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

38 #define i2s(x) NStr::NumericToString(x) 74

{

CAgpErr::E_SameGapLength

,

"same gap_length=X in all gap lines, and component_type='N' ('U' is required for gaps of unknown size)"

},

80

{

CAgpErr::W_GapObjEnd

,

"gap at the end of object (OK if X is the circular chromosome/plasmid)"

},

83  "a scaffold, two non scaffold-breaking gaps, ...)"

},

136

{

CAgpErr::W_GnlId

,

"\"gnl|\" prefix in X is deprecated inside AGP files (no \"prefix|\" is best)"

},

147

{

CAgpErr::G_BadObjLen

,

"final object_end (column 3) not equal to object length in FASTA file(s)"

},

156  "expecting 9 tab-separated columns"

,

157  "column X is empty"

,

159  "invalid value for X"

,

162  "X must be a positive integer"

,

163  "X must not exceed 4294967294"

,

164  "object_end is less than object_beg"

,

165  "component_end is less than component_beg"

,

166  "object range length not equal to the gap length"

,

167  "object range length not equal to component range length"

,

169  "duplicate object "

,

170  "first line of an object must have object_beg=1"

,

171  "first line of an object must have part_number=1"

,

172  "part number (column 4) != previous part number + 1"

,

173  "'na' or ? (formerly 0) component orientation may only be used in a singleton scaffold"

,

175  "object_beg != previous object_end + 1"

,

176  "no valid AGP lines"

,

177  "consequtive gaps lines with the same type and linkage"

,

178  "in \"Scaffold from component\" file, invalid scaffold-breaking gap"

,

179  "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap"

,

181  "scaffold X was not defined in any of \"Scaffold from component\" files"

,

182  "scaffold X is not used in any of \"Chromosome from scaffold\" files"

,

184  "same gap_length=X in all gap lines, and component_type='N' ('U' is required for gaps of unknown size)"

,

186  "invalid use of \"|\" character"

,

188  "singleton object has component_beg=1 and in minus orientation"

,

195  "gap at the end of object (OK if X is the circular chromosome/plasmid)"

,

196  "gap at the beginning of object "

,

197  "two consequtive gap lines (e.g. a gap at the end of " 198  "a scaffold, two non scaffold-breaking gaps, ...)"

,

199  "no components in object"

,

200  "the span overlaps a previous span for this component"

,

202  "component span appears out of order"

,

203  "duplicate component with non-draft type"

,

204  "line with component_type X appears to be a gap line and not a component line"

,

205  "line with component_type X appears to be a component line and not a gap line"

,

206  "extra tab or space at the end of line"

,

208  "gap line missing column 9 (null)"

,

209  "missing line separator at the end of file"

,

210  "extra text in the column 9 of the gap line"

,

211  "object names appear sorted, but not in a numerical order"

,

212  "component_id looks like a WGS accession, component_type is not W"

,

214  "component_id looks like a non-WGS accession, yet component_type is W"

,

216  "object name (column 1) is the same as component_id (column 6)"

,

220  "gap length (column 6) is not 100 for a gap of unknown size (an INSDC standard)"

,

221  "same component_id found on different scaffolds"

,

232  "in unplaced singleton scaffold, component is not used in full"

,

234  "in unplaced singleton scaffold, component orientation is not \"+\""

,

235  "gap shorter than 10 bp"

,

236  "space in object name "

,

237  "comments only allowed at the beginning of the file in AGP 2.0"

,

238  "orientation '0' is deprecated in AGP 2.0; use '?' instead"

,

240  "linkage (column 9) should be 'na' for a gap with linkage 'no' (AGP 2.0)"

,

241  "old gap type; not used in AGP 2.0"

,

242  "assuming AGP version X"

,

243  "in \"Chromosome from scaffold\" file, scaffold is not used in full"

,

244  "missing linkage evidence (column 9) (AGP 2.0)"

,

247  "AGP version comment is invalid, expecting ##agp-version 1.1 or ##agp-version 2.0"

,

248  "ignoring AGP version comment - version already set to X"

,

249  "linkage evidence term X appears more than once"

,

250  "component_id X is not an HTG accession, but is used with component_type A, D, or F"

,

251  "all objects are singletons with component_beg=1"

,

253  "\"gnl|\" prefix in X is deprecated inside AGP files (no \"prefix|\" is best)"

,

254  "component_id X is a not an accession, but is used with component_type other than W"

,

260  "invalid component_id"

,

261  "component_id not in GenBank"

,

262  "component_id X is ambiguous without an explicit version"

,

263  "component_end greater than sequence length"

,

264  "sequence data is invalid or unavailable"

,

266  "taxonomic data is not available"

,

267  "object X not found in FASTA file(s)"

,

268  "final object_end (column 3) not equal to object length in FASTA file(s)"

,

269  "run(s) of Ns within the component span"

,

281  auto

it = sMessageMap.find(

static_cast<EErrCode>

(

code

));

282  if

(it != sMessageMap.end()) {

283  return

it->second.data();

291  if

( details.size()==0 )

return msg

;

296  return msg

.substr(0, pos) + details +

msg

.substr(pos+1);

298  else if

(details.size()>2 && details[0]==

'X'

&& details[1]==

' '

&&

msg

==

"no valid AGP lines"

){

300  return

details.substr(2);

303  return msg

+ details;

378

m_agp_version(agp_version), m_reader(reader),

384

m_agp_version(agp_version), m_reader(reader),

401  int

*perror_code,

bool

log_errors)

412  if

(perror_code && 0==*perror_code) {

413

*perror_code = error_code;

420

ret_value =

static_cast<TAgpPos>

(pos);

431  bool

tabsStripped=

false

;

432  bool

extraTabOrSpace=

false

;

436  if

( line[

pcomment

-1]==

'\t'

) tabsStripped=

true

;

449  if

(line[pos-1]==

' '

) {

452

}

while

(pos>0 && line[pos-1]==

' '

);

455

extraTabOrSpace=

true

;

464  if

(

cols

.size()==10 &&

cols

[9]==

""

) {

467  else if

(

cols

.size() < 8 ||

cols

.size() > 9 ) {

470  string

(

", found "

) +

i2s

(

cols

.size()) );

478  if

( (

NPOS

!= p_space && p_space<

pcomment

) || line[0]==

' '

|| line[

cols

[0].

size

()-1]==

' '

) {

484  for

(

int i

=0;

i

<8;

i

++) {

498  if

(error_code)

return

error_code;

521  if

(

cols

.size()==8) {

535  if

(component_range_len != object_range_len) {

537  i2s

(object_range_len ) +

" != "

+

538  i2s

(component_range_len)

557  if

(

cols

.size()==8 && tabsStripped==

false

) {

573  if

(

cols

.size()==9 &&

cols

[8].size()>0 &&

583  i2s

(object_range_len ) +

" != "

+

610  if

(error_code)

return

error_code;

626  switch

( orientation_char )

721  msg

=

"1.1 since linkage evidence (column 9) is empty"

;

725  msg

=

"2 since linkage evidence (column 9) is NOT empty"

;

770  "linkage_evidence (column 9): 'na' can only be used for gaps with linkage 'no'"

);

774

vector<string> raw_linkage_evidences;

776  bool

has_unspecified=

false

;

777  ITERATE

( vector<string>, evid_iter, raw_linkage_evidences ) {

794  if

(has_unspecified && raw_linkage_evidences.size()>1) {

798  "linkage_evidence (column 9) -- \"unspecified\" cannot be combined with other terms"

);

823

(

linkage

?

"yes"

:

"no"

) +

"\t"

;

852  if

( comp_end > comp_len) {

853  string

details=

": "

;

854

details +=

i2s

(comp_end);

857

details +=

" length = "

;

858

details +=

i2s

(comp_len);

892  if

(res.size())

return

res;

895  if

(res.size()) res +=

";"

;

907  if

( !

result

.empty() ) {

910  const char

*

le

=

le_str

( *evid_iter );

912  else result

+=

"ERROR:UNKNOWN_LINKAGE_EVIDENCE_TYPE:"

+

i2s

( (

int

)*evid_iter );

916  return linkage

?

"unspecified"

:

"na"

;

931  return "ERROR:UNKNOWN_ORIENTATION:"

+

948  return "gap type=contig, linkage=no, linkage evidence=na"

;

962  return string

(

"gap type=scaffold, linkage=yes, linkage evidence="

)+

le_str

(

le

)+

" or unspecified"

;

972

m_agp_version(agp_version)

980

m_agp_version(agp_version)

1032  if

(this_row->

is_gap

) {

1040  const auto

prevGapType = prev_row->

gap_type

;

1041  const auto

currentGapType = this_row->

gap_type

;

1042  if

( prevGapType == currentGapType &&

1064  if

( !

OnError

() )

return false

;

1199  if

(filename.size()){

1212  if

(filename.size()){

1230  static const char

* kAgpVersionCommentStart =

"##agp-version"

;

1235

strlen(kAgpVersionCommentStart) );

1239  if

( versionStartPos !=

NPOS

&& versionEndPos !=

NPOS

) {

1241

(versionEndPos - versionStartPos) + 1 );

1274  out

<<

"### Errors within a single line. Lines with such errors are skipped, ###\n"

;

1275  out

<<

"### i.e. not used for: further checks, object/component/gap counts. ###\n"

;

1279  out

<<

" (X: 1..9)"

;

1282  out

<<

" (X: component_type, gap_type, linkage, orientation)"

;

1285  out

<<

" (X: object_beg, object_end, part_num, gap_length, component_beg, component_end)"

;

1290  out

<<

"### Errors that may involve several lines ###\n"

;

1294  out

<<

" in object_id"

;

1299  out

<<

"### Warnings (most are errors in -sub mode) ###\n"

;

1303  if

(lbl!=lbl_strict) lbl+=

"/"

+lbl_strict;

1304  out

<< lbl <<

"\t"

;

1306  out

<<

GetMsg

(

i

) <<

" (no longer reported)"

;

1320  out

<<

"### Errors for GenBank-based (-alt) and other component checks (-g, FASTA files) ###\n"

;

1326  "#\tErrors reported once at the end of validation:\n" 1327  "#\tunable to determine a Taxid for the AGP (less than 80% of components have one common taxid)\n" 1328  "#\tcomponents with incorrect taxids\n" 1329  "#Error with -sub, warning if no -sub option:\n" 1330  "#\tcomponent name(s)/object name(s) in FASTA not found in AGP\n" 1331  "#\tscaffold(s) not found in Chromosome from scaffold AGP\n" 1343  if

( res[0]==

'w'

) {

1349  if

(

code

<10) res +=

"0"

;

1355  const string

& filename,

int

linenum,

const string

& content)

1357  string

line=content.size()<200 ? content : content.substr(0,160)+

"..."

;

1361  SIZE_TYPE

posComment = line.find(

"#"

);

1362  if

(posComment!=

NPOS

) {

1363

comment=line.substr(posComment);

1364

line.resize(posComment);

1367  if

(posSpace!=

NPOS

) {

1369  if

(posTab!=

NPOS

&& posTab>posSpace+1 && posSpace!=0 ) {

1372

posTab = line.find(

" "

, posTab+1);

1373  if

(posTab!=

NPOS

) posSpace = posTab;

1376

line = line.substr(0, posSpace) +

"<<<SPACE!"

+ line.substr(posSpace);

1379  if

(filename.size()) ostr << filename <<

":"

;

1380

ostr<< linenum <<

":"

<< line << comment <<

"\n"

;

1387

p1 =

text

.find(

"&#"

, p1);

1388  if

(p1==

NPOS

)

break

;

1392  if

(

text

.substr(p1, p2-p1)==

"&#x9"

) {

1398  text

=

text

.substr(0,p1) +

"..."

;

1405  const string

& filename,

int

linenum,

const string

& content,

1406  bool

two_lines_involved)

1408  string

attr=

"num=\""

+

i2s

(linenum)+

"\""

;

1409  if

(filename.size()) attr+=

" filename=\""

+

NStr::XmlEncode

(filename) +

"\""

;

1410  if

(two_lines_involved) attr+=

" two_lines=\"true\""

;

1415

ostr <<

" <line "

<< attr <<

">"

<< xml_content <<

"</line>\n"

;

1420  const string

& details)

1439

ostr <<

" <text>"

<<

text

<<

"</text>\n"

;

1441

ostr <<

"</message>\n"

;

1490  "s_msg[] size != G_Last+1"

);

1494  "CAgpErrEx -- GetMsg(E_Last) not empty"

);

1498  "CAgpErrEx -- GetMsg(W_Last) not empty"

);

1500  "CAgpErrEx -- GetMsg(W_Last-1) is empty"

);

1502  "CAgpErrEx -- GetMsg(G_Last) not empty"

);

1504  "CAgpErrEx -- GetMsg(G_Last-1) is empty"

);

1617  "<line_num>current</line_num>"

,

1618  "<line_num>"

+

i2s

(

line_num

)+

"</line_num>"

, m);

1657  string

res = skip_other ?

"Printing"

:

"Skipping"

;

1658  const static char

* skipErr =

"Skipping errors, printing warnings."

;

1659  const static char

* skipWarn =

"Skipping warnings, printing errors."

;

1664  if

(

str

==

"all"

) {

1668

res+=

" all errors and warnings."

;

1670  else if

(

str

==

"alt"

) {

1674

res+=

" Accession/Length/Taxid errors."

;

1676  else if

(

str

.substr(0,4)==

"warn"

&&

str

.size()<=8 ) {

1678

res = skip_other ? skipErr : skipWarn;

1680  else if

(

str

.substr(0,4)==

"err"

&&

str

.size()<=6 ) {

1682

res = skip_other ? skipWarn : skipErr;

1685  for

(

int i

=i_from;

i

<i_to;

i

++ )

m_MustSkip

[

i

] = !skip_other;

1693  if

( matchesCode ||

string

(

GetMsg

(

i

)).find(

str

) !=

NPOS

) {

1700  if

(matchesCode)

break

;

1721  bool

strictModeErrors =

false

;

1722  bool

strictModeWarningsOnly=

false

;

1734  else if

(from==

G_Last

) {

1743  for

(

int i

=from;

i

<to;

i

++) {

1746  if

(strictModeErrors) {

1761  else if

(from<

CODE_Last

) { to=(from+1); }

1763

ostr <<

"Internal error in CAgpErrEx::PrintMessageCounts()."

;

1768  for

(

int i

=from;

i

<to;

i

++) {

1770

ostr <<

"<msg_summary>\n"

;

1773

ostr <<

" <cnt>"

<<

m_MsgCount

[

i

] <<

"</cnt>\n"

;

1774

ostr <<

"</msg_summary>\n"

;

1778

ostr <<

" <invalid_lines>"

<<

m_lines_skipped

<<

"</invalid_lines>\n"

;

1781  if

(from<to) ostr<< setw(7) <<

"Count"

<<

" Code Description\n"

;

1782  for

(

int i

=from;

i

<to;

i

++) {

1790  if

(hints && (*hints).

find

(

i

)!=(*hints).end() ) {

1791

ostr <<

" "

<< (*hints)[

i

] <<

"\n"

;

1796  " invalid lines were skipped (not subjected to all the checks, not included in most of the counts below).\n"

;

1803

ostr <<

" <notes>"

<< note_count <<

"</notes>\n"

;

1804

ostr <<

" <warnings>"

<< w_count <<

"</warnings>\n"

;

1805

ostr <<

" <errors>"

<< e_count <<

"</errors>\n"

;

1806

ostr <<

" <skipped>"

<< skipped_count <<

"</skipped>\n"

;

1811  if

(e_count==0) ostr <<

"No errors, "

;

1812  else if

(e_count==1) ostr <<

"1 error, "

;

1813  else

ostr << e_count <<

" errors, "

;

1815  if

(w_count==0) ostr <<

"no warnings"

;

1816  else if

(w_count==1) ostr <<

"1 warning"

;

1817  else

ostr << w_count <<

" warnings"

;

1820

ostr <<

", "

<< note_count <<

" note"

;

1821  if

(note_count>1) ostr <<

"s"

;

1824  if

(skipped_count) {

1825

ostr <<

"; "

<< skipped_count <<

" not printed"

;

void ReplaceUnprintableCharacters(string &text)

MAKE_CONST_MAP(sMessageMap, CAgpErr::EErrCode, const char *, { {CAgpErr::E_ColumnCount, "expecting 9 tab-separated columns"}, {CAgpErr::E_EmptyColumn, "column X is empty"}, {CAgpErr::E_EmptyLine, "empty line"}, {CAgpErr::E_InvalidValue, "invalid value for X"}, {CAgpErr::E_InvalidLinkage, "invalid linkage"}, {CAgpErr::E_MustBePositive, "X must be a positive integer"}, {CAgpErr::E_MustFitSeqPosType, "X must not exceed 4294967294"}, {CAgpErr::E_ObjEndLtBeg, "object_end is less than object_beg"}, {CAgpErr::E_CompEndLtBeg, "component_end is less than component_beg"}, {CAgpErr::E_ObjRangeNeGap, "object range length not equal to the gap length"}, {CAgpErr::E_ObjRangeNeComp, "object range length not equal to component range length"}, {CAgpErr::E_DuplicateObj, "duplicate object "}, {CAgpErr::E_ObjMustBegin1, "first line of an object must have object_beg=1"}, {CAgpErr::E_PartNumberNot1, "first line of an object must have part_number=1"}, {CAgpErr::E_PartNumberNotPlus1, "part number (column 4) != previous part number + 1"}, {CAgpErr::E_UnknownOrientation, "'na' or ? (formerly 0) component orientation may only be used in a singleton scaffold"}, {CAgpErr::E_ObjBegNePrevEndPlus1, "object_beg != previous object_end + 1"}, {CAgpErr::E_NoValidLines, "no valid AGP lines"}, {CAgpErr::E_SameConseqGaps, "consequtive gaps lines with the same type and linkage"}, {CAgpErr::E_ScafBreakingGap, "in \"Scaffold from component\" file, invalid scaffold-breaking gap"}, {CAgpErr::E_WithinScafGap, "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap"}, {CAgpErr::E_UnknownScaf, "scaffold X was not defined in any of \"Scaffold from component\" files"}, {CAgpErr::E_UnusedScaf, "scaffold X is not used in any of \"Chromosome from scaffold\" files"}, {CAgpErr::E_SameGapLength, "same gap_length=X in all gap lines, and component_type='N' ('U' is required for gaps of unknown size)"}, {CAgpErr::E_InvalidBarInId, "invalid use of \"|\" character"}, {CAgpErr::E_Last, ""}, {CAgpErr::W_GapObjEnd, "gap at the end of object (OK if X is the circular chromosome/plasmid)"}, {CAgpErr::W_GapObjBegin, "gap at the beginning of object "}, {CAgpErr::W_ConseqGaps, "two consequtive gap lines (e.g. a gap at the end of " "a scaffold, two non scaffold-breaking gaps, ...)"}, {CAgpErr::W_ObjNoComp, "no components in object"}, {CAgpErr::W_SpansOverlap, "the span overlaps a previous span for this component"}, {CAgpErr::W_SpansOrder, "component span appears out of order"}, {CAgpErr::W_DuplicateComp, "duplicate component with non-draft type"}, {CAgpErr::W_LooksLikeGap, "line with component_type X appears to be a gap line and not a component line"}, {CAgpErr::W_LooksLikeComp, "line with component_type X appears to be a component line and not a gap line"}, {CAgpErr::W_ExtraTab, "extra tab or space at the end of line"}, {CAgpErr::W_GapLineMissingCol9, "gap line missing column 9 (null)"}, {CAgpErr::W_NoEolAtEof, "missing line separator at the end of file"}, {CAgpErr::W_GapLineIgnoredCol9, "extra text in the column 9 of the gap line"}, {CAgpErr::W_ObjOrderNotNumerical, "object names appear sorted, but not in a numerical order"}, {CAgpErr::W_CompIsWgsTypeIsNot, "component_id looks like a WGS accession, component_type is not W"}, {CAgpErr::W_CompIsNotWgsTypeIs, "component_id looks like a non-WGS accession, yet component_type is W"}, {CAgpErr::W_ObjEqCompId, "object name (column 1) is the same as component_id (column 6)"}, {CAgpErr::W_GapSizeNot100, "gap length (column 6) is not 100 for a gap of unknown size (an INSDC standard)"}, {CAgpErr::W_BreakingGapSameCompId, "same component_id found on different scaffolds"}, {CAgpErr::W_UnSingleCompNotInFull, "in unplaced singleton scaffold, component is not used in full"}, {CAgpErr::W_SingleOriNotPlus, "component orientation is not \"+\" in a single component scaffold"}, {CAgpErr::W_ShortGap, "gap shorter than 10 bp"}, {CAgpErr::W_SpaceInObjName, "space in object name "}, {CAgpErr::W_CommentsAfterStart, "comments only allowed at the beginning of the file in AGP 2.0"}, {CAgpErr::W_OrientationZeroDeprecated, "orientation '0' is deprecated in AGP 2.0; use '?' instead"}, {CAgpErr::W_NaLinkageExpected, "linkage (column 9) should be 'na' for a gap with linkage 'no' (AGP 2.0)"}, {CAgpErr::W_OldGapType, "old gap type; not used in AGP 2.0"}, {CAgpErr::W_AssumingVersion, "assuming AGP version X"}, {CAgpErr::W_ScafNotInFull, "in \"Chromosome from scaffold\" file, scaffold is not used in full"}, {CAgpErr::W_MissingLinkage, "missing linkage evidence (column 9) (AGP 2.0)"}, {CAgpErr::W_AGPVersionCommentInvalid, "AGP version comment is invalid, expecting ##agp-version 1.1 or ##agp-version 2.0"}, {CAgpErr::W_AGPVersionCommentUnnecessary, "ignoring AGP version comment - version already set to X"}, {CAgpErr::W_DuplicateEvidence, "linkage evidence term X appears more than once"}, {CAgpErr::W_CompIsNotHtgTypeIs, "component_id X is not an HTG accession, but is used with component_type A, D, or F"}, {CAgpErr::W_SingletonsOnly, "all objects are singletons with component_beg=1"}, {CAgpErr::W_GnlId, "\"gnl|\" prefix in X is deprecated inside AGP files (no \"prefix|\" is best)"}, {CAgpErr::W_CompIsLocalTypeNotW, "component_id X is a not an accession, but is used with component_type other than W"}, {CAgpErr::G_InvalidCompId, "invalid component_id"}, {CAgpErr::G_NotInGenbank, "component_id not in GenBank"}, {CAgpErr::G_NeedVersion, "component_id X is ambiguous without an explicit version"}, {CAgpErr::G_CompEndGtLength, "component_end greater than sequence length"}, {CAgpErr::G_DataError, "sequence data is invalid or unavailable"}, {CAgpErr::G_TaxError, "taxonomic data is not available"}, {CAgpErr::G_InvalidObjId, "object X not found in FASTA file(s)"}, {CAgpErr::G_BadObjLen, "final object_end (column 3) not equal to object length in FASTA file(s)"}, {CAgpErr::G_NsWithinCompSpan, "run(s) of Ns within the component span"}, })

@ eAgpVersion_auto

auto-detect using the first gap line

@ eAgpVersion_1_1

AGP spec 1.1.

@ eAgpVersion_2_0

AGP spec 2.0 or later.

ncbi::TMaskedQueryRegions mask

CAgpErrEx(CNcbiOstream *out=&cerr, bool use_xml=false, EOwnership eOwnsOut=eNoOwnership)

const char * ErrorWarningOrNoteEx(int code)

int m_MsgCount[CODE_Last]

string SkipMsg(const string &str, bool skip_other=false)

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

void PrintMessageCounts(CNcbiOstream &ostr, int from, int to=E_First, bool report_lines_skipped=false, TMapCcodeToString *hints=nullptr)

AutoPtr< CNcbiOstrstream > m_messages

char m_MustSkip[CODE_Last]

static void PrintLine(CNcbiOstream &ostr, const string &filename, int linenum, const string &content)

vector< string > m_InputFiles

bool m_two_lines_involved

virtual void PrintMessage(CNcbiOstream &ostr, int code, const string &details=NcbiEmptyString)

Print the message by code, preceded by "ERROR" or "WARNING".

@ CODE_Last

This is one past the last code allowed, after built-in and user errors.

string GetPrintableCode(int code, bool strict=false) const

bool TreatAsError(int code) const

void PrintAllMessages(CNcbiOstream &out) const

AutoPtr< CNcbiOstream > m_out_destroyer

virtual void PrintMessageXml(CNcbiOstream &ostr, int code, const string &details, int appliesTo)

virtual void LineDone(const string &s, int line_num, bool invalid_line=false)

static void PrintTotalsXml(CNcbiOstream &ostr, int e_count, int w_count, int note_count, int skipped_count)

void StartFile(const string &s)

static void PrintTotals(CNcbiOstream &ostr, int e_count, int w_count, int note_count, int skipped_count)

int GetCount(EErrCode code) const

static void PrintLineXml(CNcbiOstream &ostr, const string &filename, int linenum, const string &content, bool two_lines_involved)

static bool IsStrictModeWarning(int code)

int CountTotals(int from, int to=E_First)

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

static const char * ErrorWarningOrNote(int code)

static const char * GetMsg(int code)

virtual int AppliesTo(int mask=0xFFFFFFFF)

@ W_AGPVersionCommentUnnecessary

@ W_BreakingGapSameCompId

@ W_AGPVersionCommentInvalid

@ W_UnSingleCompNotInFull

@ W_OrientationZeroDeprecated

static string FormatMessage(const string &msg, const string &details)

string m_messages_prev_line

static const TStr s_msg[]

virtual string GetErrorMessage(int mask=0xFFFFFFFF)

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

EFinalize

Whether or not the function should call Finalize() when it's done successfully.

CAgpReader(CAgpErr *arg, EAgpVersion agp_version=eAgpVersion_auto)

virtual void OnObjectChange()

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_prev_row

CRef< CAgpRow > m_this_row

virtual void OnScaffoldEnd()

EAgpVersion m_agp_version

void x_CheckPragmaComment(void)

virtual void SetVersion(EAgpVersion ver)

Change what AGP version to use for the next input that's read.

virtual void OnGapOrComponent()

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)

A container for both the original string column values (Get*() methods) and the values converted to i...

@ fLinkageEvidence_strobe

@ fLinkageEvidence_HIGHEST_BIT_MASK

@ fLinkageEvidence_align_genus

@ fLinkageEvidence_paired_ends

@ fLinkageEvidence_align_xgenus

@ fLinkageEvidence_align_trnscpt

@ fLinkageEvidence_within_clone

@ fLinkageEvidence_INVALID

@ fLinkageEvidence_clone_contig

@ fLinkageEvidence_proximity_ligation

@ fLinkageEvidence_unspecified

int ParseComponentCols(bool log_errors=true)

int ParseGapCols(bool log_errors=true)

string LinkageEvidencesToString(void)

string SubstOldGap(bool do_subst)

Returns a string describing suggested replacement, or "" if none is needed.

string & GetComponentId()

virtual void SetVersion(EAgpVersion ver)

string OrientationToString(EOrientation orientation)

static bool CheckComponentEnd(const string &comp_id, TAgpPos comp_end, TAgpLen comp_len, CAgpErr &agp_err)

static CRef< CAgpRow > New(CAgpErr *arg, EAgpVersion agp_version=eAgpVersion_auto, CAgpReader *reader=nullptr)

string LinkageEvidenceFlagsToString()

string ToString(bool reorder_linkage_evidences=false)

int linkage_evidence_flags

a bit map which holds summary of info in linkage_evidences.

map< string, EGap > TMapStrEGap

bool GapEndsScaffold() const

string & GetOrientation()

static bool GapValidAtObjectEnd(EGap gap_type)

TAgpPos ReadSeqPos(const CTempString seq_pos_str, const string &details, int *perror_code, bool log_errors=true)

static const TStr gap_types[eGapCount]

static int str_to_le(const string &str)

EAgpVersion m_agp_version

CAgpRow(CAgpErr *arg, EAgpVersion agp_version=eAgpVersion_auto, CAgpReader *reader=nullptr)

string & GetComponentType()

static TMapStrEGap * gap_type_codes_creator(void)

static const char * le_str(ELinkageEvidence le)

int FromString(const string &line)

TLinkageEvidenceVec linkage_evidences

void SetErrorHandler(CAgpErr *arg)

string & GetComponentEnd()

static CSafeStatic< TMapStrEGap > gap_type_codes

string & GetComponentBeg()

string & GetLinkageEvidence()

vector< ELinkageEvidence > TLinkageEvidenceVec

Might have duplicates, and is empty on error or if there are no actual linkage evidences (e....

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

container_type::const_iterator const_iterator

const_iterator find(const key_type &key) const

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

main entry point for tests

static unsigned int line_num

static const char * str(char *buf, int n)

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eTakeOwnership

An object can take ownership of another.

#define NCBI_ASSERT(expr, mess)

uint8_t Uint1

1-byte (8-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsOssEmpty(CNcbiOstrstream &oss)

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)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

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 & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string XmlEncode(const CTempString str, TXmlEncode flags=eXmlEnc_Contents)

Encode a string for XML.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

const char *const kEmptyCStr

Empty "C" string (points to a '\0').

@ fConvErr_NoThrow

Do not throw an exception on error.

enum ENcbiOwnership EOwnership

Ownership relations between objects.

static void text(MDB_val *v)

const string version

version string

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

bool le(T x_, T y_, T round_)

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

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