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

NCBI C++ ToolKit: CFormatGuess Class Reference

Class implements different ad-hoc unreliable file format identifications. More...

#include <util/format_guess.hpp>

enum EFormat {
  eUnknown = 0 , eBinaryASN = 1 , eRmo = 2 , eGtf_POISENED = 3 ,
  eGlimmer3 = 4 , eAgp = 5 , eXml = 6 , eWiggle = 7 ,
  eBed = 8 , eBed15 = 9 , eNewick = 10 , eAlignment = 11 ,
  eDistanceMatrix = 12 , eFlatFileSequence = 13 , eFiveColFeatureTable = 14 , eSnpMarkers = 15 ,
  eFasta = 16 , eTextASN = 17 , eTaxplot = 18 , ePhrapAce = 19 ,
  eTable = 20 , eGtf = 21 , eGff3 = 22 , eGff2 = 23 ,
  eHgvs = 24 , eGvf = 25 , eZip = 26 , eGZip = 27 ,
  eBZip2 = 28 , eLzo = 29 , eSra = 30 , eBam = 31 ,
  eVcf = 32 , eUCSCRegion = 33 , eGffAugustus = 34 , eJSON = 35 ,
  ePsl = 36 , eAltGraphX = 37 , eBed5FloatScore = 38 , eBedGraph = 39 ,
  eBedRnaElements = 40 , eBigBarChart = 41 , eBigBed = 42 , eBigPsl = 43 ,
  eBigChain = 44 , eBigMaf = 45 , eBigWig = 46 , eBroadPeak = 47 ,
  eChain = 48 , eClonePos = 49 , eColoredExon = 50 , eCtgPos = 51 ,
  eDownloadsOnly = 52 , eEncodeFiveC = 53 , eExpRatio = 54 , eFactorSource = 55 ,
  eGenePred = 56 , eLd2 = 57 , eNarrowPeak = 58 , eNetAlign = 59 ,
  ePeptideMapping = 60 , eRmsk = 61 , eSnake = 62 , eVcfTabix = 63 ,
  eWigMaf = 64 , eFlatFileGenbank = 65 , eFlatFileEna = 66 , eFlatFileUniProt = 67 ,
  eZstd = 68 , eFormat_max
} The formats are checked in the same order as declared here. More...
enum ESequenceType { eUndefined , eNucleotide , eProtein } enum EMode { eQuick , eThorough } enum ESTStrictness { eST_Lax , eST_Default , eST_Strict } enum EOnError { eDefault = 0 , eThrowOnBadSource }

Class implements different ad-hoc unreliable file format identifications.

Definition at line 50 of file format_guess.hpp.

◆ EFormat

The formats are checked in the same order as declared here.

Enumerator eUnknown

unknown format

eBinaryASN

Binary ASN.1.

eRmo

RepeatMasker Output.

eGtf_POISENED

Old and Dead GFF/GTF style annotations.

eGlimmer3

Glimmer3 predictions.

eAgp

AGP format assembly, AgpRead.

eXml

XML.

eWiggle

UCSC WIGGLE file format.

eBed

UCSC BED file format, CBedReader.

eBed15

UCSC BED15 or microarray format.

eNewick

Newick file.

eAlignment

Text alignment.

eDistanceMatrix

Distance matrix file.

eFlatFileSequence

GenBank/GenPept/DDBJ/EMBL flat-file sequence portion.

eFiveColFeatureTable

Five-column feature table.

eSnpMarkers

SNP Marker flat file.

eFasta

FASTA format sequence record, CFastaReader.

eTextASN

Text ASN.1.

eTaxplot

Taxplot file.

ePhrapAce

Phrap ACE assembly file.

eTable

Generic table.

eGtf

New GTF, CGtfReader.

eGff3

GFF3, CGff3Reader.

eGff2

GFF2, CGff2Reader, any GFF-like that doesn't fit the others.

eHgvs

HGVS, CHgvsParser.

eGvf

GVF, CGvfReader.

eZip

zip compressed file

eGZip

GNU zip compressed file.

eBZip2

bzip2 compressed file

eLzo

lzo compressed file

eSra

INSDC Sequence Read Archive file.

eBam

Binary alignment/map file.

eVcf

VCF, CVcfReader.

eUCSCRegion

USCS Region file format.

eGffAugustus

GFFish output of Augustus Gene Prediction.

eJSON

JSON.

ePsl

PSL alignment format.

eAltGraphX eBed5FloatScore eBedGraph eBedRnaElements eBigBarChart eBigBed eBigPsl eBigChain eBigMaf eBigWig eBroadPeak eChain eClonePos eColoredExon eCtgPos eDownloadsOnly eEncodeFiveC eExpRatio eFactorSource eGenePred eLd2 eNarrowPeak eNetAlign ePeptideMapping eRmsk eSnake eVcfTabix eWigMaf eFlatFileGenbank eFlatFileEna eFlatFileUniProt eZstd

Zstandard (zstd) compressed data.

eFormat_max

Max value of EFormat.

Definition at line 54 of file format_guess.hpp.

◆ EMode ◆ EOnError Enumerator eDefault

Return eUnknown.

eThrowOnBadSource

Throw an exception if the data source (stream, file) can't be read.

Definition at line 161 of file format_guess.hpp.

◆ ESequenceType ◆ ESTStrictness Enumerator eST_Lax

Implement historic behavior, risking false positives.

eST_Default

Be relatively strict, but still allow for typos.

eST_Strict

Require 100% encodability of printable non-digits.

Definition at line 155 of file format_guess.hpp.

◆ CFormatGuess() [1/3] CFormatGuess::CFormatGuess ( ) ◆ CFormatGuess() [2/3] ◆ CFormatGuess() [3/3] ◆ ~CFormatGuess() CFormatGuess::~CFormatGuess ( ) ◆ EnsureSplitLines() bool CFormatGuess::EnsureSplitLines ( ) protected

Definition at line 3693 of file format_guess.cpp.

References data, NStr::fSplit_Tokenize, i, m_bSplitDone, m_iTestBufferSize, m_iTestDataSize, m_pTestBuffer, m_TestLines, and NStr::Split().

Referenced by IsAllComment(), TestFormatAgp(), TestFormatAlignment(), TestFormatAugustus(), TestFormatBed(), TestFormatBed15(), TestFormatDistanceMatrix(), TestFormatFiveColFeatureTable(), TestFormatFlatFileEna(), TestFormatFlatFileGenbank(), TestFormatFlatFileSequence(), TestFormatFlatFileUniProt(), TestFormatGff2(), TestFormatGff3(), TestFormatGlimmer3(), TestFormatGtf(), TestFormatGvf(), TestFormatHgvs(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatPsl(), TestFormatRepeatMasker(), TestFormatSnpMarkers(), TestFormatTable(), TestFormatVcf(), and TestFormatWiggle().

◆ EnsureStats() bool CFormatGuess::EnsureStats ( ) protected

Definition at line 688 of file format_guess.cpp.

References EnsureTestBuffer(), fAlpha, fDigit, fDNA_Main_Alphabet, fProtein_Alphabet, fSpace, i, init_symbol_type_table(), m_bStatsAreValid, m_iStatsCountAaChars, m_iStatsCountAlNumChars, m_iStatsCountBraces, m_iStatsCountData, m_iStatsCountDnaChars, m_iTestDataSize, m_pTestBuffer, NcbiGetline(), ncbi::grid::netcache::search::fields::size, and symbol_type_table.

Referenced by TestFormatBed(), TestFormatBed15(), TestFormatFasta(), TestFormatFlatFileEna(), TestFormatFlatFileGenbank(), TestFormatFlatFileUniProt(), TestFormatHgvs(), TestFormatRepeatMasker(), TestFormatTextAsn(), TestFormatVcf(), and TestFormatWiggle().

◆ EnsureTestBuffer() bool CFormatGuess::EnsureTestBuffer ( ) protected

Definition at line 626 of file format_guess.cpp.

References IsAllComment(), m_iTestBufferSize, m_iTestDataSize, m_pTestBuffer, m_Stream, NULL, and CStreamUtils::Stepback().

Referenced by EnsureStats(), GuessFormat(), TestFormatAgp(), TestFormatAlignment(), TestFormatAugustus(), TestFormatBinaryAsn(), TestFormatBZip2(), TestFormatCLUSTAL(), TestFormatDistanceMatrix(), TestFormatFiveColFeatureTable(), TestFormatFlatFileSequence(), TestFormatGff2(), TestFormatGff3(), TestFormatGlimmer3(), TestFormatGtf(), TestFormatGvf(), TestFormatGZip(), TestFormatLzo(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatPsl(), TestFormatSnpMarkers(), TestFormatSra(), TestFormatTable(), TestFormatXml(), TestFormatZip(), and TestFormatZstd().

◆ Format() [1/2] ◆ Format() [2/2] ◆ GetFormatHints() ◆ GetFormatName()

Definition at line 290 of file format_guess.cpp.

References format, NStr::IntToString(), and NCBI_THROW.

Referenced by CMultiReader::LoadGFF3Fasta(), CMultiReader::LoadIndexedAnnot(), ReadProject(), CFormatGuessApp::Run(), CMakeBlastDBApp::x_AddSequenceData(), CFileLoadWizard::x_CheckFormatConflict(), CFileLoadManager::x_CheckFormatConflict(), CAgpconvertApplication::x_LoadTemplate(), CGapStatsApplication::x_ReadFileOrAccn(), xCreateASNStream(), and CMultiReader::xCreateASNStream().

◆ GuessFormat() [1/2]

Definition at line 446 of file format_guess.cpp.

References eDefault.

Referenced by CCompressedFile::CCompressedFile(), Format(), CMacroFunction_UpdateProteinSeqs::TheFunction(), CFileLoadWizard::x_CheckFormatConflict(), CAlignFilter::x_GetRegionMap(), CCompressedFile::x_GuessFormat(), CCompressedFile::x_GuessFormatNetwork(), CGapStatsApplication::x_ReadFileOrAccn(), CUpdateMultipleSeq_Input::x_ReadFromStream(), CUpdateSeq_Input::x_ReadFromStream(), and CMultiReader::xAnnotGetFormat().

◆ GuessFormat() [2/2]

Note: If the instance of the class is built upon std::istream, then on completion this function pushes whatever data it had to read (in order to detect data format) back to the stream – using CStreamUtils::Stepback()

Definition at line 453 of file format_guess.cpp.

References eNewick, EnsureTestBuffer(), eQuick, eUnknown, f, CFormatGuess::CFormatHints::IsDisabled(), CFormatGuess::CFormatHints::IsEmpty(), CFormatGuess::CFormatHints::IsPreferred(), m_Hints, m_Stream, sm_CheckOrder, sm_CheckOrder_Size, TestFormatNewick(), x_TestFormat(), and x_TestInput().

◆ Initialize() void CFormatGuess::Initialize ( void ) protected ◆ IsAllComment() bool CFormatGuess::IsAllComment ( ) protected ◆ IsAsciiText() bool CFormatGuess::IsAsciiText ( ) protected ◆ IsAsnComment() ◆ IsEnabled() ◆ IsInputRepeatMaskerWithHeader() bool CFormatGuess::IsInputRepeatMaskerWithHeader ( ) protected ◆ IsInputRepeatMaskerWithoutHeader() bool CFormatGuess::IsInputRepeatMaskerWithoutHeader ( ) protected ◆ IsLabelNewick() ◆ IsLineAgp() ◆ IsLineAugustus() ◆ IsLineFlatFileSequence() ◆ IsLineGff2() ◆ IsLineGff3() ◆ IsLineGlimmer3() ◆ IsLineGtf() ◆ IsLineGvf() ◆ IsLineHgvs() ◆ IsLinePhrapId() ◆ IsLinePsl() ◆ IsLineRmo() ◆ IsSampleNewick() ◆ IsSupportedFormat() bool CFormatGuess::IsSupportedFormat ( EFormat format ) static ◆ SequenceType()

Guess sequence type.

Function calculates sequence alphabet and identifies if the source belongs to nucleotide or protein sequence

Definition at line 308 of file format_guess.cpp.

References eNucleotide, eProtein, eST_Default, eST_Lax, eST_Strict, eUndefined, fAlpha, fDigit, fDNA_Ambig_Alphabet, fDNA_Main_Alphabet, fProtein_Alphabet, fSpace, i, init_symbol_type_table(), str(), and symbol_type_table.

Referenced by CFastaReader::AssignMolType(), CPsiBlastValidate::QueryFactory(), CAlnReader::x_GetSequenceMolType(), and x_TryProcessCLUSTALSeqData().

◆ TestFormat() [1/2] ◆ TestFormat() [2/2] ◆ TestFormatAgp() ◆ TestFormatAlignment() bool CFormatGuess::TestFormatAlignment ( EMode ) protected ◆ TestFormatAugustus() bool CFormatGuess::TestFormatAugustus ( EMode ) protected ◆ TestFormatBam() bool CFormatGuess::TestFormatBam ( EMode mode ) protected ◆ TestFormatBed()

Definition at line 1748 of file format_guess.cpp.

References columns, EnsureSplitLines(), EnsureStats(), NStr::fSplit_Tokenize, ITERATE, m_TestLines, s_IsTokenPosInt(), NStr::Split(), NStr::StartsWith(), str(), and NStr::TruncateSpaces().

Referenced by x_TestFormat().

◆ TestFormatBed15() ◆ TestFormatBinaryAsn() bool CFormatGuess::TestFormatBinaryAsn ( EMode ) protected ◆ TestFormatBZip2() ◆ TestFormatCLUSTAL() bool CFormatGuess::TestFormatCLUSTAL ( void ) protected ◆ TestFormatDistanceMatrix() bool CFormatGuess::TestFormatDistanceMatrix ( EMode ) protected ◆ TestFormatFasta() ◆ TestFormatFiveColFeatureTable() bool CFormatGuess::TestFormatFiveColFeatureTable ( EMode ) protected ◆ TestFormatFlatFileEna() bool CFormatGuess::TestFormatFlatFileEna ( EMode ) protected ◆ TestFormatFlatFileGenbank() bool CFormatGuess::TestFormatFlatFileGenbank ( EMode ) protected ◆ TestFormatFlatFileSequence() bool CFormatGuess::TestFormatFlatFileSequence ( EMode ) protected ◆ TestFormatFlatFileUniProt() bool CFormatGuess::TestFormatFlatFileUniProt ( EMode ) protected ◆ TestFormatGff2() ◆ TestFormatGff3() ◆ TestFormatGlimmer3() bool CFormatGuess::TestFormatGlimmer3 ( EMode ) protected ◆ TestFormatGtf() ◆ TestFormatGvf() ◆ TestFormatGZip() ◆ TestFormatHgvs() ◆ TestFormatJson()

Definition at line 2809 of file format_guess.cpp.

References NStr::eTrunc_Begin, NStr::IsBlank(), m_iTestDataSize, m_pTestBuffer, NStr::TruncateSpacesInPlace(), x_CheckJsonStart(), x_CheckStripJsonNumbers(), x_CheckStripJsonPunctuation(), x_IsTruncatedJsonKeyword(), x_IsTruncatedJsonNumber(), x_StripJsonKeywords(), and x_StripJsonStrings().

Referenced by x_TestFormat().

◆ TestFormatLzo() ◆ TestFormatNewick() bool CFormatGuess::TestFormatNewick ( EMode ) protected

Definition at line 1062 of file format_guess.cpp.

References EnsureSplitLines(), EnsureTestBuffer(), NStr::FindNoCase(), i, IsSampleNewick(), ITERATE, m_iTestDataSize, m_pTestBuffer, m_Stream, m_TestLines, NPOS, read_size(), and CStreamUtils::Stepback().

Referenced by GuessFormat(), and x_TestFormat().

◆ TestFormatPhrapAce() bool CFormatGuess::TestFormatPhrapAce ( EMode ) protected ◆ TestFormatPsl() bool CFormatGuess::TestFormatPsl ( EMode mode ) protected ◆ TestFormatRepeatMasker() bool CFormatGuess::TestFormatRepeatMasker ( EMode ) protected ◆ TestFormatSnpMarkers() bool CFormatGuess::TestFormatSnpMarkers ( EMode ) protected ◆ TestFormatSra() ◆ TestFormatTable() ◆ TestFormatTaxplot() bool CFormatGuess::TestFormatTaxplot ( EMode ) protected ◆ TestFormatTextAsn() bool CFormatGuess::TestFormatTextAsn ( EMode ) protected ◆ TestFormatVcf() ◆ TestFormatWiggle() bool CFormatGuess::TestFormatWiggle ( EMode ) protected ◆ TestFormatXml()

Definition at line 1278 of file format_guess.cpp.

References ArraySize(), NStr::eCase, NStr::eNocase, EnsureTestBuffer(), NStr::eTrunc_Begin, i, input(), m_iTestDataSize, m_pTestBuffer, NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

Referenced by x_TestFormat().

◆ TestFormatZip() ◆ TestFormatZstd() ◆ x_CheckJsonStart() ◆ x_CheckStripJsonNumbers() bool CFormatGuess::x_CheckStripJsonNumbers ( string & testString ) const private ◆ x_CheckStripJsonPunctuation() bool CFormatGuess::x_CheckStripJsonPunctuation ( string & testString ) const private ◆ x_FindJsonStringLimits() void CFormatGuess::x_FindJsonStringLimits ( const string & testString, list< size_t > & limits ) const private ◆ x_FindNextJsonStringStop() ◆ x_IsBlankOrNumbers() ◆ x_IsNumber() ◆ x_IsTruncatedJsonKeyword() bool CFormatGuess::x_IsTruncatedJsonKeyword ( const string & testString ) const private ◆ x_IsTruncatedJsonNumber() bool CFormatGuess::x_IsTruncatedJsonNumber ( const string & testString ) const private ◆ x_LooksLikeCLUSTALConservedInfo() bool CFormatGuess::x_LooksLikeCLUSTALConservedInfo ( const string & line ) const private ◆ x_StripJsonKeywords() void CFormatGuess::x_StripJsonKeywords ( string & testString ) const private ◆ x_StripJsonPunctuation() size_t CFormatGuess::x_StripJsonPunctuation ( string & testString ) const private ◆ x_StripJsonStrings() void CFormatGuess::x_StripJsonStrings ( string & testString ) const private ◆ x_TestFormat()

Definition at line 513 of file format_guess.cpp.

References eAgp, eAlignment, eBam, eBed, eBed15, eBinaryASN, eBZip2, eDistanceMatrix, eFasta, eFiveColFeatureTable, eFlatFileEna, eFlatFileGenbank, eFlatFileSequence, eFlatFileUniProt, eGff2, eGff3, eGffAugustus, eGlimmer3, eGtf, eGvf, eGZip, eHgvs, eJSON, eLzo, eNewick, ePhrapAce, ePsl, eRmo, eSnpMarkers, eSra, eTable, eTaxplot, eTextASN, eUCSCRegion, eVcf, eWiggle, eXml, eZip, eZstd, format, CFormatGuess::CFormatHints::IsDisabled(), m_Hints, NCBI_THROW, NStr::NumericToString(), TestFormatAgp(), TestFormatAlignment(), TestFormatAugustus(), TestFormatBam(), TestFormatBed(), TestFormatBed15(), TestFormatBinaryAsn(), TestFormatBZip2(), TestFormatDistanceMatrix(), TestFormatFasta(), TestFormatFiveColFeatureTable(), TestFormatFlatFileEna(), TestFormatFlatFileGenbank(), TestFormatFlatFileSequence(), TestFormatFlatFileUniProt(), TestFormatGff2(), TestFormatGff3(), TestFormatGlimmer3(), TestFormatGtf(), TestFormatGvf(), TestFormatGZip(), TestFormatHgvs(), TestFormatJson(), TestFormatLzo(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatPsl(), TestFormatRepeatMasker(), TestFormatSnpMarkers(), TestFormatSra(), TestFormatTable(), TestFormatTaxplot(), TestFormatTextAsn(), TestFormatVcf(), TestFormatWiggle(), TestFormatXml(), TestFormatZip(), and TestFormatZstd().

Referenced by GuessFormat(), and TestFormat().

◆ x_TestInput() ◆ x_TestTableDelimiter() ◆ x_TryProcessCLUSTALSeqData() bool CFormatGuess::x_TryProcessCLUSTALSeqData ( const string & line, string & id, size_t & seg_length ) const private ◆ m_bOwnsStream bool CFormatGuess::m_bOwnsStream protected ◆ m_bSplitDone bool CFormatGuess::m_bSplitDone protected ◆ m_bStatsAreValid bool CFormatGuess::m_bStatsAreValid protected ◆ m_Hints ◆ m_iStatsCountAaChars unsigned int CFormatGuess::m_iStatsCountAaChars protected ◆ m_iStatsCountAlNumChars unsigned int CFormatGuess::m_iStatsCountAlNumChars protected ◆ m_iStatsCountBraces unsigned int CFormatGuess::m_iStatsCountBraces protected ◆ m_iStatsCountData unsigned int CFormatGuess::m_iStatsCountData protected ◆ m_iStatsCountDnaChars unsigned int CFormatGuess::m_iStatsCountDnaChars protected ◆ m_iTestBufferSize streamsize CFormatGuess::m_iTestBufferSize protected ◆ m_iTestDataSize streamsize CFormatGuess::m_iTestDataSize protected

Definition at line 388 of file format_guess.hpp.

Referenced by EnsureSplitLines(), EnsureStats(), EnsureTestBuffer(), IsAsciiText(), TestFormatBinaryAsn(), TestFormatBZip2(), TestFormatCLUSTAL(), TestFormatFasta(), TestFormatGZip(), TestFormatHgvs(), TestFormatJson(), TestFormatLzo(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatSra(), TestFormatTextAsn(), TestFormatXml(), TestFormatZip(), TestFormatZstd(), and x_TestTableDelimiter().

◆ m_pTestBuffer char* CFormatGuess::m_pTestBuffer protected

Definition at line 386 of file format_guess.hpp.

Referenced by EnsureSplitLines(), EnsureStats(), EnsureTestBuffer(), Initialize(), IsAsciiText(), TestFormatBinaryAsn(), TestFormatBZip2(), TestFormatCLUSTAL(), TestFormatFasta(), TestFormatGZip(), TestFormatHgvs(), TestFormatJson(), TestFormatLzo(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatSra(), TestFormatTextAsn(), TestFormatXml(), TestFormatZip(), TestFormatZstd(), and ~CFormatGuess().

◆ m_Stream ◆ m_TestLines

Definition at line 397 of file format_guess.hpp.

Referenced by EnsureSplitLines(), IsAllComment(), IsInputRepeatMaskerWithHeader(), IsInputRepeatMaskerWithoutHeader(), TestFormatAgp(), TestFormatAlignment(), TestFormatAugustus(), TestFormatBed(), TestFormatBed15(), TestFormatDistanceMatrix(), TestFormatFiveColFeatureTable(), TestFormatFlatFileEna(), TestFormatFlatFileGenbank(), TestFormatFlatFileSequence(), TestFormatFlatFileUniProt(), TestFormatGff2(), TestFormatGff3(), TestFormatGlimmer3(), TestFormatGtf(), TestFormatGvf(), TestFormatHgvs(), TestFormatNewick(), TestFormatPhrapAce(), TestFormatPsl(), TestFormatSnpMarkers(), TestFormatVcf(), TestFormatWiggle(), and x_TestTableDelimiter().

The documentation for this class was generated from the following files:

include/util/format_guess.hpp
src/util/format_guess.cpp

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