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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/struc__cmt__reader_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/struc_cmt_reader.cpp Source File

69  const string

& commentID)

75  string

(

"Structured comment for \""

) +

77  "\" could not be matched to any input sequence."

;

132  if

(bioseq && !bioseq->

IsNa

())

140

matchedCommentIds.

insert

(comment.m_id);

146  auto id

= comment.m_id;

147  if

(!

id

|| matchedCommentIds.

find

(

id

) == matchedCommentIds.

end

()) {

148  string

commentId(

"[Unrecognized SeqID]"

);

149  if

(

id

&& id->IsLocal() && id->GetLocal().IsStr()) {

150

commentId = comment.m_id->GetLocal().GetStr();

160  for

(

const auto

& new_desc : comments.m_descs)

162  bool

append_desc =

true

;

167  for

(

auto

& desc : descr.

Set

())

169  if

(!desc->IsUser())

continue

;

171  auto

& user = desc->SetUser();

178

append_desc =

false

;

180  for

(

const auto

& field : new_desc->GetUser().GetData())

182

user.SetFieldRef(field->GetLabel().GetStr())->SetValue(field->GetData().GetStr());

189

add_desc->Assign(*new_desc);

190

descr.

Set

().push_back(add_desc);

196  CSeq_entry

& entry,

const

CStructComment& comments)

198  bool

matchFound(

false

);

201  if

(!bioseq.

IsNa

())

204  if

(comments.m_id.NotEmpty())

206

bool matched = false;

207

for (const auto& id : bioseq.GetId())

209

if (CStructuredCommentsReader::SeqIdMatchesCommentId(*id, *comments.m_id))

229  for

(

auto

& desc : comments.

m_descs

) {

230  string

prefix, suffix;

231  const auto

& user = desc->GetUser();

232  for

(

const auto

&

data

: user.GetData()) {

233  if

(

data

->IsSetLabel() &&

data

->GetLabel().IsStr()) {

234  const string

&

label

=

data

->GetLabel().GetStr();

235  if

(

label

==

"StructuredCommentPrefix"

) {

236

prefix =

data

->GetData().GetStr();

238  else if

(

label

==

"StructuredCommentSuffix"

) {

239

suffix =

data

->GetData().GetStr();

243  if

(!prefix.empty() && suffix.empty()) {

244

desc->SetUser().AddField(

"StructuredCommentSuffix"

, prefix);

254  if

(!reader.

AtEOF

())

257

vector<CTempString> values;

259

vert = values.size()<=2;

User-defined methods of the data storage class.

static CLineErrorEx * Create(EProblem eProblem, EDiagSev eSeverity, int code, int subcode, const std::string &strSeqId, unsigned int uLine, const std::string &strErrorMessage=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

@Seq_descr.hpp User-defined methods of the data storage class.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

Abstract base class for lightweight line-by-line reading.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Warning

Warning message.

CTempString GetCurrentLine(void) const

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual void UngetLine(void)=0

Unget current line, which must be valid.

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static const char label[]

void SetDescr(TDescr &value)

Assign a value to Descr data member.

Tdata & Set(void)

Assign a value to data member.

if(yy_accept[yy_current_state])

Lightweight interface for getting lines of data with minimal memory copying.

void VisitAllSeqDesc(objects::CSeq_entry &entry, bool skip_nucprot, _M m)

void VisitAllBioseqs(objects::CSeq_entry &entry, _M &&m)

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

static void sReportUnappliedStructuredComment(ILineErrorListener *pEC, const string &commentID)

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