 if ( ! loc.
IsInt() ) {
359 switch( fuzz.
Which() ) {
376 "Start_range",
min +
string(
",."));
380 "Start_range",
string(
".,") +
min);
394 if ( ! loc.
IsInt() ) {
403 switch( fuzz.
Which() ) {
435 string strAttributes;
438 if ( priority != temp_attrs.
end() ) {
440 temp_attrs.
erase( priority );
442 priority = temp_attrs.
find(
"Parent");
443 if ( priority != temp_attrs.
end() ) {
445 temp_attrs.
erase( priority );
447 priority = temp_attrs.
find(
"Name");
448 if ( priority != temp_attrs.
end() ) {
450 temp_attrs.
erase( priority );
452 priority = temp_attrs.
find(
"Start_range");
453 if ( priority != temp_attrs.
end() ) {
455 temp_attrs.
erase( priority );
457 priority = temp_attrs.
find(
"End_range");
458 if ( priority != temp_attrs.
end() ) {
460 temp_attrs.
erase( priority );
463 while ( other != temp_attrs.
end() ) {
467 return strAttributes;
473 string& strAttributes )
const
476 string key = it->first;
477 string value = it->second.front();
480 if ( !strAttributes.empty() ) {
481 strAttributes +=
";";
483 strAttributes +=
key;
484 strAttributes +=
"=";
486 strAttributes +=
"\"";
488 strAttributes +=
value;
490 strAttributes +=
"\"";
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.
void GetLabel(string *label) const
bool SetAttribute(const string &, const string &)
TAttributes::iterator TAttrIt
TAttributes::const_iterator TAttrCit
virtual bool x_AssignAttributeName(const CMappedFeat &)
virtual bool x_AssignAttributesCustom(const CMappedFeat &)
virtual bool x_AssignAttributeEndRange(const CMappedFeat &)
virtual ~CGvfWriteRecord()
virtual bool x_AssignAttributeVarType(const CMappedFeat &)
string StrAttributes() const override
virtual bool x_AssignAttributeID(const CMappedFeat &)
virtual bool AssignSource(const CMappedFeat &)
virtual bool x_AssignAttributeStartRange(const CMappedFeat &)
CGvfWriteRecord(CGffFeatureContext &)
void x_AppendAttribute(TAttrCit, string &) const
virtual bool AssignAttributes(const CMappedFeat &, unsigned int=0)
virtual bool AssignType(const CMappedFeat &, unsigned int=0)
virtual bool x_AssignAttributeParent(const CMappedFeat &)
ESubtype GetSubtype(void) const
bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const
Verify that a named field exists.
const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const
Access a named field in this user object.
const_iterator begin() const
const_iterator end() const
const_iterator find(const key_type &key) const
Include a standard set of the NCBI C++ Toolkit most basic headers.
const CSeqFeatData & GetData(void) const
const CUser_object & GetExt(void) const
bool IsSetExt(void) const
const CSeq_loc & GetLocation(void) const
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)
Check if a string starts with a specified prefix value.
const TStr & GetStr(void) const
Get the variant data.
bool IsStr(void) const
Check if variant Str is selected.
bool IsSetType(void) const
type of object within class Check if a value has been assigned to Type data member.
const TData & GetData(void) const
Get the Data member data.
TLim GetLim(void) const
Get the variant data.
TMin GetMin(void) const
Get the Min member data.
const TStr & GetStr(void) const
Get the variant data.
const TData & GetData(void) const
Get the Data member data.
E_Choice Which(void) const
Which variant is currently selected.
const TType & GetType(void) const
Get the Type member data.
TMax GetMax(void) const
Get the Max member data.
vector< CRef< CUser_field > > TData
const TRange & GetRange(void) const
Get the variant data.
const TVariation & GetVariation(void) const
Get the variant data.
const TFuzz_from & GetFuzz_from(void) const
Get the Fuzz_from member data.
const TFuzz_to & GetFuzz_to(void) const
Get the Fuzz_to member data.
TFrom GetFrom(void) const
Get the From member data.
bool IsSetFuzz_to(void) const
Check if a value has been assigned to Fuzz_to data member.
TTo GetTo(void) const
Get the To member data.
bool IsInt(void) const
Check if variant Int is selected.
const TInt & GetInt(void) const
Get the variant data.
bool IsSetFuzz_from(void) const
Check if a value has been assigned to Fuzz_from data member.
TType GetType(void) const
Get the Type member data.
const TInstance & GetInstance(void) const
Get the variant data.
const TId & GetId(void) const
Get the Id member data.
bool IsSetConsequence(void) const
Check if a value has been assigned to Consequence data member.
const TData & GetData(void) const
Get the Data member data.
bool IsInstance(void) const
Check if variant Instance is selected.
list< CRef< C_E_Consequence > > TConsequence
const TConsequence & GetConsequence(void) const
Get the Consequence member data.
bool IsSetParent_id(void) const
Check if a value has been assigned to Parent_id data member.
const TParent_id & GetParent_id(void) const
Get the Parent_id member data.
const TName & GetName(void) const
Get the Name member data.
bool IsSetId(void) const
ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334',...
bool IsSetName(void) const
names and synonyms some variants have well-known canonical names and possible accepted synonyms Check...
@ eType_snv
delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...
const struct ncbi::grid::netcache::search::fields::KEY key
const GenericPointer< typename T::ValueType > T2 value