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NCBI C++ ToolKit: src/objtools/format/genome_project_item.cpp Source File

84 const string

&url_prefix,

const string

&alt_prefix,

const bool

is_html )

86 const char

* pchPrefix =

""

;

90 const string

id

= *str_iter;

91 if

(

id

empty

() ) {

95 if

( is_html && ! url_prefix.empty() ) {

96 string

url = url_prefix;

100

url =

"https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis="

;

102 result

"<a href=\""

<< url <<

id

"\">"

;

105 if

( is_html && ! url_prefix.empty() ) {

117 const char

* pchPrefix =

""

;

121 if

( *int_iter == 0 ) {

126

pchPrefix = separator.c_str();

132 struct

SDBLinkLineLessThan {

133 bool

operator()(

const string

line1

const string

line2

) {

134 const int

line1_prefix_order = x_GetPrefixOrder(

line1

);

135 const int

line2_prefix_order = x_GetPrefixOrder(

line2

);

136 if

( line1_prefix_order != line2_prefix_order ) {

137 return

(line1_prefix_order < line2_prefix_order);

146 int

x_GetPrefixOrder(

const string

& line)

149 const static int

kDefaultPrefixOrder =

kMax_Int

;

152

string::size_type colon_pos = line.find(

':'

);

153 if

( colon_pos == string::npos ) {

154 return

kDefaultPrefixOrder;

157 const string

sPrefix = line.substr(0, colon_pos);

161 static const

TPrefixElem sc_prefix_map[] = {

166

{

"BioProject"

, 10 },

167

{

"BioSample"

, 20 },

169

{

"Sequence Read Archive"

, 40 },

170

{

"Trace Assembly Archive"

, 60 }

175

TPrefixMap::const_iterator find_iter = sc_PrefixMap.find(sPrefix.c_str());

176 if

( find_iter == sc_PrefixMap.end() ) {

178 return

kDefaultPrefixOrder;

181 return

find_iter->second;

185 struct

SDbLinkLabelInfo {

194 const bool

bHtml =

ctx

.Config().DoHTML();

196 const CUser_object

* genome_projects_user_obje =

nullptr

;

208 if

(! genome_projects_user_obje) {

209

genome_projects_user_obje = &uo;

213 if

(! dblink_user_obj) {

214

dblink_user_obj = &uo;

221 if

(genome_projects_user_obje) {

234 static const

TDbLinkLabelToInfo kDbLinkLabelToInfo[] = {

235

{

"Assembly"

, {

true

false

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

} },

236

{

"BioProject"

, {

true

false

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

} },

237

{

"BioSample"

, {

true

false

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

} },

238

{

"ProbeDB"

, {

true

false

""

} },

239

{

"Sequence Read Archive"

, {

true

false

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

} },

240

{

"Trace Assembly Archive"

, {

false

true

""

} }

248

vector<string> dblinkLines;

249 if

(dblink_user_obj) {

255

TDbLinkLabelToInfoMap::const_iterator find_iter =

256

kDbLinkLabelToInfoMap.find(

label

.c_str());

257 if

( find_iter == kDbLinkLabelToInfoMap.end() ) {

261 const char

* pchNormalizedDbLinkLabel = find_iter->first;

262 const

SDbLinkLabelInfo & dbLinkLabelInfo = find_iter->second;

265 const

TFieldData & field_data = field.

GetData

();

267 if

( dbLinkLabelInfo.allow_text &&

268

(field_data.IsStrs() || field_data.IsStr()) )

270 const

TFieldData::TStrs* pStrs =

nullptr

;

274

unique_ptr<TFieldData::TStrs> pStrsDestroyer;

276 if

( field_data.IsStrs() ) {

277

pStrs = & field_data.

GetStrs

();

279 _ASSERT

( field_data.IsStr() );

280

pStrsDestroyer.reset(

new

TFieldData::TStrs );

281

pStrsDestroyer->push_back( field_data.GetStr() );

282

pStrs = pStrsDestroyer.get();

287

alt_url =

"https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?analysis="

;

290

*pStrs, dbLinkLabelInfo.url, alt_url, bHtml );

291 if

( ! dblinkValue.empty() ) {

292

dblinkLines.push_back(

293

pchNormalizedDbLinkLabel +

string

(

": "

) + dblinkValue );

299

}

else if

( dbLinkLabelInfo.allow_numeric &&

300

(field_data.IsInts() || field_data.IsInt()) )

303 const

TFieldData::TInts* pInts =

nullptr

;

305

unique_ptr<TFieldData::TInts> pIntsDestroyer;

307 if

( field_data.IsInts() ) {

308

pInts = & field_data.GetInts();

309

}

else if

( field_data.IsInt() ) {

310

pIntsDestroyer.reset(

new

TFieldData::TInts );

311

pIntsDestroyer->push_back( field_data.GetInt() );

312

pInts = pIntsDestroyer.get();

316 if

( ! dblinkValue.empty() ) {

317

dblinkLines.push_back(

318

pchNormalizedDbLinkLabel +

string

(

": "

) +

325 sort

( dblinkLines.begin(), dblinkLines.end(), SDBLinkLineLessThan() );

void x_SetObject(const CSerialObject &obj)

EItem GetItemType() const override

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const override

vector< int > m_ProjectNumbers

TDBLinkLineVec m_DBLinkLines

const TDBLinkLineVec & GetDBLinkLines(void) const

vector< TDBLinkLine > TDBLinkLineVec

const vector< int > & GetProjectNumbers(void) const

void x_GatherInfo(CBioseqContext &ctx) override

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

virtual void FormatGenomeProject(const CGenomeProjectItem &, IFlatTextOStream &)

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

static char line1[1024 *16]

static char line2[1024 *16]

static string s_JoinNumbers(const CUser_field_Base::C_Data::TInts &ints, const string &separator)

static string s_JoinLinkableStrs(const CUser_field_Base::C_Data::TStrs &strs, const string &url_prefix, const string &alt_prefix, const bool is_html)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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[]

bool IsStr(void) const

Check if variant Str is selected.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CStringUTF8 > TStrs

vector< CRef< CUser_field > > TData

@ e_User

user defined object

constexpr auto sort(_Init &&init)

constexpr bool empty(list< Ts... >) noexcept

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

void TryToSanitizeHtml(std::string &str)

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/genome__project__item_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/genome_project_item.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/genomeprojectitem_8cpp_source.html below: