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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cav__seqset_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/cddalignview/cav_seqset.cpp Source File

67 #define NCBI_USE_ERRCODE_X Objtools_CAV_Seqset 75

CBioseq_set::TSeq_set::const_iterator q, qe = bss.

GetSeq_set

().end();

76 for

(q=bss.

GetSeq_set

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

77 if

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

101 if

(seqEntry.

IsSeq

()) {

123

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

124 for

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

131

SequenceList::iterator s, se =

sequences

.end();

132 for

(s=

sequences

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

delete

*s;

138 #define FIRSTOF2(byte) (((byte) & 0xF0) >> 4) 139 #define SECONDOF2(byte) ((byte) & 0x0F) 144 str

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

146 str

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

150 for

(

=0;

<vec.size(); ++

) {

156 for

(

=0;

str

->size(); ++

) {

157 switch

(

str

->at(

)) {

158 case

str

->at(

) =

'A'

;

break

;

159 case

str

->at(

) =

'C'

;

break

;

160 case

str

->at(

) =

'G'

;

break

;

161 case

8: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

163 str

->at(

) =

'X'

;

168 #define FIRSTOF4(byte) (((byte) & 0xC0) >> 6) 169 #define SECONDOF4(byte) (((byte) & 0x30) >> 4) 170 #define THIRDOF4(byte) (((byte) & 0x0C) >> 2) 171 #define FOURTHOF4(byte) ((byte) & 0x03) 175 str

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

179 for

(

=0;

<vec.size(); ++

) {

187 for

(

=0;

str

->size(); ++

) {

188 switch

(

str

->at(

)) {

189 case

str

->at(

) =

'A'

;

break

;

190 case

str

->at(

) =

'C'

;

break

;

191 case

str

->at(

) =

'G'

;

break

;

192 case

3: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

199 static const char

*stdaaMap =

"-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

;

201 str

->resize(vec.size());

202 for

(

unsigned int i

=0;

<vec.size(); ++

)

203 str

->at(

) = stdaaMap[(

unsigned int

) vec[

]];

211

CSeq_descr::Tdata::const_iterator d, de = bioseq.

GetDescr

().

Get

().end();

212 for

(d=bioseq.

GetDescr

().

Get

().begin(); d!=de; ++d) {

213 if

(d->GetObject().IsTitle()) {

214

description = d->GetObject().GetTitle();

216

}

else if

(d->GetObject().IsPdb() && d->GetObject().GetPdb().GetCompound().size() > 0) {

217

description = d->GetObject().GetPdb().GetCompound().front();

225

CBioseq::TAnnot::const_iterator

, ae = bioseq.

GetAnnot

().end();

226 for

(

=bioseq.

GetAnnot

().begin();

!=ae; ++

) {

227 if

(

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

228

CSeq_annot::C_Data::TIds::const_iterator

, ie =

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

229 for

(

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

!=ie; ++

) {

230 if

(

->GetObject().IsGeneral() &&

231 i

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

"mmdb"

232 i

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

233

mmdbLink =

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

237 if

(

!= ie)

break

;

241 if

(mmdbLink != NOT_SET)

274

": confused by sequence string format"

);

278 ERR_POST_X

(5,

Critical

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

);

283

": confused by sequence representation"

);

295

SeqIdList::const_iterator s, se =

seqIDs

.end();

296 for

(s=

seqIDs

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

298 string title

= (*s)->GetPdb().GetMol();

299 string

_chain_id = (*s)->GetPdb().GetEffectiveChain_id();

300 if

(!_chain_id.empty() && _chain_id[0] !=

' '

)

306 for

(s=

seqIDs

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

310 return seqIDs

.front()->GetSeqIdString();

319

SeqIdList::const_iterator s, se =

seqIDs

.end();

320 for

(s=

seqIDs

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

322 label

= (*s)->GetPdb().GetMol();

323 string

_chain_id = (*s)->GetPdb().GetEffectiveChain_id();

324 if

(!_chain_id.empty() && _chain_id[0] !=

' '

)

330 for

(s=

seqIDs

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

343

SeqIdList::const_iterator s, se =

seqIDs

.end();

344 for

(s=

seqIDs

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

345 if

((*s)->Match(seqID))

352

SeqIdList::const_iterator o, oe = others.end();

353 for

(o=others.begin(); o!=oe; ++o)

User-defined methods of the data storage class.

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

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

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

C interface header for cddalignview as function call.

#define CAV_ERROR_SEQUENCES

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

void UnpackSeqSet(const objects::CBioseq_set &bss)

SequenceSet(SeqEntryList &seqEntries)

void UnpackSeqEntry(const objects::CSeq_entry &seqEntry)

bool Matches(const objects::CSeq_id &seqID) const

string GetLabel(void) const

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

string GetTitle(void) const

list< CRef< objects::CSeq_id > > SeqIdList

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

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

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Critical(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

const TPrim & Get(void) const

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,...

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

#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.

static const char label[]

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

TRepr GetRepr(void) const

Get the Repr member data.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

bool IsSetAnnot(void) const

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

const TAnnot & GetAnnot(void) const

Get the Annot member data.

bool IsNcbi4na(void) const

Check if variant Ncbi4na is selected.

const Tdata & Get(void) const

Get the member data.

bool IsNcbi8na(void) const

Check if variant Ncbi8na is selected.

TLength GetLength(void) const

Get the Length member data.

TMol GetMol(void) const

Get the Mol member data.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

bool IsNcbi2na(void) const

Check if variant Ncbi2na is selected.

const TNcbi8na & GetNcbi8na(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

unsigned int

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

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

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