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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tabular__fmt_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/align/util/tabular_fmt.hpp Source File

1 #ifndef GPIPE_COMMON___TABULAR_FORMAT__HPP 2 #define GPIPE_COMMON___TABULAR_FORMAT__HPP 64

{ m_Scores = scores; }

70  const

objects::CSeq_align& align) = 0;

79  const string

&unavailable_string =

""

);

80  void

SetFormat(

const string

&

format

);

90  void Format

(

const

objects::CSeq_align& align);

93 

{

return

m_FormatterMap; }

96 

{

return

m_Formatters; }

119  const

objects::CSeq_align& align);

134  const

objects::CSeq_align& align);

152  const

objects::CSeq_align& align);

168  const

objects::CSeq_align& align);

184  const

objects::CSeq_align& align);

199  const

objects::CSeq_align& align);

213  const

objects::CSeq_align& align);

224  const

objects::CSeq_align& align);

237  const

objects::CSeq_align& align);

256  const

objects::CSeq_align& align);

271  const

objects::CSeq_align& align);

282  const

objects::CSeq_align& align);

293  const

objects::CSeq_align& align);

305  const

objects::CSeq_align& align);

319  const

objects::CSeq_align& align);

332  const

objects::CSeq_align& align);

343  const

objects::CSeq_align& align);

354  const

objects::CSeq_align& align);

365  const

objects::CSeq_align& align);

376  const

objects::CSeq_align& align);

387  const

objects::CSeq_align& align);

397  const string

& col_name);

401  const

objects::CSeq_align& align);

418  const

objects::CSeq_align& align);

431  const

objects::CSeq_align& align);

445  const

objects::CSeq_align& align);

463  const

objects::CSeq_align& align);

480  const

objects::CSeq_align& align);

496  const

objects::CSeq_align& align);

520  const

objects::CSeq_align& align);

546  const

objects::CSeq_align& align);

564  const

objects::CSeq_align& align);

579  const

objects::CSeq_align& align);

593  const

objects::CSeq_align& align);

607  const

objects::CSeq_align& align);

621  const

objects::CSeq_align& align);

625  void x_RecurseStrands

(

const

objects::CSeq_align& align,

bool

& Plus,

bool

& Minus);

637  const

objects::CSeq_align& align);

659  const

objects::CSeq_align& align);

681  const

objects::CSeq_align& align);

696  const

objects::CSeq_align& align);

709  const

objects::CSeq_align& align);

731  const

objects::CSeq_align& align);

748  const

objects::CSeq_align& align);

763  const

objects::CSeq_align& align);

779  const

objects::CSeq_align& align);

794  const

objects::CSeq_align& align);

808  const

objects::CSeq_align& align);

821  const

objects::CSeq_align& align);

834  const

objects::CSeq_align& align);

virtual void PrintHelpText(CNcbiOstream &ostr) const =0

virtual void PrintHeader(CNcbiOstream &ostr) const =0

virtual void SetGencoll(CConstRef< objects::CGC_Assembly >)

objects::CScoreLookup * m_Scores

void SetScoreLookup(objects::CScoreLookup *scores)

virtual void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)=0

CTabularFormatter_AlignEnd(int row, bool nominus=false)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping alignment identifiers

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_AlignStart(int row, bool nominus=false)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_AlignStrand(int row)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_AllSeqIds(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping any score in an alignment

CTabularFormatter_AnyScore(const string &score_name, const string &col_name)

formatter for dumping any score in an alignment

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_AssemblyInfo(int row, EAssemblyType type, EInfo info)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CConstRef< objects::CGC_Assembly > m_Gencoll

virtual void SetGencoll(CConstRef< objects::CGC_Assembly > gencoll)

formatter for dumping alignment identifiers

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

TSeqPos x_CalcBiggestGap(const objects::CSeq_align &align)

CTabularFormatter_BiggestGapBases(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping cigar of alignments

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Cigar()

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

formatter for dumping sequence deflines

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_Defline(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

objects::sequence::CDeflineGenerator generator

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void x_RecurseStrands(const objects::CSeq_align &align, bool &Plus, bool &Minus)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_DiscStrand(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

formatter for Shannon's entropy

CTabularFormatter_Entropy(size_t row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping exons

CTabularFormatter_ExonIntrons(unsigned sequence, EIntervalType interval, EInfoType info)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_FixedText(const string &col_name, const string &text)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_GapRanges(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_GeneSymbol(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_Indels(EIndelType indel_type, int coordinate_row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_MismatchPositions(int row)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CConstRef< objects::CGC_Assembly > m_Gencoll

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_NearestGap(int row, CConstRef< objects::CGC_Assembly > gencoll)

formatter for dumping organism names

std::unique_ptr< objects::CTaxon1 > m_Taxon1

~CTabularFormatter_OrgName()

CTabularFormatter_OrgName(int row, EField field=eFullTaxName)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CConstRef< objects::CGC_Assembly > m_Gencoll

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_PatchType(int row, CConstRef< objects::CGC_Assembly > gencoll)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_PercentCoverage(int row, const string &header)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_PercentId(bool gapped=false)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping sequence Prot-refs (protein only)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_ProtRef(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

formatter for BLAST seg %

CTabularFormatter_SegPercent(size_t row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_SeqChrom(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_SeqClone(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_SeqId(int row, objects::sequence::EGetIdType id_type, bool tag_only=false, bool protein=false)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

objects::sequence::EGetIdType m_GetIdType

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_SeqLength(int row)

CTabularFormatter_StartCodonChanges(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_StopCodonChanges(int row)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping tax-ids

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_TaxId(int row)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Tech(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Traceback()

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

Simple tabular alignment formatter This is a replacement for the BLAST tabular formatter that support...

void RegisterField(const string &field_name, IFormatter *field_formatter)

objects::CScoreLookup * m_Scores

const list< CIRef< IFormatter > > & Formatters() const

string m_UnavailableString

map< string, CIRef< IFormatter > > TFormatterMap

list< CIRef< IFormatter > > m_Formatters

TFormatterMap m_FormatterMap

const TFormatterMap & AvailableFormatters() const

API (CDeflineGenerator) for computing sequences' titles ("definitions").

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

static void text(MDB_val *v)

#define row(bind, expected)

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