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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/entry_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/flatfile/entry.cpp Source File

50 #define THIS_FILE "entry.cpp" 63  const string

& line = *lineIt;

64  auto

firstCharPos = line.find_first_not_of(

" "

);

66  if

(firstCharPos >= 12) {

72  if

(line.starts_with(subKw)) {

74

subEnd = subBegin + 1;

89  const int

COL_FEATKEY = 5;

96  auto

firstCharPos = line.find_first_not_of(

" "

);

98  if

(firstCharPos > COL_FEATKEY) {

114  if

(firstCharPos == COL_FEATKEY) {

116

subEnd = subBegin + 1;

139  throw

std::runtime_error(

"xInitNidSeqId: Details not yet implemented"

);

150  return

(mol ==

"aa"

);

162  auto

& seqInst = bioseq.SetInst();

169  int

topology =

CheckTPG

(topologyStr);

192  const char

* p =

nullptr

;

196  for

(p = ffbuf.

current

, q = to,

i

= 0;

i

<

len

&& *p !=

'\0'

;

i

++)

240  for

(q = entry->

mBuf

.

ptr

; q < eptr; q++) {

244  if

(*q > 126 || (*q < 32 && *q != 10)) {

254  for

(

i

= 0; q > entry->

mBuf

.

ptr

;) {

261

(*q ==

'\n'

|| (q - 2 >= entry->

mBuf

.

ptr

&& *(q - 2) ==

'\n'

))) {

277  if

(q + 3 < eptr && q[3] ==

'.'

) {

322  char

* wasx =

nullptr

;

323  for

(q = entry->

mBuf

.

ptr

; q < eptr; q++) {

330

entry->

mBuf

.

len

-= q - wasx;

333  if

(q + 3 < eptr && q[1] ==

'X'

&& q[2] ==

'X'

)

339  for

(q = entry->

mBuf

.

ptr

; q < eptr; q++) {

343  if

(*q > 126 || (*q < 32 && *q != 10)) {

353  for

(

i

= 0; q > entry->

mBuf

.

ptr

;) {

360

(*q ==

'\n'

|| (q - 2 >= entry->

mBuf

.

ptr

&& *(q - 2) ==

'\n'

))) {

376  if

(q + 3 < eptr && q[3] ==

'.'

) {

User-defined methods of the data storage class.

void SetEntryData(EntryBlk *)

struct DataBlk::@1166 mBuf

EntryPtr LoadEntryGenbank(ParserPtr pp, size_t offset, size_t len)

static size_t FileReadBuf(char *to, size_t len, FileBuf &ffbuf)

DataBlk * LoadEntry(ParserPtr pp, size_t offset, size_t len)

#define ParFlat_ENTRYNODE

char * StringNew(size_t sz)

#define FtaErrPost(sev, level,...)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

ETopology

topology of molecule

EStrand

strandedness in living organism

@ eRepr_raw

continuous sequence

@ eRepr_virtual

no seq data

int CheckTPG(const string &str)

int CheckSTRAND(const string &str)

#define ERR_INPUT_CannotReadEntry

#define ERR_FORMAT_NonAsciiChar

#define ERR_FORMAT_DirSubMode

bool xInitSeqInst(const unsigned char *pConvert)

bool xInitNidSeqId(objects::CBioseq &, int type, int dataOffset, Parser::ESource)

CRef< objects::CSeq_entry > mSeqEntry

SectionPtr GetFirstSectionOfType(int type)

void set_offs(size_t offs)

vector< IndexblkPtr > entrylist

Section(int type_, const vector< string > &textLines)

vector< Section * > mSubSections

vector< string > mTextLines

void xBuildFeatureBlocks()

void xBuildSubBlock(int subtype, string_view subKw)

void fta_StringCpy(char *dst, const char *src)

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