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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/agp__read_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/agp_read.cpp Source File

55

vector<vector<char> >* component_types)

57

vector<CRef<CSeq_entry> >

entries

;

58 AgpRead

(is,

entries

, component_id_rule, set_gap_data, component_types);

71

vector<vector<char> >* component_types)

73

vector<CRef<CBioseq> > bioseqs;

74 AgpRead

(is, bioseqs, component_id_rule, set_gap_data, component_types);

87

vector<vector<char> >* component_types)

89 if

(component_types) {

90

component_types->clear();

93

vector<string> fields;

94 string

current_object;

98 int

part_num, last_part_num = 0;

106 SIZE_TYPE

first_hash_pos = line.find_first_of(

'#'

);

107 if

(first_hash_pos !=

NPOS

) {

108

line.resize(first_hash_pos);

112 if

(line.find_first_not_of(

" \t\n\r"

) ==

NPOS

) {

117 if

( ! line.empty() && *line.rbegin() ==

'\r'

) {

118

line.resize( line.size() - 1 );

127 for

(index = (

int

) fields.size() - 1; index > 0; --index) {

128 if

(!fields[index].

empty

()) {

132

fields.resize(index + 1);

137 if

(fields.size() != 9) {

138 if

(fields.size() >= 5 && fields[4] !=

"N"

&& fields[4] !=

"U"

) {

140 string

(

"error at line "

) +

143 " columns; there should be 9"

145

}

else if

(fields.size() != 8) {

147 string

(

"error at line "

) +

150 " columns; there should be 8 or 9"

155 if

(fields[0] != current_object || !bioseq) {

160

bioseqs.push_back(bioseq);

163

current_object = fields[0];

171

current_object, current_object));

172

bioseq->

SetId

().push_back(

id

);

178 if

(component_types) {

179

component_types->push_back(vector<char>());

185 if

(part_num != last_part_num + 1) {

187 string

(

"error at line "

) +

189 ": part number out of order"

192

last_part_num = part_num;

195 string

(

"error at line "

) +

197 ": begining not equal to previous end + 1"

207 if

(fields[4] ==

"N"

|| fields[4] ==

"U"

) {

210

delta_seq->SetLiteral().SetLength(gap_len);

211 if

(fields[4] ==

"U"

) {

212

delta_seq->SetLiteral().SetFuzz().SetLim();

238 throw

runtime_error(

"invalid gap type in column 7: " 242 const string

& linkage_string = fields[7];

243 if

(linkage_string ==

"yes"

) {

245

}

else if

(linkage_string ==

"no"

) {

248 throw

runtime_error(

"invalid linkage in column 8: " 252

delta_seq->SetLiteral().SetSeq_data()

253

.SetGap().SetType(

type

);

254

delta_seq->SetLiteral().SetSeq_data()

255

.SetGap().SetLinkage(linkage);

258

}

else if

(fields[4].

size

() == 1 &&

259

fields[4].find_first_of(

"ADFGPOW"

) == 0) {

260 CSeq_loc

& loc = delta_seq->SetLoc();

277

loc.

SetInt

().SetId(*comp_id);

282 if

(fields[8] ==

"+"

) {

284

}

else if

(fields[8] ==

"-"

) {

286

}

else if

(fields[8] ==

"0"

) {

288

}

else if

(fields[8] ==

"na"

) {

292 string

(

"error at line "

) +

294 "orientation "

+ fields[8],

299 string

(

"error at line "

) +

301 "component type "

+ fields[4],

304

seq_inst->

SetExt

().SetDelta().Set().push_back(delta_seq);

305 if

(component_types) {

306

component_types->back().push_back(fields[4][0]);

314

bioseqs.push_back(bioseq);

User-defined methods of the data storage class.

CRef< CBioseq_set > AgpRead(CNcbiIstream &is, EAgpRead_IdRule component_id_rule, bool set_gap_data, vector< vector< char > > *component_types)

static unsigned int line_num

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

TStr & SetStr(void)

Select the variant.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

TLocal & SetLocal(void)

Select the variant.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

@ e_not_set

No variant selected.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TId & SetId(void)

Assign a value to Id data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ eType_clone

Deprecated. Used only for AGP 1.1.

@ eType_fragment

Deprecated. Used only for AGP 1.1.

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

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

static wxAcceleratorEntry entries[3]

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