IntaRNA::BasePairProbabilityWriter Class Reference

#include <BasePairProbabilityWriter.h>

Static Public Member Functions
static void	write (std::ostream &out, const BasePairProbabilities &result, const RnaSequence &target, const RnaSequence &query, const std::string &separator=";")
static void	writeFile (const std::string &filename, const BasePairProbabilities &result, const RnaSequence &target, const RnaSequence &query, const std::string &separator=";")
static void	writeSvg (std::ostream &out, const BasePairProbabilities &result, const InteractionEnergy &energy, Z_type targetRT, Z_type queryRT, const Interaction *mfe=nullptr)
static void	writeSvgFile (const std::string &filename, const BasePairProbabilities &result, const InteractionEnergy &energy, Z_type targetRT, Z_type queryRT, const Interaction *mfe=nullptr)

Detailed Description

Explicit writer for a completed actual-pair matrix, independent of trackers. Whole blocks are synchronized for shared streams. No destructor emits data.

Member Function Documentation

write()

static void IntaRNA::BasePairProbabilityWriter::write ( std::ostream &  out, const BasePairProbabilities &  result, const RnaSequence &  target, const RnaSequence &  query, const std::string &  separator = ";"  )

static

Validate and write one matrix with original 5'-to-3' nucleotide/index labels.

Parameters

out	destination stream; an I/O failure throws
result	explicitly finalized raw result
target	original target sequence
query	original query sequence
separator	CSV-style separator, shared with ordinary output

writeFile()

static void IntaRNA::BasePairProbabilityWriter::writeFile ( const std::string &  filename, const BasePairProbabilities &  result, const RnaSequence &  target, const RnaSequence &  query, const std::string &  separator = ";"  )

static

Write to a filename or STDOUT/STDERR, using existing gzip stream support. Checks stream flush and explicit close; does not publish pending/failed data.

Parameters

filename	destination (already expanded for multi-FASTA)
result	finalized raw result
target	original target sequence
query	original query sequence
separator	CSV-style separator

writeSvg()

static void IntaRNA::BasePairProbabilityWriter::writeSvg ( std::ostream &  out, const BasePairProbabilities &  result, const InteractionEnergy &  energy, Z_type  targetRT, Z_type  queryRT, const Interaction *  mfe = nullptr  )

static

Write a complete SVG dot plot with original target rows/query columns. Includes intramolecular pairing, signed coordinate guides and a CSS color legend. Seed outlines are included if the result collected admitted seed pairs.

Parameters

out	destination stream; an I/O failure throws
result	explicitly finalized raw result
energy	original, unshifted energy/accessibility model used in prediction
targetRT	positive finite energy scale used to convert target ED to Pu
queryRT	positive finite energy scale used to convert query ED to Pu; accessibility scales can differ from the interaction model's RT
mfe	optional traced MFE structure in original coordinates for region/pair outlines

writeSvgFile()

static void IntaRNA::BasePairProbabilityWriter::writeSvgFile ( const std::string &  filename, const BasePairProbabilities &  result, const InteractionEnergy &  energy, Z_type  targetRT, Z_type  queryRT, const Interaction *  mfe = nullptr  )

static

Write a complete SVG to a file or STDOUT/STDERR, including gzip support. Validates the whole document before opening the destination.

Parameters

filename	destination (already expanded for multi-FASTA)
result	explicitly finalized raw result
energy	original, unshifted energy/accessibility model
targetRT	positive finite target accessibility energy scale
queryRT	positive finite query accessibility energy scale
mfe	optional traced MFE structure in original coordinates for region/pair outlines

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

• src/IntaRNA/BasePairProbabilityWriter.h