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

: m_TopSeqEntry(entry), m_SeqSubmit(submit)

vector<const char*> s_FeatSelectors {

it = find_if( s_FeatSelectors.begin(), s_FeatSelectors.end(),

[&selector](

* elem) { return NStr::EqualNocase(selector, elem); } );

(it != s_FeatSelectors.end());

& named_annot,

& range)

& named_annot,

& feat_interval)

(!named_annot.empty()) {

CMacroBioData_AutodefOptsIter - iterates over all AutodefOptions in the seq-entry.

CMacroBioData_BioSourceIter - iterates over all biosource descriptors and features in the seq-entry.

CMacroBioData_DBLinkIter - iterates over all DBlinks in the seq-entry.

CMacroBioData_FeatIntervalIter - iterates over features within [|(left, right]|) intervals.

CMacroBioData_FeatIterBase - iterates over any type of features.

CMacroBioData_MolInfoIter - iterates over all molinfos in the seq-entry.

CMacroBioData_PubdescIter - iterates over all publication descriptors and features in the seq-entry.

CMacroBioData_SeqAlignIter - iterates over sequence alignments.

CMacroBioData_SeqSetIter- iterates over sets.

CMacroBioData_SeqdescIter- iterates over all types of sequence descriptors.

CMacroBioData_TSEntryIterBase - iterator pointing to the top seq-entry.

CMacroBioData_UserObjectIter - iterates over all user objects in the seq-entry.

The following asn-selectors are defined to be used in the FOR EACH statement:

class CMacroExecException

IMacroBioDataIter - common interface of all iterators used in the editing macros The type of the iter...

static const char * sm_SeqAa

IMacroBioDataIter * CreateIterator(const string &selector, const string &named_annot, const TSeqRange &range, CNcbiOstream *ostr=nullptr) const

Create specific iterator as a subclass of IMacroBioDataIter.

static const char * sm_Protein

static const char * sm_Miscfeat

IMacroBioDataIter * x_CreateFeatIterator(const string &selector, const string &named_annot, const TSeqRange &range) const

static const char * sm_ImpFeat

static const char * sm_Seqdesc

static const char * sm_SeqNa

static const char * sm_BioSource

bool IsSetSeqSubmit(void) const

static const char * sm_SeqSet

static CMacroBioData_SeqIter * s_MakeSeqIterator(const objects::CSeq_entry_Handle &entry, objects::CSeq_inst::EMol mol_type)

static const char * sm_TSEntry

static const char * sm_SNP

static const char * sm_RNA

static const char * sm_DBLink

static bool s_IsFeatSelector(const string &selector)

void SetSeqSubmit(const objects::CSeq_submit &submit)

objects::SAnnotSelector x_GetAnnotSelector(const string &selector, const string &named_annot) const

CConstRef< objects::CSeq_submit > m_SeqSubmit

static const char * sm_Pubdesc

static const char * sm_rRNA

static const char * sm_UserObject

static const char * sm_StrComm

static const char * sm_MolInfo

static const char * sm_mRNA

objects::CSeq_entry_Handle m_TopSeqEntry

static const char * sm_Gene

static const char * sm_SeqFeat

static const char * sm_miscRNA

static const char * sm_SeqAlign

void SetOutputStream(CNcbiOstream *str)

static const char * sm_Seq

IMacroBioDataIter * x_CreateNonFeatIterator(const string &selector) const

static const char * sm_AutodefOpts

static const char * sm_CdRegion

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

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

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

TObjectType & GetObject(void) const

Get object.

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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

Case-insensitive equality of a substring with another string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

Neutral sequence alignment (for representing an HSP in BLAST)

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