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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/app_2cn3d_2sequence__set_8cpp_source.html below:

NCBI C++ ToolKit: src/app/cn3d/sequence_set.cpp Source File

81

CBioseq_set::TSeq_set::iterator q, qe = bss.SetSeq_set().end();

82 for

(q=bss.SetSeq_set().begin(); q!=qe; ++q) {

83 if

(q->GetObject().IsSeq()) {

94 FATALMSG

(

"Can't create Sequence object, aborting..."

);

95

seqlist.push_back(sequence);

105 if

(seqEntry.

IsSeq

()) {

108 FATALMSG

(

"Can't create Sequence object, aborting..."

);

109

seqlist.push_back(sequence);

118

SeqEntryList::iterator s, se = seqEntries.end();

119 for

(s=seqEntries.begin(); s!=se; ++s)

126

SequenceList::const_iterator s, se =

sequences

.end();

127 for

(s=

sequences

.begin(); s!=se; ++s) {

128

CBioseq::TId::const_iterator

, ie = ids.end();

129 for

(

=ids.begin();

!=ie; ++

)

130 if

((*s)->identifier->MatchesSeqId(**

))

136 #define FIRSTOF2(byte) (((byte) & 0xF0) >> 4) 137 #define SECONDOF2(byte) ((byte) & 0x0F) 142 str

->resize(vec.size() * 2);

144 str

->resize(vec.size() * 2 - 1);

148 for

(

=0;

<vec.size(); ++

) {

154 for

(

=0;

str

->size(); ++

) {

155 switch

(

str

->at(

)) {

156 case

str

->at(

) =

'A'

;

break

;

157 case

str

->at(

) =

'C'

;

break

;

158 case

str

->at(

) =

'G'

;

break

;

159 case

8: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

161 str

->at(

) =

'X'

;

166 #define FIRSTOF4(byte) (((byte) & 0xC0) >> 6) 167 #define SECONDOF4(byte) (((byte) & 0x30) >> 4) 168 #define THIRDOF4(byte) (((byte) & 0x0C) >> 2) 169 #define FOURTHOF4(byte) ((byte) & 0x03) 173 str

->resize(vec.size() * 4);

177 for

(

=0;

<vec.size(); ++

) {

185 for

(

=0;

str

->size(); ++

) {

186 switch

(

str

->at(

)) {

187 case

str

->at(

) =

'A'

;

break

;

188 case

str

->at(

) =

'C'

;

break

;

189 case

str

->at(

) =

'G'

;

break

;

190 case

3: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

197 str

->resize(vec.size());

198 for

(

unsigned int i

=0;

<vec.size(); ++

)

205 if

(bioseq.IsSetDescr()) {

206 string

defline, taxid;

207

CSeq_descr::Tdata::const_iterator d, de = bioseq.GetDescr().Get().end();

208 for

(d=bioseq.GetDescr().Get().begin(); d!=de; ++d) {

211 if

((*d)->IsTitle()) {

212

defline = (*d)->GetTitle();

213

}

else if

(defline.size() == 0 && (*d)->IsPdb() && (*d)->GetPdb().GetCompound().size() > 0) {

214

defline = (*d)->GetPdb().GetCompound().front();

218 if

((*d)->IsSource()) {

219 if

((*d)->GetSource().GetOrg().IsSetTaxname())

220

taxid = (*d)->GetSource().GetOrg().GetTaxname();

221 else if

((*d)->GetSource().GetOrg().IsSetCommon())

222

taxid = (*d)->GetSource().GetOrg().GetCommon();

225 if

(taxid.size() > 0)

227 if

(defline.size() > 0) {

239 if

(bioseq.IsSetAnnot()) {

240

CBioseq::TAnnot::const_iterator

, ae = bioseq.GetAnnot().end();

241 for

(

=bioseq.GetAnnot().begin();

!=ae; ++

) {

242 if

(

->GetObject().GetData().IsIds()) {

243

CSeq_annot::C_Data::TIds::const_iterator

, ie =

->GetObject().GetData().GetIds().end();

244 for

(

->GetObject().GetData().GetIds().begin();

!=ie; ++

) {

245 if

(

->GetObject().IsGeneral() &&

246 i

->GetObject().GetGeneral().GetDb() ==

"mmdb"

247 i

->GetObject().GetGeneral().GetTag().IsId()) {

248

mmdbID =

->GetObject().GetGeneral().GetTag().GetId();

252 if

(

!= ie)

break

;

261 if

(bioseq.GetInst().GetSeq_data().IsNcbieaa()) {

262 sequenceString

= bioseq.GetInst().GetSeq_data().GetNcbieaa().Get();

264

}

else if

(bioseq.GetInst().GetSeq_data().IsIupacaa()) {

265 sequenceString

= bioseq.GetInst().GetSeq_data().GetIupacaa().Get();

267

}

else if

(bioseq.GetInst().GetSeq_data().IsNcbistdaa()) {

273 else if

(bioseq.GetInst().GetSeq_data().IsIupacna()) {

274 sequenceString

= bioseq.GetInst().GetSeq_data().GetIupacna().Get();

282

}

else if

(bioseq.GetInst().GetSeq_data().IsNcbi4na()) {

285

}

else if

(bioseq.GetInst().GetSeq_data().IsNcbi8na()) {

288

}

else if

(bioseq.GetInst().GetSeq_data().IsNcbi2na()) {

291 if

(bioseq.GetInst().IsSetLength() && bioseq.GetInst().GetLength() <

sequenceString

.length())

296 ERRORMSG

(

"Sequence::Sequence() - sequence "

<< bioseq.GetId().front()->GetSeqIdString()

297

": confused by sequence string format"

);

302 if

(bioseq.GetInst().IsSetLength() && bioseq.GetInst().GetLength() !=

sequenceString

.length()) {

303 ERRORMSG

(

"Sequence::Sequence() - sequence string length mismatch"

);

312 ERRORMSG

(

"Sequence::Sequence() - sequence "

<< bioseq.GetId().front()->GetSeqIdString() <<

": confused by sequence representation"

);

325 if

(

title

.size() > 0) {

326 if

(descr.size() > 0)

332 if

(object->

graph

name

.size() > 0) {

333 if

(descr.size() > 0)

344

CBioseq::TAnnot::const_iterator

, ae =

bioseqASN

->GetAnnot().end();

345

CSeq_annot::C_Data::TIds::const_iterator

, ie;

347 for

(

bioseqASN

->GetAnnot().begin();

!=ae; ++

) {

348 if

((*a)->GetData().IsIds()) {

349 for

(

=(*a)->GetData().GetIds().begin(), ie=(*a)->GetData().GetIds().end();

!=ie; ++

) {

350 if

((*i)->IsGeneral() && (*i)->GetGeneral().GetDb() ==

"mmdb"

351

(*i)->GetGeneral().GetTag().IsId())

355 if

((*i)->GetGeneral().GetTag().GetId() != mmdbID ||

358 ERRORMSG

(

"Sequence::AddMMDBAnnotTag() - mmdbID mismatch"

);

370

annot->

SetData

().SetIds().push_back(seqid);

371

(

const_cast<Sequence

>

(

this

))->bioseqASN->SetAnnot().push_back(annot);

385

CBioseq::TId::const_iterator

, ie =

bioseqASN

->GetId().end();

428 ERRORMSG

(

"Sequence::GetOrSetMMDBLink() - mismatched MMDB ID: identifier says " 439

oss <<

"https://www.ncbi.nlm.nih.gov/"

<< (

isProtein

"protein"

"nuccore"

) <<

"/"

;

449 if

(

label

"query"

label

"consensus"

)

462 static

unique_ptr < CRegexp > regexp;

463 static string

previousPrositePattern;

465 if

(!regexp.get() || prositePattern != previousPrositePattern) {

469 if

Prosite2Regex

(prositePattern, &regexPattern, &nGroups))

470 throw "error converting ProSite to regex syntax"

;

473 TRACEMSG

(

"creating CRegexp with pattern '"

<< regexPattern <<

"'"

);

476

previousPrositePattern = prositePattern;

481 while

(start < (

int

)

Length

()) {

485 if

(regexp->NumFound() <= 0)

493 bool

addMatch =

true

;

494 if

(restrictTo.size() > 0) {

495

MoleculeHighlightMap::const_iterator

= restrictTo.find(

identifier

);

496 if

(

!= restrictTo.end()) {

497 for

(

=1;

<regexp->NumFound(); ++

) {

498 for

(

int

j=regexp->GetResults(

)[0]; j<=regexp->GetResults(

)[1]-1; ++j) {

499 if

->second[j]) {

513 for

(

=1;

<regexp->NumFound(); ++

)

517

start = regexp->GetResults(regexp->NumFound() - 1)[1];

520

}

catch

(

const char

*err) {

521 ERRORMSG

(

"Sequence::HighlightPattern() - "

<< err);

523

}

catch

(exception& e) {

524 ERRORMSG

(

"Sequence::HighlightPattern() - caught exception: "

<< e.what());

User-defined methods of the data storage class.

static void StringFromStdaa(const vector< char > &vec, string *str)

static void UnpackSeqSet(CBioseq_set &bss, SequenceSet *parent, SequenceSet::SequenceList &seqlist)

static void StringFrom4na(const vector< char > &vec, string *str, bool isDNA)

static void UnpackSeqEntry(CSeq_entry &seqEntry, SequenceSet *parent, SequenceSet::SequenceList &seqlist)

static void StringFrom2na(const vector< char > &vec, string *str, bool isDNA)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void AddHighlights(const Sequence *sequence, unsigned int seqIndexFrom, unsigned int seqIndexTo)

std::string GetLabel(void) const

static const int VALUE_NOT_SET

std::string ToString(void) const

static const MoleculeIdentifier * GetIdentifier(const Molecule *molecule, const SeqIdList &ids)

static const TGi GI_NOT_SET

std::list< ncbi::CRef< ncbi::objects::CSeq_entry > > SeqEntryList

std::list< ncbi::CRef< Sequence > > SequenceList

const Sequence * FindMatchingSequence(const ncbi::objects::CBioseq::TId &ids) const

SequenceSet(SeqEntryList &seqEntries)

void UnpackSeqEntry(const objects::CSeq_entry &seqEntry)

void FillOutSeqId(ncbi::objects::CSeq_id *sid) const

const Molecule * molecule

std::string GetDescription(void) const

const MoleculeIdentifier * identifier

unsigned int Length(void) const

void AddMMDBAnnotTag(int mmdbID) const

void LaunchWebBrowserWithInfo(void) const

bool HighlightPattern(const std::string &pattern, const MoleculeHighlightMap &restrictTo) const

Sequence(ncbi::objects::CBioseq &bioseq)

int GetOrSetMMDBLink(void) const

std::map< const MoleculeIdentifier *, std::vector< bool > > MoleculeHighlightMap

ncbi::objects::CSeq_id * CreateSeqId(void) const

CConstRef< objects::CBioseq > bioseqASN

bool GetParentOfType(const T **ptr, bool warnIfNotFound=true) const

const ChemicalGraph * graph

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

bool Prosite2Regex(const std::string &prosite, std::string *regex, std::string *errString)

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

TObjectType & GetObject(void) const

Get object.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

@ eNocase

Case insensitive compare.

static const char label[]

void SetTag(TTag &value)

Assign a value to Tag data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

TGeneral & SetGeneral(void)

Select the variant.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

Messenger * GlobalMessenger(void)

The NCBI C++/STL use hints.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

char LookupCharacterFromNCBIStdaaNumber(unsigned char n)

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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