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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/agp__renumber_8cpp_source.html below:

NCBI C++ ToolKit: src/app/agp_validate/agp_renumber.cpp Source File

45 "Clean up an AGP file:\n" 46 "https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/\n" 48 "USAGE: agp_renumber <in.agp >out.agp\n" 50 " - Recalculate the object begin and end coordinates from\n" 51 " the length of the component span or gap length.\n" 52 " - Renumber the part numbers for each object.\n" 53 " - Lowercase gap type and linkage.\n" 54 " - Reorder linkage evidence terms: paired-ends;align_genus;align_xgenus;align_trnscpt;within_clone;clone_contig;map;strobe;pcr\n" 55 " - Reformat white space to conform to the AGP format specification:\n" 56 " - add missing tabs at the ends of gap lines;\n" 57 " - drop blank lines;\n" 58 " - remove extra tabs and spaces at the end of lines;\n" 59 " - add a missing line separator at the end of the file;\n" 60 " - replace spaces with tabs (except in comments).\n"

;

238 bool

had_space =

false

;

239 bool

had_extra_tab=

false

;

240 bool

no_eol_at_eof=

false

;

241 bool

bad_case_gap =

false

;

249 char

component_type=0;

254 if

(at_beg)

continue

;

258 if

(prev_ch!=

'\t'

) {

262 if

( tab_count==9 &&

<s.size()-1 && s[

+1]==

'#'

) {

266 else if

(!had_space){

267

had_extra_tab=

true

;

271 else if

(!had_space){

273

had_extra_tab=

true

;

278

buf

<< s.substr(

);

282 if

(prev_ch==

'\t'

&& tab_count==4) {

285 if

( (component_type==

'N'

|| component_type==

'U'

) &&

286

(tab_count==6 || tab_count==7) &&

tolower

(ch)!=ch

288

ch=

tolower

(ch); bad_case_gap=

true

;

293

buf

'\t'

<< s.substr(

);

316 if

(

.eof()) no_eol_at_eof=

true

;

327

cerr << renum.

GetErrorMessage

()<<

"\nRenumbering not completed because of errors.\n"

;

331 if

(had_space ) cerr <<

"Spaces converted to tabs.\n"

;

332 if

(had_extra_tab ) cerr <<

"Extra tabs removed.\n"

;

336 if

(no_eol_at_eof ) cerr <<

"Line break added at the end of file.\n"

;

337 if

(bad_case_gap ) cerr <<

"Gap type/linkage converted to lower case.\n"

;

338 if

(renum.

reordered_ln_ev

) cerr <<

"Linkage evidence terms reordered.\n"

;

342

cerr << renum.

no_renum_objs

" object(s) did not need renumbering.\n"

;

344

cerr <<

"All lines have proper object_beg, object_end, part_number.\n"

;

354 int main

(

int

argc,

char

* argv[])

359 else if

(argv[1][0]==

'-'

|| argc > 1+1) {

365 if

( !

.good() ) {

366

cerr <<

"Error - cannot open for reading: "

<< argv[1] <<

"\n"

;

int main(int argc, char *argv[])

int ProcessStream(istream &in, ostream &out)

@ eAgpVersion_auto

auto-detect using the first gap line

virtual void Msg(int code, const string &details, int appliesTo=fAtThisLine)

static const char * GetMsg(int code)

Detects scaffolds, object boundaries, errors that involve 2 consecutive lines, and is intended as a s...

CAgpErr * GetErrorHandler()

virtual int Finalize()

This is called at the end of the file, usually automatically but can be called manually if the automa...

CRef< CAgpRow > m_this_row

virtual string GetErrorMessage(const string &filename=NcbiEmptyString)

Return a string with one (or two, depending on error) source line(s) on which the error occured,...

virtual int ReadStream(CNcbiIstream &is, EFinalize eFinalize=eFinalize_Yes)

Read an AGP file from the given input stream.

bool ProcessThisRow()

Invoked from ReadStream(), after the row has been parsed, and seldom needs to be invoked by user.

void SetErrorHandler(CAgpErr *arg)

CRef< CCustomErrorHandler > custom_err

virtual void OnObjectChange()

virtual void OnGapOrComponent()

set< string > m_obj_names

CAgpRenumber(ostream &out)

string ToString(bool reorder_linkage_evidences=false)

static bool IsGap(char c)

static bool MustRenumber(int code)

virtual void Msg(int code, int appliesTo=fAtThisLine)

virtual void Msg(int code, const string &details, int appliesTo=fAtThisLine)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

iterator_bool insert(const value_type &val)

std::ofstream out("events_result.xml")

main entry point for tests

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

CNcbistrstream_Base< IO_PREFIX::ostrstream, IOS_BASE::out > CNcbiOstrstream

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert int to string.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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

std::istream & in(std::istream &in_, double &x_)

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