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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/feature_filter.cpp Source File

*

=

;

*

=

;

*

=

;

(filter.empty())

;

filter_str = filter;

);

objects::CSeq_feat& feat =

->GetOriginalFeature();

(feat.GetData().IsClone()) {

(feat.GetData().GetClone().IsSetConcordant()) {

= feat.GetData().GetClone().GetConcordant();

(feat.GetData().GetClone().IsSetConcordant()) {

= !feat.GetData().GetClone().GetConcordant();

(identifier ==

) {

objects::CSeq_loc& loc =

->GetLocation();

= loc.GetTotalRange().GetLength();

}

(identifier ==

) {

objects::CSeq_loc& loc =

->GetLocation();

= loc.GetTotalRange().GetFrom();

}

(identifier ==

) {

objects::CSeq_loc& loc =

->GetLocation();

= loc.GetTotalRange().GetTo();

(

& iter :

->GetOriginalFeature().GetExts()) {

(iter->GetType().IsStr() &&

iter->GetType().GetStr() ==

&&

iter->GetFieldRef(

) &&

!iter->GetFieldRef(

).IsNull()) {

& d = iter->GetFieldRef(

)->GetData();

= float(d.GetReal() + 0.5);

);

objects::CSeq_feat& feat =

->GetOriginalFeature();

= feat.GetNamedQual(

);

(

.empty()) {

}

(identifier ==

) {

= feat.GetNamedQual(

);

feat.GetData().IsVariation()) {

objects::CVariation_ref& var = feat.GetData().GetVariation();

(objects::CVariation_ref::TPhenotype, pnt_iter, var.GetPhenotype()) {

((*pnt_iter)->CanGetClinical_significance()) {

((*pnt_iter)->GetClinical_significance()) {

objects::CPhenotype::eClinical_significance_non_pathogenic:

objects::CPhenotype::eClinical_significance_pathogenic:

=

;

objects::CPhenotype::eClinical_significance_probable_pathogenic:

=

;

objects::CPhenotype::eClinical_significance_probable_non_pathogenic:

=

;

objects::CPhenotype::eClinical_significance_unknown:

=

;

objects::CPhenotype::eClinical_significance_untested:

=

;

objects::CPhenotype::eClinical_significance_other:

(

.empty()) {

feat.GetData().IsVariation()) {

= feat.GetNamedQual(

);

(feat.IsSetExts()) {

objects::CSeq_feat::TExts& exts = feat.GetExts();

(objects::CSeq_feat::TExts, iter, exts) {

( (*iter)->GetType().IsStr() &&

(*iter)->GetFieldRef(

) &&

(*iter)->GetFieldRef(

)->GetData().IsStr()) {

= (*iter)->GetFieldRef(

)->GetData().GetStr();

success =

;

= (*m_Node)->GetInt();

= (double)(*m_Node)->GetInt();

= (*m_Node)->GetBool();

= (*m_Node)->GetStrValue();

tr->SetUserObject(v);

&

= tr->GetOriginalText();

);

((*iter)->IsLeaf() && !sub_v->

()) {

);

);

(valid && ++iter != tr.

()) {

((*iter)->IsLeaf()) {

&

= node->GetStrValue();

}

( !sub_v2->

() ) {

+ node->GetOriginalText());

is_between =

;

is_between = sub_v1->

>= sub_v2->

;

is_between = (

>= 0);

is_between = sub_v1->

<= sub_v3->

;

is_between = (

<= 0);

(

= 1;

< args.size() && !found; ++

) {

+ node->GetOriginalText());

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Query parser exceptions class CFeatFilterQueryException.

TIdentifierDict m_IdDict

Identifier dictionary.

const TIdentifierDict * GetIdDictionary() const

virtual bool ResolveIdentifier(const std::string &identifier, bool &value)

The following functions search in the feature asn for a value with the name 'identifier' and,...

bool NeedFiltering() const

bool Pass(const objects::CMappedFeat *feat)

CFeatureFilter()

class CFeatureFilter implementation

const objects::CMappedFeat * m_EvalFeat

Evaluated object.

void Init(const string &filter)

void AddId(const string &id, CQueryParseNode::EType type)

virtual bool HasIdentifier(const std::string &id)

Search for 'identifier' in nodes feature list and true if it exists.

class CSGQueryFunctionCompare

virtual void Evaluate(CQueryParseTree::TNode &node)

class CSGQueryFunctionCompare

class CSGQueryFunctionLogic

virtual void Evaluate(CQueryParseTree::TNode &node)

class CSGQueryFunctionLogic

class CSGQueryFunctionValue

virtual void Evaluate(CQueryParseTree::TNode &node)

class CSGQueryFunctionValue

class CSGQueryNodePreprocessor

TIdentifierDict * m_Dictionary

CSGQueryNodePreprocessor(TIdentifierDict *d)

class CSGQueryNodePreprocessor implementation

ETreeTraverseCode operator()(CTreeNode< CQueryParseNode > &tr, int delta)

Int8 m_Int

Int data, if data was an integer or converted into one.

bool PromoteTo(CQueryParseNode::EType type)

promote this value to the given type.

bool IsDataField() const

Get to indicate if this is a field from the tree or simple string.

void SetDataType(CQueryParseNode::EType dt)

Set/get underlying data type.

double m_Double

Floating point data, if data was a double or converted into one.

std::string m_String

String data, if data came from a string or data fied in the tree.

CQueryParseNode::EType GetDataType() const

bool m_Bool

Bool data, if data base a constant boolean or converted into one.

void SetDataField(bool f)

definition of a Culling tree

Base class for query node user defined object.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static const char * kConcordant

static const char * kValidationStatus

static const char * kDiscordant

static const char * kClinicalAssertion

static const char * kSamplesetType

static const char * kVariantQuality

static const char * kIntronReads

static const char * kPilot

static const char * kFrom

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

int64_t Int8

8-byte (64-bit) signed integer

const IQueryParseUserObject * GetUserObject() const

Get user object.

void Parse(const char *query_str, ECase case_sense=eCaseInsensitive, ESyntaxCheck syntax_check=eSyntaxCheck, bool verbose=false, const TFunctionNames &functions=TFunctionNames(0), unsigned line=0, unsigned linePos=0)

Query parser front-end function.

vector< CQueryParseTree::TNode * > TArgVector

Vector for easy argument access.

const TNode * GetQueryTree() const

virtual bool ResolveIdentifier(const std::string &, bool &)

If query has an identifier, this will resolve it in an application-specific way.

void AddFunc(CQueryParseNode::EType func_type, CQueryFunctionBase *func)

Register function implementation.

void MakeArgVector(CQueryParseTree::TNode &qnode, TArgVector &args)

Created vector of arguments (translate sub-nodes to vector)

virtual void Evaluate(CQueryParseTree &qtree)

Run query tree evaluation.

@ eCaseInsensitive

Case insensitive parsing (AnD)

@ eNotSet

Produced by the (private) default constructor.

@ eFloatConst

Floating point const.

@ eIntConst

Integer const.

@ eBoolConst

Boolean (TRUE or FALSE)

@ eString

String ("free text")

@ eSyntaxCheck

Best possible check for errors.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StringToBool(const CTempString str)

Convert string to bool.

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

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

Convert double to string.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

static bool MatchesMask(CTempString str, CTempString mask, ECase use_case=eCase)

Match "str" against the "mask".

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static const string BoolToString(bool value)

Convert bool to string.

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 bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another 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.

@ eNocase

Case insensitive compare.

TNodeList::iterator TNodeList_I

Fun TreeDepthFirstTraverse(TTreeNode &tree_node, Fun func)

Depth-first tree traversal algorithm.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

unsigned int CountNodes(unsigned int depth=1, TCountNodes how=0) const

Count nodes of the tree of which this node is a root.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

bool IsLeaf() const

Report whether this is a leaf node.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

@ eTreeTraverse

Keep traversal.

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

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

Int4 delta(size_t dimension_, const Int4 *score_)

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