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NCBI C++ ToolKit: src/algo/sequence/align_group.cpp Source File

& annot_name_base,

( !tax_id_tag.empty() ) {

org_ref->GetLabel(&tax_id_tag);

tax_id_tag +=

;

name(annot_name_base);

( !name.empty() ) {

annot->

().SetAlign().swap(iter->second);

align_groups.push_back(annot);

& annot_name_base,

(iter->first.size() == 1) {

tax_id = *iter->first.begin();

( !tax_id_tag.empty() ) {

org_ref->GetLabel(&tax_id_tag);

tax_id_tag +=

;

name(annot_name_base);

( !name.empty() ) {

annot->

().SetAlign().swap(iter->second);

align_groups.push_back(annot);

( !mixed_annot ) {

name(annot_name_base);

( !name.empty() ) {

name +=

;

mixed_annot->

().SetAlign()

.insert(mixed_annot->

().SetAlign().end(),

iter->second.begin(), iter->second.end());

align_groups.push_back(mixed_annot);

& annot_name_base,

objects::CScope& scope,

TSequenceAlignMap seq_aligns;

( ; id_iter; ++id_iter) {

seq_aligns[ids].push_back(align);

(TSequenceAlignMap, iter, seq_aligns) {

( !iter->second.size() ) {

(TSeqIds, it, iter->first) {

( !

.empty() ) {

it->GetSeqId()->GetLabel(&

,

.insert(annot->

().SetAlign().begin(),

iter->second.begin(), iter->second.end());

name(annot_name_base);

( !name.empty() ) {

align_groups.push_back(annot);

& annot_name_base,

objects::CScope& scope)

TSequenceAlignMap seq_aligns;

seq_aligns[strands].push_back(align);

(TSequenceAlignMap, iter, seq_aligns) {

( !iter->second.size() ) {

(TStrands, it, iter->first) {

( !

.empty() ) {

.insert(annot->

().SetAlign().begin(),

iter->second.begin(), iter->second.end());

name(annot_name_base);

( !name.empty() ) {

align_groups.push_back(annot);

& annot_name_base,

objects::CScope& scope,

TSequenceAlignMap seq_aligns;

TSequenceTypes

;

( ; id_iter; ++id_iter) {

this_flags |=

;

.insert(this_flags);

seq_aligns[

].push_back(align);

(TSequenceAlignMap, iter, seq_aligns) {

( !iter->second.size() ) {

(TSequenceTypes, it, iter->first) {

( !

.empty() ) {

+=

;

+=

;

.insert(annot->

().SetAlign().begin(),

iter->second.begin(), iter->second.end());

name(annot_name_base);

( !name.empty() ) {

align_groups.push_back(annot);

( ; id_iter; ++id_iter) {

tax_aligns[ids].push_back(align);

org_ref =

->GetOrgRef(tax_id, is_species,

is_uncultured, blast_name);

org_ref = tax_iter->second;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void GroupBySequenceType(const TAlignList &aligns, TAnnotList &align_groups, const string &annot_base_name, objects::CScope &scope, TSequenceFlags flags=fSequenceDefaults)

Group alignments into sequence-related categories.

void GroupByLikeTaxIds(const TAlignList &aligns, TAnnotList &align_groups, const string &annot_base_name, objects::CScope &scope)

Separate a set of alignments into groups that describe how the alignments relate taxonomically.

TTaxId x_GetTaxId(const objects::CSeq_id_Handle &id, objects::CScope &scope)

void GroupByTaxIds(const TAlignList &aligns, TAnnotList &align_groups, const string &annot_base_name, objects::CScope &scope)

Separate a set of alignments into groups that describe how the alignments relate taxonomically.

CConstRef< objects::COrg_ref > x_GetOrgRef(TTaxId tax_id)

unique_ptr< objects::CTaxon1 > m_Taxon1

void GroupBySeqIds(const TAlignList &aligns, TAnnotList &align_groups, const string &annot_base_name, objects::CScope &scope, TSeqIdFlags flags=0)

Group alignments into bins for each set of seq-ids.

void x_SeparateByTaxId(const TAlignList &alignments, TTaxAlignMap &tax_aligns, objects::CScope &scope)

void GroupByStrand(const TAlignList &aligns, TAnnotList &align_groups, const string &annot_base_name, objects::CScope &scope)

Group alignments into bins for each set of strands.

list< CRef< objects::CSeq_align > > TAlignList

list< CRef< objects::CSeq_annot > > TAnnotList

TDim CheckNumRows(void) const

Validatiors.

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

Template class for iteration on objects of class C (non-medifiable version)

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ fLabel_Version

Show the version.

@ fLabel_GeneralDbIsContent

For type general, use the database name as the tag and the (text or numeric) key as the content.

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

@ e_Other

for historical reasons, 'other' = 'refseq'

void SetData(TData &value)

Assign a value to Data data member.

void SetName(const TName &value)

Assign a value to Name data member.

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