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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/process__explore_8hpp_source.html below:

NCBI C++ ToolKit: src/app/streamtest/process_explore.hpp Source File

1 #ifndef __process_explore__hpp__ 2 #define __process_explore__hpp__ 35 m_out

= args[

"o"

] ? &(args[

"o"

].AsOutputFile()) : &cout;

36 m_accn

= args[

"accn"

].AsString();

38 m_from

= args[

"from"

].AsInteger();

41 m_to

= args[

"to"

].AsInteger();

43 if

(args[

"revcomp"

]) {

47 if

(args[

"policy"

]) {

48 m_policy

= args[

"policy"

].AsInteger();

51 if

(args[

"flags"

]) {

52 m_flags

= args[

"flags"

].AsInteger();

55 if

(args[

"depth"

]) {

56 m_depth

= args[

"depth"

].AsInteger();

94

sel.SetFlags(CSeqMap::fFindAny);

95

CBioseq_Handle bsh = bsx.GetBioseqHandle();

96

for ( CSeqMap_CI seg(ConstRef(&bsh.GetSeqMap()), &bsh.GetScope(), sel); seg; ++seg ) {

97

*x_out <<

"# "

<< seg.GetType() <<

" @ "

<< seg.GetPosition() <<

" - "

<< seg.GetEndPosition() << endl;

100

}

else if

(bsx.

IsAA

()) {

105

m_out

"Record has "

<< num_nucs <<

" nucleotide"

<< ((num_nucs != 1) ?

"s"

""

);

106

m_out

" and "

<< num_prots <<

" protein"

<< ((num_prots != 1) ?

"s"

""

);

113 for

(

auto

&bsx : idx.GetBioseqIndices()) {

116

}

else if

(bsx->

IsAA

()) {

121

m_out

"Second has "

<< num_nucs <<

" nucleotide"

<< ((num_nucs != 1) ?

"s"

""

);

122

m_out

" and "

<< num_prots <<

" protein"

<< ((num_prots != 1) ?

"s"

""

);

133

}

else if

m_accn

.empty()) {

136

bsx = idx.GetBioseqIndex(

m_accn

);

143 if

(num_nucs == 1 && num_prots > 0) {

146

bsx = idx.GetBioseqIndex(2);

153

bsx = idx.GetBioseqIndex();

164 if

(idx.IsFetchFailure()) {

165

m_out

"IsFetchFailure"

'\n'

;

174

*m_out <<

"\nBIOSEQ\n"

;

176

*m_out <<

"Accession: "

<< bsx.

GetAccession

() <<

'\n'

;

177

*m_out <<

"Length: "

<< bsx.

GetLength

() <<

'\n'

;

180

*m_out <<

"Taxname: "

<< bsx.

GetTaxname

() <<

'\n'

;

181

*m_out <<

"Title: "

<< bsx.

GetTitle

() <<

'\n'

;

189

*m_out <<

"Parent Bioseq-set class: "

<< prnt->

GetClass

() <<

'\n'

;

191

*m_out <<

"Unable to process GetParent"

'\n'

;

197

*m_out <<

"First 10 bases '"

<< subseq <<

"'"

'\n'

;

203

*m_out <<

"Best Protein subtype: "

<< bestprot->

GetSubtype

() <<

'\n'

;

222 string

gap_type =

""

;

223 int

num_gaps = (

int

) gaps.size();

227 bool

has_gap =

false

;

230

gap_start =

sgr

->GetStart();

231

gap_end =

sgr

->GetEnd();

232

gap_type =

sgr

->GetGapType();

238 int

num_feats = (

int

) bsx.

IterateFeatures

([

this

, &bsx, gaps, num_gaps, &next_gap, &has_gap, &gap_start, &gap_end, &gap_type](

CFeatureIndex

& sfx) {

245 while

(has_gap && gap_start < feat_start) {

246

*m_out <<

"Gap type: "

<< gap_type <<

", from: "

<< gap_start <<

", to: "

<< gap_end <<

'\n'

;

247 if

(next_gap < num_gaps) {

249

gap_start =

sgr

->GetStart();

250

gap_end =

sgr

->GetEnd();

251

gap_type =

sgr

->GetGapType();

262

*m_out <<

"Feature subtype: "

<< sbt <<

", Start: "

<< feat_start <<

", Stop: "

<< sfx.

GetEnd

() <<

'\n'

;

267 if

(sbt != CSeqFeatData::ESubtype::eSubtype_gene) {

276

*m_out <<

"Best gene: "

<< locus <<

'\n'

;

279

*m_out <<

"Best gene: "

<< locus <<

'\n'

;

288

*m_out <<

"Location: "

<< loc_str <<

'\n'

;

297

*m_out <<

"MappedLoc: "

<< sloc_str <<

'\n'

;

302 if

(sbt == CSeqFeatData::ESubtype::eSubtype_cdregion) {

305

*m_out <<

"CdRegion seq: "

<< feat_seq <<

'\n'

;

318

}

else if

(bsx.

IsAA

()) {

320 if

(sbt == CSeqFeatData::ESubtype::eSubtype_prot) {

323

*m_out <<

"Protein seq: "

<< feat_seq <<

'\n'

;

334

*m_out <<

"CDS gene: "

<< locus <<

'\n'

;

343

*m_out <<

"Feature count "

<< num_feats <<

'\n'

;

385 m_out

= args[

"o"

] ? &(args[

"o"

].AsOutputFile()) : &cout;

408 string

ucode =

"Î²-carotene 1Â¾ COâ H2O NH3 Tn&lt;i&gt;3&lt;/i&gt; Ã§ Å Ã¥ Ã Ã Ä"

;

409 string

phrase =

"selective serotonin reuptake inhibitor and monoamine-oxidase inhibitor and ((NH4+)3) hydroxide"

;

412

m_out

"\nUcode: "

<< ucode <<

'\n'

;

414

m_out

"Ascii: "

<< ascii <<

'\n'

;

416

m_out

"Clean: "

<< mixed <<

'\n'

;

418

m_out

"\nPhrase:\n"

<< phrase <<

'\n'

;

421

m_out

"\nNORM:\n"

;

423

m_out

<< norm <<

'\n'

;

426

m_out

"\nPAIR:\n"

;

428

m_out

<< pair <<

'\n'

;

CSeq_inst::TLength GetLength(void) const

const vector< CRef< CGapIndex > > & GetGapIndices(void)

CRef< CFeatureIndex > GetFeatureForProduct(void)

CRef< CSeqsetIndex > GetParent(void) const

const string & GetAccession(void) const

const string & GetTitle(void)

size_t IterateFeatures(Fnc m)

const string & GetTaxname(void)

CRef< CFeatureIndex > GetBestProteinFeature(void)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

void ProcessInitialize(const CArgs &args)

void DoOneBioseq(CBioseqIndex &bsx)

CSeqFeatData::ESubtype GetSubtype(void) const

TSeqPos GetStart(void) const

CRef< CFeatureIndex > GetBestGene(void)

const CMappedFeat GetMappedFeat(void) const

CConstRef< CSeq_loc > GetMappedLocation(void) const

TSeqPos GetEnd(void) const

void ProcessInitialize(const CArgs &args)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

CSeq_entry_Handle m_topseh

void SetFeatDepth(int featDepth)

size_t IterateBioseqs(Fnc m)

namespace ncbi::objects::

CBioseq_set::TClass GetClass(void) const

static string TrimMixedContent(const string &str)

void PopulateWordPairIndex(string str)

static string ConvertUTF8ToAscii(const string &str)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

void ProcessInitialize(const CArgs &args)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators â.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

const CSeqFeatData & GetData(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

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.

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.

const TLocation & GetLocation(void) const

Get the Location member data.

const TGene & GetGene(void) const

Get the variant data.

unsigned int

A callback function used to compare two keys in a database.

static SLJIT_INLINE sljit_ins sgr(sljit_gpr dst, sljit_gpr src)

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