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NCBI C++ ToolKit: src/gui/core/test_table_reader/test_table_reader.cpp Source File

66 const string

& parms_file,

67 const string

& table_xform,

68 const string

& accession);

81

arg_desc->AddOptionalKey(

"xform"

"TransformationType"

82 "Desired transformation for table - none, seqlocs or features. Default: none"

85

arg_desc->AddOptionalKey(

"acc"

"Accession"

86 "Optional accession, e.g. GCF_000001405.17, used to look up ids for chromosome fields"

89

arg_desc->AddOptionalKey(

"table-format"

"TableFormatDescription"

90 "ASN table format description for table(s) being imported"

100 const string

& parms_file,

101 const string

& table_xform,

102 const string

& accession)

108 string

transformation_type = table_xform;

112 if

(parms_file ==

""

) {

124 for

(

size_t i

=0;

<delims.size(); ++

)

134 if

(accession !=

""

) {

148 LOG_POST

(

Error

"Could not find a delimiter for table: "

<< fname);

154 LOG_POST

(

Error

"Could not open parameters file: "

<< parms_file);

159 LOG_POST

(

Info

"Loading Parameters file: "

<< parms_file);

164 if

(table_xform ==

""

165

user_object.

HasField

(

"conversion-type"

) &&

167

transformation_type = user_object.

168

GetField(

"conversion-type"

GetData

().GetStr();

171

success = ds->

LoadTable

(fname, user_object);

187 string

output_type =

""

;

197 if

(transformation_type ==

"seqlocs"

) {

198

vector<CTableAnnotDataSource::STableLocation> locations =

201 if

(locations.size() == 0) {

205 for

(

size_t i

=0;

<locations.size(); ++

) {

206 if

(!locations[

].m_IsRsid)

207

success = annot_table_ds->

AddSeqLoc

(locations[

static_cast<int>

(

+1),

NULL

);

209

success = annot_table_ds->

AddSnpSeqLoc

(locations[

static_cast<int>

(

+1),

NULL

);

211

output_type =

".locs"

;

214 else if

(transformation_type ==

"features"

) {

215

vector<CTableAnnotDataSource::STableLocation> locations =

220 if

(locations.size() > 1) {

221 LOG_POST

(

Error

"Unable to create features - table has more than 1 location per row"

);

224 else if

(locations.size() == 0) {

228 if

(!locations[0].m_IsRsid)

232

output_type =

".feats"

;

236 string

out_fname = fname + output_type +

".asn"

;

238

annot_table_ds->

WriteAsn

(out_fname);

253 if

(args.

Size

() == 0)

257 string

table_xform =

""

;

258 string

accession =

""

;

264 if

(parsed_args[

"table-format"

HasValue

()) {

265

parms_file = parsed_args[

"table-format"

].AsString();

266 LOG_POST

(

Info

"Loading tables using format from asn file: "

270 if

(parsed_args[

"xform"

HasValue

()) {

271

table_xform = parsed_args[

"xform"

].AsString();

275 if

(parsed_args[

"acc"

HasValue

()) {

276

accession = parsed_args[

"acc"

].AsString();

279 for

(

size_t

idx = 1; idx<=parsed_args.

GetNExtra

(); ++idx) {

280 string

arg = parsed_args[idx].AsString();

289 string

ext =

file

.GetExt();

291

cout <<

"Skipping asn file: "

<< arg << endl;

296 if

(

file

.IsFile()) {

297 LoadTable

(arg, parms_file, table_xform, accession);

300

cout <<

"file: "

<< arg <<

" is not a file name"

<< endl;

302 " is not a file name.\n"

);

void SetAssemblyAcc(string value)

bool AddSeqLoc(const STableLocation &fc, int loc_number, ICanceled *cancel=NULL)

Add a location to the table based on the specified columns.

CRef< CSeq_annot > GetContainer()

vector< STableLocation > FindLocations(string &msg, bool strand_required)

Find colums that can be combined to form locations based on column info If no locations are found,...

bool CreateSnpFeature(const STableLocation &fc, ICanceled *cancel=NULL)

Create a region feature for each snp using specified snp (rsid) column.

bool AddSnpSeqLoc(const STableLocation &fc, int loc_number, ICanceled *cancel=NULL)

Add a location to the table using the rsid (snp/variation) ids location from the snp db.

bool CreateFeature(const STableLocation &fc, ICanceled *cancel=NULL)

Create a feature using specified columns.

void WriteAsn(const string &fname)

Write seqtable to file 'fname'.

CTableColumnTypeGuesser -.

void GuessColumns()

Update columns in data source with type info based on best-guesses.

const vector< char > & GetDelimiters() const

bool GetMergeDelimiters() const

CTableImportDataSource -.

const CTableDelimiterRules & GetDelimiterRules() const

Get set all delimiter rules (for delimited tables)

vector< CTableImportColumn > & GetColumns()

return the array of column data

EFieldSeparatorType GetTableType() const

bool LoadTable(const wxString &fname, CUser_object &user_object)

void ConvertToSeqAnnot(CRef< CSeq_annot > annot_container)

Save data in table into annot_container.

int Run(void)

Run the application.

void LoadTable(const string &fname, const string &parms_file, const string &table_xform, const string &accession)

void Init(void)

Initialize the application.

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ eRegularArgs

Regular application.

@ eString

An arbitrary string.

void SetDiagPostFlag(EDiagPostFlag flag)

Set the specified flag (globally).

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

void SetDiagTrace(EDiagTrace how, EDiagTrace dflt=eDT_Default)

Set the diagnostic trace settings.

#define LOG_POST(message)

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

@ eDPF_All

All flags (except for the "unusual" ones!)

@ eDS_ToMemory

Keep in a temp.memory buffer, see FlushMessages()

@ eDT_Enable

Enable messages of severity "eDiag_Trace".

@ eDiag_Info

Informational message.

SIZE_TYPE Size(void) const

Get size (number) of arguments.

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators â.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string & ToLower(string &str)

Convert string to lower case â string& version.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Process information in the NCBI Registry, including working with configuration files.

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

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

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NCBI C++ ToolKit: src/gui/core/test_table_reader/test_table_reader.cpp Source File

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