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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tms__utils_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/objects/tms_utils.cpp Source File

54 static string s_GetParams

(

const string

& accession,

const string

& assembly,

const string

context

)

71 return "dev.ncbi.nlm.nih.gov"

;

73 return "www.ncbi.nlm.nih.gov"

;

79 return "/projects/sviewer/seqconfig.cgi"

;

84 if

(!tracks.

CanGet

())

return

;

88 for

(

const auto

: tracks.

Get

()) {

90 if

(

->CanGetId()) trackId =

->GetId();

96 string

accession,

subkey

, annotType,

key

->GetKey();

97 if

(

key

"alignment_track"

) annotType =

"align"

;

98 else if

(

key

"graph_track"

) annotType =

"graph"

;

99 else if

(

key

"feature_track"

) annotType =

"ftable"

;

100 else if

(

key

"gene_model_track"

) annotType =

"ftable"

subkey

"gene"

;

101 else if

(

key

"SNP_track"

) annotType =

"ftable"

;

102 else if

(

key

"SNP_Bins_track"

) annotType =

"seq-table"

subkey

"citedvar"

;

103 else if

(

key

"dbvar_track"

) annotType =

"ftable"

subkey

"variation"

;

104 else if

(

key

"aggregate_feature_track"

) annotType =

"biological_region"

;

110 if

(

key

"SNP_track"

) {

111 if

(

->CanGetFilter()) {

112

accession =

->GetFilter();

115 if

->CanGetAnnots() ||

->GetAnnots().empty()) {

119 subkey

->GetAnnots().front();

123 if

(accession.empty()) {

128 if

->CanGetAnnots() ||

->GetAnnots().empty()) {

132

accession =

->GetAnnots().front();

137

track->

m_Name

= accession;

140 if

(

->CanGetDisplay_name())

143 if

(

->CanGetHelp())

146 if

(

->CanGetCategory())

147

track->

m_xClass

->GetCategory().GetName();

149 if

(

->CanGetSubcategory())

155 if

(

->CanGetSubkey()) {

161 if

(

->CanGetShown())

164 if

((

key

"aggregate_feature_track"

) && !

subkey

.empty()) {

166 if

((

subkey

"biological_region"

) && (

subkey

"aggregate_features"

)) {

167 if

(

->CanGetId() &&

->CanGetDisplay_name()) {

168 LOG_POST

(

Warning

"CTMSUtils: ignored track "

->GetId() <<

" - \""

->GetDisplay_name() <<

"\", due to invalid subkey - "

subkey

);

177 data

.push_back(track);

188 string

params =

s_GetParams

(accession, assembly, tms_context);

189 string

url =

"https://"

+ host + path +

"?"

+ params;

196

}

NCBI_CATCH

(

"CTMSUtils::GetTrackMetaData()"

);

198 if

(!res->CanGetSuccess()) {

199 LOG_POST

(

Error

"CTMSUtils: failed to get valid response from server"

);

203 if

(!res->GetSuccess()) {

205 if

(res->CanGetErr_msg())

206

errMsg = res->GetErr_msg();

208

errMsg =

"Unknown error"

;

209 LOG_POST

(

Error

"CTMSUtils: failed to get TMS tracks. "

<< errMsg);

213 if

(res->CanGetTrack_config_set())

User-defined methods of the data storage class.

CNcbiIstream & GetResponseStream()

iterator_bool insert(const value_type &val)

The NCBI C++ standard methods for dealing with std::string.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

void Warning(CExceptionArgs_Base &args)

string m_AssmAcc

GenColl assembly accession.

string m_AnnotType

annot type, such as ftable, seq-table, align

string m_xClass

annotation category

set< string > m_Subtypes

feature/track types (track-specific)

string m_SubCategory

annotation subcategory

string m_Descr

annotation description (or comment)

static void GetTrackMetaData(vector< CRef< CAnnotMetaData > > &data, const string &accession, const string &assembly, const string &context)

string m_Title

annotation title

static bool IsExtendedNAA(const string &annot, bool isStrict=false)

check if a given annotation is an extended NAA (named accession[.version][number],...

string m_Name

annotation name, e.g. named annotation accession

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string HtmlDecode(const CTempString str, EEncoding encoding=eEncoding_Unknown, THtmlDecode *result_flags=NULL)

Decode HTML entities and character references.

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

Check if a string starts with a specified prefix value.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

static string & ToLower(string &str)

Convert string to lower case â string& version.

@ eNocase

Case insensitive compare.

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

bool CanGet(void) const

Check if it is safe to call Get method.

const struct ncbi::grid::netcache::search::fields::KEY key

const struct ncbi::grid::netcache::search::fields::SUBKEY subkey

static string s_GetParams(const string &accession, const string &assembly, const string &context)

static string s_GetHost()

static string s_GetPath()

static void s_ConvertMetaData(vector< CRef< CAnnotMetaData > > &data, const CTrackConfigSet &tracks, const string &assembly)

static CS_CONTEXT * context

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