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NCBI C++ ToolKit: src/app/objmgr/demo/objmgr_demo.cpp Source File

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prog_description =

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arg_desc->SetUsageContext(

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C::E_Choice E_Choice;

(

e =

; e < C::e_MaxChoice; ++e ) {

( C::SelectionName(E_Choice(e)) ==

.AsString() ) {

(

j = 0; j < 2; ++j ) {

<<

[(c>>4)&15];

( vector<CSeq_id_Handle>,

, v ) {

(

!= v.begin() ) {

<< setw(10) << range.

()

<<

->AsFastaString();

<< p1 <<

<< index[

] <<

<< feat <<

;

( ++it2 != cc.

() ) {

vector<CMappedFeat> cc = feat_tree.GetChildren(parent);

( vector<CMappedFeat>, it, cc ) {

<<

<<parent<<

<<

<<*it<<

<<

<<parent<<

<<

<<*it<<

<<

<<parent<<

<<

<<*it<<

<<

<< exc.

()

<<

<<parent<<

<<

<<*it<<

<<

<<parent<<

<<

<<*it<<

<<

<<parent<<

<<

<<*it<<

<<

<< exc.

()

<<

;

<<

;

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

vector<CSeq_id_Handle> ids = scope.

(idh);

( vector<CSeq_id_Handle>, it, ids ) {

(

<<exc);

(

.Which() ) {

(

.GetNcbi2na().Get().size()*4);

(

.GetNcbi2na().Get().size()*2);

( args[

] ) {

( args[

] ) {

.Reset(

(args[

].AsString()));

( args[

] ) {

= args[

].AsString();

(

.find(

) ==

) {

h =

.ReadFileHeader();

( h ==

) {

.ReadObject(&*

, CSeq_id::GetTypeInfo());

( h ==

) {

.ReadObject(&*range_loc, CSeq_loc::GetTypeInfo());

(

<<args[

].AsString());

(

);

( args[

].AsString() ==

)

( args[

].AsString() ==

)

( args[

].AsString() ==

)

( args[

].AsString() ==

)

( args[

].AsString() ==

)

( args[

].AsString() ==

)

externals_only = args[

];

limit_tse = args[

];

repeat_count = args[

].AsInteger();

pause = args[

].AsInteger();

pause_key = args[

];

only_features = args[

];

by_product = args[

];

count_types = args[

];

count_subtypes = args[

];

get_types = args[

];

get_names = args[

];

( get_types || get_names ) {

only_features =

;

( count_types || count_subtypes ) {

only_features =

;

get_cost = args[

];

print_tse = args[

];

print_seq = args[

];

print_descr = args[

];

GetVariant<CSeqdesc>(args[

]);

print_cds = args[

];

print_features = args[

];

print_mapper = args[

];

get_mapped_location = args[

];

get_original_feature = args[

];

get_mapped_feature = args[

];

get_feat_handle = args[

];

print_graphs = args[

];

print_graph_stats = args[

];

print_alignments = args[

];

print_annot_desc = args[

];

check_seq_data = args[

];

seq_vector_tse = args[

];

skip_features = args[

];

skip_graphs = args[

];

skip_alignments = args[

];

skip_tables = args[

];

get_mapped_alignments = args[

];

( args[

] )

sort_seq_feat = args[

];

save_mapped_feat = args[

];

labels = args[

];

max_feat = args[

].AsInteger();

= args[

].AsInteger();

adaptive = args[

];

no_feat_policy = args[

];

only_feat_policy = args[

];

exact_depth = args[

];

nosnp = args[

];

include_unnamed = args[

];

include_allnamed = args[

];

noexternal = args[

];

whole_tse = args[

];

whole_sequence = args[

];

scan_whole_sequence = args[

];

scan_whole_sequence2 = args[

];

check_gaps = args[

];

dump_seq_id = args[

];

used_memory_check = args[

];

get_synonyms = args[

];

get_ids = args[

];

get_blob_id = args[

];

make_tree = args[

];

tse_feat_tree = args[

];

feature::CFeatTree::EFeatIdMode feat_id_mode =

feature::CFeatTree::eFeatId_by_type;

( args[

].AsString() ==

) {

feat_id_mode = feature::CFeatTree::eFeatId_ignore;

( args[

].AsString() ==

) {

feat_id_mode = feature::CFeatTree::eFeatId_always;

feature::CFeatTree::ESNPStrandMode snp_strand_mode =

feature::CFeatTree::eSNPStrand_both;

( args[

].AsString() ==

) {

snp_strand_mode = feature::CFeatTree::eSNPStrand_same;

( args[

].AsString() ==

) {

snp_strand_mode = feature::CFeatTree::eSNPStrand_both;

print_tree = args[

];

verify_tree = args[

];

vector<string> include_named;

( args[

] ) {

(args[

].AsString(),

, include_named);

vector<string> exclude_named;

( args[

] ) {

(args[

].AsString(),

, exclude_named);

vector<string> include_named_accs;

( args[

] ) {

(args[

].AsString(),

, include_named_accs);

save_NA_prefix = args[

]? args[

].AsString():

;

scan_seq_map = args[

];

scan_gaps = args[

];

get_seg_labels = args[

];

vector<int> types_counts, subtypes_counts;

vector<string> other_loaders;

( args[

] ) {

genbank_readers = args[

].AsString();

( genbank_readers !=

) {

( args[

] ) {

( genbank_readers ==

) {

( args[

] || args[

] ) {

lds_db, lds_dir;

( args[

] ) {

lds_db = args[

].AsString();

( args[

] ) {

lds_dir = args[

].AsString();

lds_dir = args[

].AsString();

( !

(lds_db).Exists() && !lds_dir.empty() ) {

( args[

] || args[

] ) {

( args[

] ) {

db = args[

].AsString();

( args[

] ) {

s = args[

].AsString();

( s.size() > 0 && s[0] ==

) {

( s.size() > 0 && s[0] ==

) {

( args[

] ) {

old_param =

().

(

,

);

().

(

,

, args[

].AsString());

(args[

]) {

vector<string>

;

( args[

] ) {

vector<string> bams;

(

& bam : bams ) {

old_param =

().

(

,

);

old_param1 =

().

(

,

);

( args[

] ) {

().

(

,

, args[

].AsString());

().

(

,

, old_param1);

( vector<string>, it, other_loaders ) {

( args[

] ) {

( used_memory_check ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

(

.HaveMoreData() ) {

annot->

().SetAlign().push_back(align);

( args[

] ) {

(

.HaveMoreData() ) {

annot->

().SetAlign().push_back(align);

( args[

] ) {

= args[

].AsString();

vector<string> keys;

( keys.size() < 2 || keys.size() > 3 ) {

(

<<

<<

);

(

);

sat, satkey, subsat = 0;

( keys.size() == 3 ) {

(

<<

<<

);

gb_blob_id, seq_blob_id;

( get_blob_id ) {

(

<<idh<<

);

(

<<idh<<

<<exc);

( get_blob_id ) {

(

<<idh);

seq_blob_id = blob_id.

();

seq_blob_id = loader->GetName()+

+seq_blob_id;

( !gb_blob_id.empty() && gb_blob_id != seq_blob_id ) {

= !handle;

( handle && args[

] ) {

<<

<< sequence::CDeflineGenerator().GenerateDefline(handle) <<

( handle && get_synonyms ) {

( handle && print_tse ) {

<<

;

<<

;

( handle && print_seq ) {

<<

;

<<

;

plus_strand = args[

];

minus_strand = args[

];

ignore_strand = args[

];

( plus_strand || minus_strand || args[

] || args[

] ) {

( args[

] ) {

range_from = args[

].AsInteger();

( args[

] ) {

range_to = args[

].AsInteger();

range_loc->

().SetId(*search_id);

range_loc->

().SetFrom(range_from);

range_loc->

().SetTo(range_to);

range.

(range_from).SetTo(range_to);

( plus_strand ) {

( minus_strand ) {

( range_loc ) {

range_from = range.

();

range_to = range.

();

range_strand = range_loc->

();

range_from = range_to = 0;

range_loc = whole_loc;

( args[

] ) {

( args[

].AsString() ==

)

( args[

].AsString() ==

)

no_map = args[

];

table_field_name;

( args[

] )

table_field_name = args[

].AsString();

table_field_id = -1;

( args[

] )

table_field_id = args[

].AsInteger();

modify = args[

];

vector<CRef<CPrefetchRequest> > prefetch_snp;

vector<CRef<CPrefetchRequest> > prefetch_seq;

(

pass = 0; pass < repeat_count; ++pass ) {

( pass && pause ) {

( args[

] && range_loc != whole_loc ) {

step = args[

].AsInteger();

range_loc->

().SetFrom(range_from);

range_loc->

().SetTo(range_to);

( handle && get_seg_labels ) {

(

, pause_key);

( exact_depth ) {

( ; seg; ++seg ) {

( handle && !only_features ) {

<<

<<bit->GetSeqId()->DumpAsFasta()<<

(

, pause_key);

( seq_vector_tse ) {

( check_seq_data ) {

sout += seq_vect[

];

c = seq_vect[0];

(

<<exc.

());

c = seq_vect[seq_vect.

()-1];

(

<<exc.

());

( whole_sequence ) {

(

<= 20u ) {

(

<<exc);

( scan_whole_sequence ) {

( check_gaps && it.IsInGap() ) {

<<

<< it.GetGapSizeForward()

<<

<<it.GetPos()<<

;

it.GetGapSeq_literal();

pos += it.GetGapSizeForward();

( (pos & 0xffff) == 0 ) {

(

<<pos<<

<<exc);

( scan_whole_sequence2 ) {

( ; pos < seq_vect.

(); ++pos ) {

( check_gaps && seq_vect.

(pos) ) {

<<

<<pos<<

;

( (pos & 0xffff) == 0 ) {

(

<<pos<<

<<exc);

(

, pause_key);

(

desc_it(handle, desc_type); desc_it; ++desc_it) {

( print_descr ) {

(

, pause_key);

( print_descr ) {

<<

<<

<<

<<

<<

( args[

] ) {

( args[

] ) {

& action = args[

].AsString();

( action ==

) {

( action ==

) {

( action ==

) {

( args[

] ) {

base_sel.

(

(args[

].AsDouble()));

( args[

] ) {

( args[

] ) {

base_sel.

(args[

].AsInt8(),

args[

].AsInt8());

base_sel.

(args[

].AsInt8());

( args[

] ) {

( no_feat_policy ) {

( only_feat_policy ) {

( handle && externals_only ) {

( added_annot ) {

( added_entry ) {

( handle ) {

( include_allnamed ) {

( include_unnamed ) {

( vector<string>, it, include_named ) {

( vector<string>, it, include_named_accs ) {

( vector<string>, it, exclude_named ) {

sel_msg =

;

( args[

] ) {

feat_type = GetVariant<CSeqFeatData>(args[

]);

( args[

] ) {

( args[

] ) {

( args[

] ) {

(args[

]) {

TTableField;

unique_ptr< CTableFieldHandle<TTableField> > table_field;

( table_field_id >= 0 ) {

( !table_field_name.empty() ) {

( prefetch_manager ) {

prefetch_seq.clear();

prefetch_snp.clear();

step = args[

].AsInteger();

(

= 0;

< 2; ++

) {

from = range_from + step/2*

;

to = range_to + step/2*

;

prefetch_snp.push_back

prefetch_seq.push_back

( get_types || get_names ) {

<<

<< setw(2) <<

<<

( vector<string>, it, include_named_accs ) {

( vector<string>,

, include_named_accs ) {

scope, *range_loc, &sel2);

( name.IsNamed() ) {

<<

<< name.GetName()

it(scope, *range_loc, sel);

(

->IsNamed() ) {

<<

<<

->GetName()

(

->IsNamed() ) {

<<

<<

->GetName()

(

->IsNamed() ) {

<<

<<

->GetName()

(

->IsNamed() ) {

<<

<<

->GetName()

(

->IsNamed() ) {

<<

<<

->GetName()

( !skip_features ) {

( count_types ) {

( count_subtypes ) {

( handle && print_features && print_mapper ) {

( handle && args[

] ) {

feat_id = args[

].AsInteger();

vector<CSeq_feat_Handle> feats;

(

= 0;

< 4; ++

) {

<< feat_id <<

;

<< feat_id <<

;

<< feat_id <<

;

<< feat_id <<

;

( print_features ) {

( vector<CSeq_feat_Handle>, it, feats ) {

( handle && args[

] ) {

feat_id = args[

].AsString();

vector<CSeq_feat_Handle> feats;

(

= 0;

< 4; ++

) {

<< feat_id <<

;

<< feat_id <<

;

<< feat_id <<

;

<< feat_id <<

;

( print_features ) {

( vector<CSeq_feat_Handle>, it, feats ) {

matches = 0, mismatches = 0;

vector<CConstRef<CSeq_feat> > feats;

vector<CMappedFeat> mapped_feats;

vector<CConstRef<CSeq_loc> > mapped_locs;

(

, pause_key);

it(scope, *range_loc, base_sel);

<<

<<

;

( count_types ) {

( count_subtypes ) {

( print_annot_desc ) {

( get_mapped_location )

( get_original_feature )

( get_mapped_feature ) {

( sort_seq_feat ) {

( save_mapped_feat ) {

mapped_feats.push_back(*it);

( table_field.get() &&

( table_field->TryGet(it,

) ) {

= table_field->Get(it);

( print_features ) {

<<

<<

<<

<<

( handle && print_features &&

sequence;

<<

;

<<

;

( print_features &&

sequence;

( print_features &&

sequence;

<<

<<

<<

<< sel_msg <<

( print_annot_desc ) {

(

& annot : annots ) {

( annot.Seq_annot_IsSetDesc() ) {

( sort_seq_feat && !feats.empty() ) {

<<

<< feats.size() <<

vector<CConstRef<CSeq_feat> > sorted_feats = feats;

( sorted_feats != feats ) {

<<

(

= 0;

< sorted_feats.size(); ++

) {

( feats[

] != sorted_feats[

] ) {

( exception& exc ) {

<<

<< exc.what()

( save_mapped_feat ) {

(

= 0;

< mapped_feats.size(); ++

) {

<< *mapped_locs[

];

<< mapped_feats[

].GetMappedFeature();

( count_types ) {

( vector<int>, vit, types_counts ) {

( count_subtypes ) {

( vector<int>, vit, subtypes_counts ) {

setw(3) << subtype <<

feature::CFeatTree feat_tree;

feat_tree.SetFeatIdMode(feat_id_mode);

feat_tree.SetSNPStrandMode(snp_strand_mode);

( tse_feat_tree ) {

it2 =

(scope, *range_loc, base_sel);

feat_tree.AddFeatures(it2);

list<CMappedFeat> q;

( list<CMappedFeat>, pit, q ) {

vector<CMappedFeat> cc =

feat_tree.GetChildren(parent);

( vector<CMappedFeat>, cit, cc ) {

gene = feat_tree.GetBestGene(child, feat_tree.eBestGene_OverlappedOnly);

( gene != gene1 ) {

( gene && !by_gene.count(gene) ) {

( gene2 != gene1 ) {

<<

<<

<<

<< fit->first;

<<

<<index[*fit] <<

;

( !by_gene.

() ) {

( verify_tree ) {

no_product_count = 0;

(

it(scope, *range_loc, sel); it; ++it ) {

cds_vect =

(it->GetLocation(), scope,

( it->IsSetProduct() ) {

cds_vect =

(it->GetProduct(), scope,

<< cds_vect.

() <<

;

( cds_vect.

() == 0 ) {

it->GetOriginalFeature().GetLocation();

it->GetMappedFeature().GetLocation();

* mapped_id = 0;

it->GetMappedFeature().GetLocation().CheckId(mapped_id);

sout += cds_vect[

];

( no_product_count ) {

<<

<< no_product_count <<

( !skip_features && handle ) {

(

it(handle, range, range_strand, base_sel); it; ++it ) {

<<

<< sel_msg <<

( !only_features ) {

( handle && whole_tse ) {

( !skip_graphs ) {

it(scope, *range_loc, base_sel);

( print_annot_desc ) {

( get_mapped_location )

( get_original_feature )

( get_mapped_feature )

( print_graph_stats ) {

actual_size = vv.size();

asn_max =

.GetMax();

actual_max = *max_element((

*)vv.data(),

(

*)vv.data()+actual_size);

(

c : vv ) {

sum.

((

*)&v,

(v));

<<

<<accumulate(vv.begin(), vv.end(), 0ull);

actual_size = vv.size();

asn_max =

.GetMax();

actual_max = *max_element(vv.data(), vv.data()+actual_size);

sum.

((

*)vv.data(), actual_size*

(vv[0]));

<<

<<accumulate(vv.begin(), vv.end(), 0ull);

( actual_size !=

(graph.

()) ) {

( actual_max != asn_max ) {

( print_graphs ) {

( print_annot_desc ) {

(

& annot : annots ) {

( annot.Seq_annot_IsSetDesc() ) {

( !skip_alignments ) {

it(scope, *range_loc, base_sel);

( get_mapped_alignments ) {

( print_alignments ) {

<< it.GetOriginalSeq_align();

(

& uoref : align.

() ) {

cout <<

<<field->GetInt()<<endl;

( args[

] ) {

(

it(scope, *range_loc, base_sel); it; ++it) {

( !skip_tables ) {

(

it(scope, *range_loc, sel); it; ++it) {

table_counts[annot.

()].first += 1;

table_counts[annot.

()].second += rows;

( args[

] ) {

( table_field.get() ) {

(

= 0;

< rows; ++

) {

( table_field->TryGet(annot,

,

) ) {

(

& c : table_counts ) {

( c.first.IsNamed() ) {

<<

<< c.first.GetName();

<<

<< c.second.first <<

<< c.second.second <<

( !skip_tables ) {

(

it(scope, *range_loc, base_sel); it; ++it) {

( args[

] ) {

table_counts[annot.

()].first += 1;

table_counts[annot.

()].second += rows;

( it.IsMapped() ) {

( table_field.get() ) {

(

= 0;

< rows; ++

) {

( table_field->TryGet(annot,

,

) ) {

(

& c : table_counts ) {

( c.first.IsNamed() ) {

<<

<< c.first.GetName();

<<

<< c.second.first <<

<< c.second.second <<

( !skip_features ) {

(

it(scope, *range_loc, sel); it; ++it) {

( !save_NA_prefix.empty() ) {

& acc = *nit;

(

it(handle, sel); it; ++it ) {

name = save_NA_prefix+acc;

( handle && scan_gaps ) {

max_level =

(5,

);

cout <<

<<max_level<<endl;

gap_count = 0;

sel.

(range_from, range_length);

(

level = 0; level < max_level; ++level ) {

has_refs =

;

cout <<

<<level

<<

<< seg.GetPosition() <<

<< seg.GetEndPosition()

<<

<< seg.GetLength() <<

cout <<

<< level <<

<< sw2.

() <<

cout <<

<< gap_count <<

<<

.

() <<

( handle && scan_seq_map ) {

actual_length = actual_end; actual_length -= range_from;

max_level =

(5,

);

(

level = 0; level < max_level; ++level) {

( exact_depth ) {

( ; seg; ++seg ) {

(

&& 0);

(

&& 0);

(level || total_length == actual_length);

( --seg; seg; --seg ) {

(total_length == new_length);

( ++seg; seg; ++seg ) {

(total_length == new_length);

total_length += iter.GetLength();

total_length += iter.GetLength();

<<

<< seq.

().substr(0, 10) <<

( handle && args[

] ) {

<<

<< id;

( print_features ) {

<<

<< oid;

( print_features ) {

( handle && modify ) {

(pseh == pseh.GetEditHandle());

pseh.GetEditHandle().AttachBioseq(*newseq);

( dump_seq_id ) {

cout <<

<<bytes<<endl;

( args[

] ) {

cout <<

<< endl;

( used_memory_check ) {

( args[

] ) {

( args[

] ) {

cout <<

<< exc.

() << endl;

handle && !

? 0: 1;

(

argc,

* argv[])

ret =

().AppMain(argc, argv);

User-defined methods of the data storage class.

bool check_cds(const DataBlk &entry, Parser::EFormat format)

Data loader implementation that uses the blast databases.

Checksum and hash calculation classes.

const TAnnotNames & GetAnnotNames(void) const

bool MaxSearchSegmentsLimitIsReached(void) const

vector< SAnnotTypeSelector > TAnnotTypes

size_t GetSize(void) const

Uint8 GetCostOfLoadingInBytes(void) const

Get collected cost of loading requested data in bytes.

CSeq_annot_Handle GetAnnot(void) const

const TAnnotTypes & GetAnnotTypes(void) const

double GetCostOfLoadingInSeconds(void) const

Get collected cost of loading requested data in seconds.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

@ eProtein

protein database

@ eUnknown

protein is attempted first, then nucleotide

CChecksum – Checksum calculator.

Derive our application class from CwxNCBIApp and use it together with standard CNCBIwxApplication.

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

void GetIds(CScope &scope, const CSeq_id_Handle &idh)

virtual void Exit(void)

Cleanup on application exit.

virtual TNamedAnnotNames GetNamedAnnotAccessions(const CSeq_id_Handle &idh)=0

virtual TBlobId GetBlobIdFromSatSatKey(int sat, int sat_key, int sub_sat=0) const =0

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Argument-less loader - for compatibility only, unusable.

Class for managing LDS2 database and related data files.

void AddDataDir(const string &data_dir, EDirMode mode=eDir_Recurse)

Add data directory.

void UpdateData(void)

Rescan all indexed files, check for modifications, update the database.

@ eDir_Recurse

Automatically scan sub-directories (default).

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CObjectIStreamAsnBinary –.

CPrefetchSeqData(const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, CBioseq_Handle::EVectorCoding vector_coding)

CRange< TSeqPos > m_Range

const string & GetResult(void) const

CBioseq_Handle::EVectorCoding m_VectorCoding

virtual bool Execute(CRef< CPrefetchRequest > token)

CPrefetchSeqData(const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, CSeq_data::E_Choice encoding)

const string & GetSequence(void) const

CSeq_data::E_Choice m_Encoding

static E_Choice GetTypeFromSubtype(ESubtype subtype)

static CSeq_id_Handle GetSeq_id_Handle(const const_iterator &iter)

TBlobId GetBlobId(void) const

TSeq_feat_Handles GetFeaturesWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CConstRef< TObject > GetCompleteObject(void) const

TSeq_feat_Handles GetFeaturesWithXref(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CDataLoader * GetDataLoader(void) const

const CSeq_submit & GetTopLevelSeq_submit() const

Return reference to top-level Seq-submit object Throw an exception if it's not available.

ETopLevelObjectType GetTopLevelObjectType() const

Get type of top level object added to scope.

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

iterator_bool insert(const value_type &val)

iterator_bool insert(const value_type &val)

const_iterator end() const

parent_type::const_iterator const_iterator

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

static unsigned char depth[2 *(256+1+29)+1]

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

static const char * str(char *buf, int n)

#define GI_FROM(T, value)

const CNcbiRegistry & GetConfig(void) const

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

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CNcbiRegistry & GetRWConfig(void)

Get the application's cached configuration parameters, accessible for read-write for an application's...

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fBinary

Open as binary file; for eInputFile, eOutputFile, eIOFile.

@ eInt8

Convertible into an integer number (Int8 only)

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

Uint4 GetChecksum(void) const

Return calculated checksum.

void AddChars(const char *str, size_t len)

Update current control sum with data provided.

void DBAPI_RegisterDriver_FTDS(void)

#define ERR_FATAL(message)

Posting fatal error and abort.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define MSerial_AsnBinary

C * SerialClone(const C &src)

Create on heap a clone of the source object.

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static ESNPScaleLimit GetSNPScaleLimit_Value(const string &name)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

static CRef< CSeq_id_Mapper > GetInstance(void)

string GetLabel(const CSeq_id &id)

size_t Dump(CNcbiOstream &out, EDumpDetails details=eDumpTotalBytes) const

@ fLabel_Version

Show the version.

@ eContent

Untagged human-readable accession or the like.

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

CMappedFeat GetBestParentForFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype parent_subtype, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

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,...

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_Contained

2nd contained within 1st extremes

string GetAccessionForGi(TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession for a given GI.

@ eWithoutAccessionVersion

accession only, even if version is available

@ 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

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

static void Wait(CRef< CPrefetchRequest > token)

string ToString(void) const

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

TLoader * GetLoader(void) const

Get pointer to the loader.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

virtual bool Execute(CRef< CPrefetchRequest > token)

void RemoveFromHistory(const CTSE_Handle &tse, EActionIfLocked action=eKeepIfLocked)

Remove single TSE from the scope's history.

CSeq_id_Handle GetAccVer(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn'...

TTaxId GetTaxId(const CSeq_id &id, TGetFlags flags=0)

Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxono...

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CSeq_entry_Handle AddSeq_submit(CSeq_submit &submit, TPriority pri=kPriority_Default)

Add Seq-submit, return its CSeq_entry_Handle.

string GetName(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

string GetLabel(const CSeq_id &id, TGetFlags flags=0)

Get short description of bioseq, usually "accession.version" Returns empty string if the sequence is ...

const CFeat_CI & GetResult(void) const

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CDataLoader * RegisterDataLoader(TPluginManagerParamTree *params=0, const string &driver_name=kEmptyStr)

Add data loader using plugin manager.

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

static CRef< CPrefetchRequest > GetFeat_CI(CPrefetchManager &manager, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)

const CBioseq_Handle & GetBioseqHandle(void) const

CBioseq_Handle::TBioseqStateFlags GetSequenceState(const CSeq_id &id, TGetFlags flags=0)

Get sequence GenBank state Return (fState_not_found|fState_no_data) if sequence is not found.

CRef< CPrefetchRequest > AddAction(TPriority priority, IPrefetchAction *action, IPrefetchListener *listener=0)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

@ eSeqMap_Up

map from segments to the top level bioseq

bool IsSetExcept(void) const

bool GetExcept(void) const

const CFeat_id & GetId(void) const

const CSeq_feat::TXref & GetXref(void) const

bool IsSetComment(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

bool GetPseudo(void) const

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const CSeq_submit & GetTopLevelSeq_submit(void) const

void SelectNone(void) const

Make this Seq-entry to be empty.

bool IsSetDbxref(void) const

CConstRef< TObject > GetCompleteObject(void) const

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

bool IsSetExp_ev(void) const

CSeq_feat::EExp_ev GetExp_ev(void) const

const CTSE_Handle & GetTSE_Handle(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetTitle(void) const

bool IsSetXref(void) const

const CTSE_Handle & GetTSE_Handle(void) const

bool IsSetExcept_text(void) const

const CSubmit_block & GetTopLevelSubmit_block(void) const

bool IsSetProduct(void) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

TSeq SelectSeq(CBioseq &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

EVectorCoding

CSeqVector constructor flags.

const string & GetComment(void) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

size_t GetSeq_tableNumRows(void) const

const CUser_object & GetExt(void) const

bool IsTopLevelSeq_submit(void) const

Seq-submit access functions.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

const string & GetExcept_text(void) const

void Reset(void)

Reset handle and make it not to point to any bioseq.

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CConstRef< TObject > GetCompleteObject(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

const string & GetTitle(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

const CSeq_feat::TDbxref & GetDbxref(void) const

bool IsSetQual(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

bool IsTableFeat(void) const

Check if this is non-SNP table feature.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

const string & GetName(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

bool IsSetPseudo(void) const

bool IsPlainFeat(void) const

Check if this is plain feature.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const CSeq_feat::TQual & GetQual(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsSetExt(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

const CSeq_data & GetRefData(void) const

will allow any data segments, user should check for position and strand

SAnnotSelector & ExcludeFeatSubtype(TFeatSubtype subtype)

Exclude feature subtype from the search.

ESortOrder

Flag to indicate sorting method.

SAnnotSelector & SetAllNamedAnnots(void)

Look for all named Seq-annots Resets the filter, and then excludes unnamed annots.

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

SAnnotSelector & SetCollectTypes(bool value=true)

Collect available annot types rather than annots.

SAnnotSelector & ExcludeFeatType(TFeatType type)

Exclude feature type from the search.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

bool IsSetPartial(void) const

SAnnotSelector & SetSearchExternal(const CTSE_Handle &tse)

Set all flags for searching standard GenBank external annotations.

TSeqPos GetRefPosition(void) const

SAnnotSelector & SetMaxSearchSegmentsAction(EMaxSearchSegmentsAction action)

SAnnotSelector & SetResolveMethod(EResolveMethod resolve_method)

SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together wit...

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetByProduct(bool byProduct=true)

Set flag indicating if the features should be searched by their product rather than location.

bool GetPartial(void) const

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

SAnnotSelector & SetOverlapType(EOverlapType overlap_type)

Set overlap type.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

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

SAnnotSelector & SetNoMapping(bool value=true)

SAnnotSelector & SetExcludeIfGeneIsSuppressed(bool exclude=true)

Exclude features with empty gene xref: xref { { data gene { } } }.

SAnnotSelector & SetAdaptiveDepthFlags(TAdaptiveDepthFlags flags)

SetAdaptiveDepthFlags() sets flags for adaptive depth heuristics.

SAnnotSelector & SetLimitSeqAnnot(const CSeq_annot_Handle &limit)

Limit annotations to those from the seq-annot only.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & SetFeatComparator(IFeatComparator *comparator)

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

const CSeq_graph & GetMappedGraph(void) const

Graph mapped to the master sequence.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

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.

EOverlapType

Flag to indicate location overlapping method.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

EUnresolvedFlag

Flag to indicate handling of unresolved seq-ids.

SAnnotSelector & SetSNPScaleLimit(TSNPScaleLimit value)

bool GetRefMinusStrand(void) const

TAdaptiveDepthFlags GetAdaptiveDepthFlags(void) const

GetAdaptiveDepthFlags() returns current set of adaptive depth heuristics flags.

const CSeq_loc & GetProduct(void) const

CSeqMap::ESegmentType GetType(void) const

EResolveMethod

Flag to indicate references resolution method.

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & SetMaxSearchTime(TMaxSearchTime max_time)

Set maximum time (in seconds) to search before giving up.

SSeqMapSelector & SetRange(TSeqPos start, TSeqPos length)

Set range for iterator.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

SAnnotSelector & SetBitFilter(TBitFilter filter_bits, TBitFilter filter_mask=TBitFilter(-1))

TRange GetRange(void) const

Get range for mapped seq-feat's location.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

SAnnotSelector & SetUnresolvedFlag(EUnresolvedFlag flag)

Set method of handling unresolved seq-ids.

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

SAnnotSelector & SetCollectCostOfLoading(bool value=true)

Collect cost of loading requested data.

TSeqPos GetRefEndPosition(void) const

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

const CSeq_loc & GetLoc(void) const

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

TSeqPos GetPosition(void) const

return position of current segment in sequence

SAnnotSelector & AddUnnamedAnnots(void)

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

SAnnotSelector & SetMaxSearchSegments(TMaxSearchSegments max_segments)

Set maximum number of empty segments to search before giving up.

SAnnotSelector & ResetNamedAnnotAccessions(void)

Add named annot accession (NA*) in the search.

TSeqPos GetLength(void) const

return length of current segment

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

SAnnotSelector & SetLimitSeqEntry(const CSeq_entry_Handle &limit)

Limit annotations to those from the seq-entry only.

CSeq_id_Handle GetLocationId(void) const

@ eSortOrder_Reverse

decresing end, decreasing length

@ eSortOrder_Normal

default - increasing start, decreasing length

@ eSortOrder_None

do not sort annotations for faster retrieval

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eOverlap_TotalRange

overlapping of total ranges only

@ eIgnoreUnresolved

Ignore unresolved ids (default)

@ eSearchUnresolved

Search annotations for unresolvable IDs.

@ eFailUnresolved

Throw exception for unresolved ids.

@ eResolve_TSE

default - search only on segments in the same TSE

@ eResolve_All

Search annotations for all referenced sequences.

@ eResolve_None

Do not search annotations on segments.

@ eMaxSearchSegmentsSilent

@ eMaxSearchSegmentsThrow

const_iterator begin(CScope *scope) const

STL style methods.

const_iterator end(CScope *scope) const

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

bool CanGetRange(TSeqPos start, TSeqPos stop) const

Check if the sequence data is available for the interval [start, stop).

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

CConstRef< CSeq_literal > GetGapSeq_literal(TSeqPos pos) const

returns gap Seq-literal object ref returns null if it's not a gap or an unspecified gap

TMutex & GetMutex(void) const

Get mutex for a few non-MT-safe methods to make them MT-safe at a cost of performance.

void SetCoding(TCoding coding)

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

TSeqPos GetGapSizeForward(TSeqPos pos) const

returns number of gap symbols ahead including base at position 'pos' returns 0 if the position is not...

@ eSeqData

real sequence data

@ eSeqRef

reference to Bioseq

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

position_type GetToOpen(void) const

static TThisType GetWhole(void)

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

Get the parameter value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified 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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ fSplit_ByPattern

Require full delimiter strings.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

@ eStart

Start timer immediately after creating.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

TId & SetId(void)

Select the variant.

EField_id

identification of the column data in the objects described by the table known column data types posit...

const TExt & GetExt(void) const

Get the Ext member data.

vector< CRef< CDbtag > > TDbxref

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

const TGene & GetGene(void) const

Get the variant data.

TPartial GetPartial(void) const

Get the Partial member data.

vector< CRef< CSeqFeatXref > > TXref

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

vector< CRef< CGb_qual > > TQual

@ e_not_set

No variant selected.

@ e_MaxChoice

== e_Variation+1

ENa_strand

strand of nucleic acid

const TInt & GetInt(void) const

Get the variant data.

const TGraph & GetGraph(void) const

Get the Graph member data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TByte & GetByte(void) const

Get the variant data.

bool IsByte(void) const

Check if variant Byte is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

TNumval GetNumval(void) const

Get the Numval member data.

bool IsSetTitle(void) const

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

void SetData(TData &value)

Assign a value to Data data member.

E_Choice

Choice variants.

const TId & GetId(void) const

Get the Id member data.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_not_set

No variant selected.

@ e_Locs

used for communication between tools

const TSub & GetSub(void) const

Get the Sub member data.

static void hex(unsigned char c)

static void text(MDB_val *v)

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

void SleepSec(unsigned long sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Sleep.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

std::istream & in(std::istream &in_, double &x_)

CSeq_id_Handle s_Normalize(const CSeq_id_Handle &id, CScope &scope)

map< CMappedFeat, TOrderedFeatures > TOrderedTree

TSeqPos s_GetLength(const CSeq_data &data)

map< TFeatureKey, size_t > TFeatureIndex

bool s_VerifyTree(feature::CFeatTree &feat_tree, const CMappedFeat &parent)

CNcbiOstream & operator<<(CNcbiOstream &out, const vector< char > &v)

set< TFeatureKey > TOrderedFeatures

C::E_Choice GetVariant(const CArgValue &value)

int main(int argc, const char *argv[])

void s_PrintTree(const string &p1, const string &p2, TOrderedTree &tree, TFeatureKey key, TFeatureIndex &index)

TFeatureKey s_GetFeatureKey(const CMappedFeat &child)

CAtomicCounter newCObjects

pair< string, CMappedFeat > TFeatureKey

void x_Pause(const char *msg, bool pause_key)

void GenBankReaders_Register_Pubseq2(void)

void GenBankReaders_Register_Pubseq(void)

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

Compare objects pointed to by (smart) pointer.

PStateFlags(CBioseq_Handle::TBioseqStateFlags state)

CBioseq_Handle::TBioseqStateFlags state

Selector used in CSeqMap methods returning iterators.

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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