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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqidlist__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/seqidlist_writer.cpp Source File

69 const char

null_byte = 0;

71 Uint8

total_num_ids = 0;

73 char

create_date_size = 0;

74 Uint8

total_length = 0;

76 Uint4

vol_names_size = 0;

77 Uint4

title_size = title.size();

79 char

db_date_size = 0;

80 const unsigned char

byte_max = 0xFF;

82

vector<string> tmplist;

83

tmplist.reserve(idlist.size());

91 ITERATE

(vector<string>, itr, vols) {

92 if

(itr != vols.begin()) {

99

vol_names_size = vol_names.size();

102

db_date_size = db_date.size();

106 for

(

unsigned int i

=0;

< idlist.size();

++) {

109 if

(seqid.

IsGi

()) {

115

tmplist.push_back(

id

);

126 if

(tmplist.size() == 0) {

130 sort

(tmplist.begin(), tmplist.end());

131

vector<string>::iterator it = unique (tmplist.begin(), tmplist.end());

132

tmplist.resize(distance(tmplist.begin(),it));

133 if

(seqdb !=

NULL

) {

134

vector<blastdb::TOid> oids;

135

vector<string> check_ids(tmplist);

138 for

(

unsigned int i

=0;

< check_ids.size();

++) {

140

tmplist.push_back(check_ids[

]);

145

total_num_ids = tmplist.size();

148

create_date_size = create_date.size();

150

os.write(&null_byte, 1);

151

os.write((

char

*)&file_size, 8);

152

os.write((

char

*)&total_num_ids, 8);

153

os.write((

char

*) &title_size, 4);

154

os.write(title.c_str(), title_size);

155

os.write(&create_date_size, 1);

156

os.write(create_date.c_str(), create_date_size);

157

os.write((

char

*)&total_length, 8);

159

os.write(&db_date_size, 1);

160

os.write(db_date.c_str(), db_date_size);

161

os.write((

char

*) &vol_names_size, 4);

162

os.write(vol_names.c_str(), vol_names_size);

165 for

(

unsigned int i

=0;

< tmplist.size();

++) {

166 Uint4

id_len = tmplist[

].size();

168 if

(id_len >= byte_max) {

169

os.write((

char

*)&byte_max, 1);

170

os.write((

char

*)&id_len, 4);

173 char l

= byte_max & id_len;

176

os.write(tmplist[

].c_str(), id_len);

180

file_size = (

Uint8

) os.tellp();

182

os.write((

char

*)&file_size, 8);

CSeqDB_Substring FindBaseName() const

Returns the portion of this path containing the base name.

void GetString(string &s) const

Return the data by assigning it to a string.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

Uint8 GetVolumeLength() const

Returns the sum of the lengths of all volumes.

string GetDate() const

Returns the construction date of the database.

static const char * kBlastDbDateFormat

Format string for the date returned by CSeqDB::GetDate.

EBlastDbVersion GetBlastDbVersion() const

Return blast db version.

void AccessionsToOids(const vector< string > &accs, vector< blastdb::TOid > &oids) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_AnyLocal

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

@ eCurrent

Use current time. See also CCurrentTime.

bool IsPrf(void) const

Check if variant Prf is selected.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsPir(void) const

Check if variant Pir is selected.

constexpr auto sort(_Init &&init)

Defines exception class and several constants for SeqDB.

const blastdb::TOid kSeqDBEntryNotFound

This file defines several SeqDB utility functions related to byte order and file system portability.

int WriteBlastSeqidlistFile(const vector< string > &idlist, CNcbiOstream &os, const string &title, const CSeqDB *seqdb)

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

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