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NCBI C++ ToolKit: include/objtools/readers/agp_util.hpp Source File

(

(arg, agp_version, reader));

(

(agp_version, reader) );

FromString(

& line);

GetErrorMessage();

(

reorder_linkage_evidences=

);

(cols.size()==8) {

(cols.size()==8) {

eOrientationPlus = 43,

eOrientationMinus = 45,

eOrientationUnknown = 48,

eOrientationIrrelevant = 110

eGapYes_count=eGapContamination+1

fLinkageEvidence_paired_ends = (1 << 0),

fLinkageEvidence_align_genus = (1 << 1),

fLinkageEvidence_align_xgenus = (1 << 2),

fLinkageEvidence_align_trnscpt= (1 << 3),

fLinkageEvidence_within_clone = (1 << 4),

fLinkageEvidence_clone_contig = (1 << 5),

fLinkageEvidence_map = (1 << 6),

fLinkageEvidence_strobe = (1 << 7),

fLinkageEvidence_pcr = (1 << 8),

fLinkageEvidence_proximity_ligation = (1 << 9),

fLinkageEvidence_HIGHEST_BIT_MASK = fLinkageEvidence_proximity_ligation,

fLinkageEvidence_unspecified = 0,

fLinkageEvidence_INVALID = -1,

fLinkageEvidence_na = -2

c==

|| c==

;

c==

|| c==

|| c==

;

gap_type==eGapCentromere || gap_type==eGapTelomere ||

gap_type==eGapShort_arm || gap_type==eGapHeterochromatin ||

gap_type==eGapContamination;

IsDraftComponent(component_type);

( gap_type==eGapFragment)

;

linkage==

;

GapValidAtObjectEnd(gap_type);

CheckComponentEnd(

& comp_id,

comp_end,

comp_len,

CheckComponentEnd(GetComponentId(), component_end, comp_len, *m_AgpErr);

LinkageEvidencesToString(

);

LinkageEvidenceFlagsToString(

);

LinkageEvidenceFlagsToString(linkage_evidence_flags);

* le_str(ELinkageEvidence

);

str_to_le(

&

);

SubstOldGap(

do_subst);

*perror_code,

log_errors =

);

ParseComponentCols(

log_errors=

);

ParseGapCols(

log_errors=

);

gap_types[eGapCount];

* gap_type_codes_creator(

);

SetErrorHandler(

* arg);

gap_types[

];

m_agp_version;

ReadStream(

& is, EFinalize eFinalize = eFinalize_Yes );

ReadStream(is, (bFinalize ? eFinalize_Yes : eFinalize_No) );

Finalize();

GetErrorMessage(

& filename=

);

ProcessThisRow();

x_CheckPragmaComment(

);

SetErrorHandler(

* arg);

m_agp_version;

Msg(

,

& details,

appliesTo=fAtThisLine);

(

,

appliesTo=fAtThisLine)

GetErrorMessage(

=0xFFFFFFFF);

AppliesTo(

=0xFFFFFFFF);

E_Last, E_First=1, E_LastToSkipLine=E_ObjRangeNeComp,

G_First = G_InvalidCompId,

(

==W_ShortGap ||

==W_AssumingVersion)

;

* GetMsg(

);

FormatMessage(

&

,

& details);

CODE_First = E_First,

CODE_Extended = ((((G_Last / 10 ) + 2) * 10) + 1),

CODE_Last=CODE_Extended+20

GetPrintableCode(

,

strict=

)

;

& filename,

linenum,

& content);

PrintLineXml(

& ostr,

& filename,

linenum,

& content,

two_lines_involved);

s_StrictModeWarningMask =

(

(1) << (W_ExtraTab -W_First)) |

(

(1) << (W_GapLineMissingCol9 -W_First)) |

(

(1) << (W_NoEolAtEof -W_First)) |

(

(1) << (W_GapLineIgnoredCol9 -W_First)) |

(

(1) << (W_ObjOrderNotNumerical -W_First)) |

(

(1) << (W_GapSizeNot100 -W_First)) |

(

(1) << (W_ShortGap -W_First)) |

(

(1) << (W_CommentsAfterStart -W_First)) |

(

(1) << (W_AssumingVersion -W_First)) |

(

(1) << (W_AGPVersionCommentInvalid -W_First)) |

(

(1) << (W_AGPVersionCommentUnnecessary-W_First)) ;

s_StrictModeWarningMask & (

(1) << (

-W_First));

* ErrorWarningOrNoteEx(

);

PrintMessageXml(

& ostr,

,

& details,

appliesTo);

PrintTotals(

& ostr,

e_count,

w_count,

note_count,

skipped_count);

PrintTotals(ostr, e_count, w_count, 0, skipped_count);

PrintTotalsXml(

& ostr,

e_count,

w_count,

note_count,

skipped_count);

use_xml=

,

Msg(

,

& details,

appliesTo=fAtThisLine);

(

,

appliesTo=fAtThisLine)

LineDone(

& s,

,

invalid_line=

);

StartFile(

& s);

SkipMsg(

&

,

skip_other=

);

(

>=E_First &&

<CODE_Last) m_MustSkip[

] = !skip_other;

MustSkip(

);

CountTotals(

from,

to=E_First);

GetCount(EErrCode

)

;

PrintMessageCounts(

& ostr,

from,

to=E_First,

report_lines_skipped=

,

* hints=

);

m_MsgCount[CODE_Last];

m_MustSkip[CODE_Last];

(m_InputFiles.size());

m_InputFiles[num-1];

m_UpgradedWarnings.insert(

);

(m_UpgradedWarnings.find(

) != m_UpgradedWarnings.end());

GetExpandedPattern(

* p);

@ 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

Accession naming patterns; find ranges for consequtive digits.

vector< double > TDoubleVec

multimap< int, string > TMapCountToString

Correctly print multiple errors and warnings on consequitive lines; suppress undesired or higly repet...

map< int, string > TMapCcodeToString

void UpgradeToError(EErrCode code)

AutoPtr< CNcbiOstrstream > m_messages

vector< string > m_InputFiles

bool m_two_lines_involved

set< EErrCode > m_UpgradedWarnings

bool TreatAsError(EErrCode code) const

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

bool TreatAsError(int code) const

AutoPtr< CNcbiOstream > m_out_destroyer

void SkipMsg(int code, bool skip_other=false)

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

const string & GetFile(int num)

static bool IsStrictModeWarning(int code)

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

static const char * ErrorWarningOrNote(int code)

@ W_AGPVersionCommentUnnecessary

@ W_BreakingGapSameCompId

@ W_AGPVersionCommentInvalid

@ W_UnSingleCompNotInFull

@ W_OrientationZeroDeprecated

string m_messages_prev_line

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.

CAgpErr * GetErrorHandler()

virtual void OnObjectChange()

CRef< CAgpRow > m_prev_row

CRef< CAgpRow > m_this_row

virtual void OnScaffoldEnd()

EAgpVersion m_agp_version

virtual void OnGapOrComponent()

int ReadStream(CNcbiIstream &is, bool bFinalize)

Deprecated backward-compatibility wrapper.

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

bool CheckComponentEnd(TAgpLen comp_len)

string & GetComponentId()

bool GapValidAtObjectEnd() const

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

string LinkageEvidenceFlagsToString()

CAgpErr * GetErrorHandler()

int linkage_evidence_flags

a bit map which holds summary of info in linkage_evidences.

map< string, EGap > TMapStrEGap

static bool IsGap(char c)

bool GapEndsScaffold() const

string & GetOrientation()

static bool GapValidAtObjectEnd(EGap gap_type)

EAgpVersion m_agp_version

static bool IsDraftComponent(char c)

string & GetComponentType()

TLinkageEvidenceVec linkage_evidences

static const char * GapTypeToString(int i)

CRef< CAgpRow > Clone(void) const

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

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....

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

container_type::iterator iterator

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

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

main entry point for tests

static unsigned int line_num

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

unsigned int TSeqPos

Type for sequence locations and lengths.

@ eNoOwnership

No ownership is assumed.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

enum ENcbiOwnership EOwnership

Ownership relations between objects.

#define NCBI_XOBJREAD_EXPORT

double value_type

The numeric datatype used by the parser.

Static variables safety - create on demand, destroy on application termination.

Multi-threading – mutexes; rw-locks; semaphore.

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)

string ToString(const wxRect &rc)

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