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NCBI C++ ToolKit: src/algo/structure/struct_util/su_sequence_set.cpp Source File

76

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

77 for

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

78 if

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

88

seqlist.push_back(sequence);

98 if

(seqEntry.

IsSeq

()) {

100

seqlist.push_back(sequence);

108

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

109 for

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

115 #define FIRSTOF2(byte) (((byte) & 0xF0) >> 4) 116 #define SECONDOF2(byte) ((byte) & 0x0F) 121 str

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

123 str

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

127 for

(

=0;

<vec.size(); ++

) {

133 for

(

=0;

str

->size(); ++

) {

134 switch

(

str

->at(

)) {

135 case

str

->at(

) =

'A'

;

break

;

136 case

str

->at(

) =

'C'

;

break

;

137 case

str

->at(

) =

'G'

;

break

;

138 case

8: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

140 str

->at(

) =

'X'

;

145 #define FIRSTOF4(byte) (((byte) & 0xC0) >> 6) 146 #define SECONDOF4(byte) (((byte) & 0x30) >> 4) 147 #define THIRDOF4(byte) (((byte) & 0x0C) >> 2) 148 #define FOURTHOF4(byte) ((byte) & 0x03) 152 str

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

156 for

(

=0;

<vec.size(); ++

) {

164 for

(

=0;

str

->size(); ++

) {

165 switch

(

str

->at(

)) {

166 case

str

->at(

) =

'A'

;

break

;

167 case

str

->at(

) =

'C'

;

break

;

168 case

str

->at(

) =

'G'

;

break

;

169 case

3: isDNA ?

str

->at(

) =

'T'

str

->at(

) =

'U'

;

break

;

176 static const char

*stdaaMap =

"-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

;

178 str

->resize(vec.size());

179 for

(

unsigned int i

=0;

<vec.size(); ++

)

180 str

->at(

) = stdaaMap[(

unsigned int

) vec[

]];

184

m_bioseqASN(&bioseq), m_isProtein(

false

)

187 if

(bioseq.IsSetDescr()) {

188 string

defline, taxid;

189

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

190 for

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

193 if

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

194

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

195

}

else if

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

196

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

200 if

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

201 if

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

202

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

203 else if

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

204

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

207 if

(taxid.size() > 0)

209 if

(defline.size() > 0) {

210 if

(taxid.size() > 0)

220 if

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

223

}

else if

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

226

}

else if

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

232 else if

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

241

}

else if

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

244

}

else if

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

247

}

else if

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

250 if

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

m_sequenceString

.length())

255 THROW_MESSAGE

(

"Sequence::Sequence(): confused by sequence format"

);

258 if

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

m_sequenceString

.length())

259 THROW_MESSAGE

(

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

);

266 THROW_MESSAGE

(

"Sequence::Sequence(): confused by sequence representation"

);

273 #define RETURN_FIRST_SEQID_THAT_(is) \ 274 for (i=m_bioseqASN->GetId().begin(); i!=ie; ++i) \ 280

CBioseq::TId::const_iterator

, ie =

m_bioseqASN

->GetId().end();

292

CBioseq::TId::const_iterator

, ie =

m_bioseqASN

->GetId().end();

User-defined methods of the data storage class.

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

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

SequenceSet(SeqEntryList &seqEntries)

void UnpackSeqEntry(const objects::CSeq_entry &seqEntry)

std::string m_sequenceString

std::string m_description

const ncbi::objects::CSeq_id & GetPreferredIdentifier(void) const

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

ncbi::CRef< ncbi::objects::CBioseq > m_bioseqASN

bool MatchesSeqId(const ncbi::objects::CSeq_id &seqID) const

std::string IdentifierString(void) const

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

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

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static string GetStringDescr(const CBioseq &bioseq, EStringFormat fmt)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

unsigned int

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

The NCBI C++/STL use hints.

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

#define THROW_MESSAGE(str)

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

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

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

#define RETURN_FIRST_SEQID_THAT_(is)

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

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

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/su__sequence__set_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/struct_util/su_sequence_set.cpp Source File

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