IntaRNA::OutputHandlerCsv Class Reference

#include <OutputHandlerCsv.h>

Inheritance diagram for IntaRNA::OutputHandlerCsv:

Collaboration diagram for IntaRNA::OutputHandlerCsv:

Public Types
enum	ColType {   id1 = 0 , id2 , seq1 , seq2 ,   subseq1 , subseq2 , subseqDP , subseqDB ,   start1 , end1 , start2 , end2 ,   hybridDP , hybridDB , hybridDPfull , hybridDBfull ,   bpList , E , Etotal , ED1 ,   ED2 , Pu1 , Pu2 , E_init ,   E_loops , E_dangleL , E_dangleR , E_endL ,   E_endR , E_hybrid , E_norm , E_hybridNorm ,   E_add , seedStart1 , seedEnd1 , seedStart2 ,   seedEnd2 , seedE , seedED1 , seedED2 ,   seedPu1 , seedPu2 , w , Eall ,   Eall1 , Eall2 , Zall , Zall1 ,   Zall2 , EallTotal , P_E , RT ,   ColTypeNumber }
	the column types supported More...
typedef std::list< ColType >	ColTypeList
	list of ColTypes

Public Member Functions
	OutputHandlerCsv (const OutputConstraint &outConstraint, std::ostream &out, const InteractionEnergy &energy, const ColTypeList columns, const std::string &colSep=";", const bool printHeader=false, const std::string &listSep=":")
virtual	~OutputHandlerCsv ()
virtual void	add (const Interaction &interaction)
Public Member Functions inherited from IntaRNA::OutputHandler
	OutputHandler (const OutputConstraint &outConstraint)
virtual	~OutputHandler ()
virtual size_t	reported () const
virtual void	incrementZ (const Z_type subZ)
virtual Z_type	getZ () const
const OutputConstraint &	getOutputConstraint () const

Static Public Member Functions
static const std::map< ColType, std::string > &	getColType2string ()
static std::string	list2string (const ColTypeList &colTypes, const std::string &sep)
static ColTypeList	string2list (const std::string &listString)
static bool	needsZall (const ColTypeList &colTypes)
static bool	needBPs (const ColTypeList &colTypes)
static std::string	getHeader (const ColTypeList &colTypes, const std::string &colSep)
Static Public Member Functions inherited from IntaRNA::OutputHandler
static std::string	reverse (const std::string &str)

Static Public Attributes
static const std::string	notAvailable
	string to encode not available values
static const ColTypeList	colTypeNumericSort
	list of ColTypes that have to be sorted numerically

Static Protected Member Functions
static void	initColType2string ()

Protected Attributes
std::ostream &	out
	the output stream to write to
const InteractionEnergy &	energy
	the interaction energy function used for interaction computation
const std::list< ColType >	columns
	the sequence of columns to be reported
std::string	colSep
	the column separator to be used
std::string	listSep
	the list separator to be used within single columns
Z_type	Z
	overall partition function (if set)
Protected Attributes inherited from IntaRNA::OutputHandler
const OutputConstraint	outConstraint
	the output constraints to be applied
size_t	reportedInteractions
	number of reported interactions
Z_type	Z
	overall partition function for the sequences provided in Z_energy

Static Protected Attributes
static std::map< ColType, std::string >	colType2string
	mapping of ColTypes to according strings

Detailed Description

OutputHandler that stores interactions in CSV stream output.

Member Typedef Documentation

ColTypeList

typedef std::list<ColType> IntaRNA::OutputHandlerCsv::ColTypeList

list of ColTypes

Member Enumeration Documentation

ColType

enum IntaRNA::OutputHandlerCsv::ColType

the column types supported

Enumerator
id1	id of first sequence
id2	id of second sequence
seq1	full first sequence
seq2	full second sequence
subseq1	interacting subsequence of first sequence
subseq2	interacting subsequence of second sequence
subseqDP	hybrid subsequences compatible with hybridDP
subseqDB	hybrid subsequences compatible with hybridDB
start1	start index of hybrid in seq1
end1	end index of hybrid in seq1
start2	start index of hybrid in seq2
end2	end index of hybrid in seq2
hybridDP	hybrid in VRNA dot-bracket notation
hybridDB	hybrid in dot-bar notation
hybridDPfull	hybrid in VRNA dot-bracket notation for full sequence lengths
hybridDBfull	hybrid in dot-bar notation for full sequence lengths
bpList	list of hybrid base pairs like (1,3),(4,2),...
E	overall interaction energy
Etotal	overall energy of the interaction including the intra-molecular ensemble energies (E+Eall1+Eall2)
ED1	ED value of seq1.
ED2	ED value of seq2.
Pu1	probability to be accessible for seq1
Pu2	probability to be accessible for seq2
E_init	initiation energy
E_loops	sum of loop energies (excluding E_init)
E_dangleL	dangling end contribution of base pair (start1,end2)
E_dangleR	dangling end contribution of base pair (end1,start2)
E_endL	penalty of closing base pair (start1,end2)
E_endR	penalty of closing base pair (end1,start2)
E_hybrid	energy of hybridization only = E - ED1 - ED2
E_norm	length normalized energy = E/ln(length(seq1)*length(seq2))
E_hybridNorm	length normalized energy of hybridization only = E_hybrid / ln(length(seq1)*length(seq2))
E_add	user provided energy shift
seedStart1	start index of the seed in seq1
seedEnd1	end index of the seed in seq1
seedStart2	start index of the seed in seq2
seedEnd2	end index of the seed in seq2
seedE	overall energy of the seed only (including accessibility etc)
seedED1	ED value of seq1 of the seed only (excluding rest)
seedED2	ED value of seq2 of the seed only (excluding rest)
seedPu1	probability of seed region to be accessible for seq1
seedPu2	probability of seed region to be accessible for seq2
w	Boltzmann weight of the interaction energy.
Eall	ensemble energy of all interactions (outConstraint.needZall)
Eall1	ensemble energy of all intra-molecular structures of seq1
Eall2	ensemble energy of all intra-molecular structures of seq2
Zall	partition function of all interactions (outConstraint.needZall)
Zall1	partition function of all intra-molecular structures of seq1
Zall2	partition function of all intra-molecular structures of seq2
EallTotal	total ensemble energy (Eall+Eall1+Eall2) of all interactions including the intra-molecular ensemble energies (outConstraint.needZall)
P_E	probability of mfe within interaction ensemble (outConstraint.needZall)
RT	the scaled temperature used for Boltzmann weight computation
ColTypeNumber	number of column types

Constructor & Destructor Documentation

OutputHandlerCsv()

IntaRNA::OutputHandlerCsv::OutputHandlerCsv	(	const OutputConstraint &	outConstraint,
		std::ostream &	out,
		const InteractionEnergy &	energy,
		const ColTypeList	columns,
		const std::string &	colSep = ";",
		const bool	printHeader = false,
		const std::string &	listSep = ":"
	)

Construct a CSV table output handler for interaction reporting.

Parameters

outConstraint	the output constraint applied to find the reported interaction
out	the stream to write to
energy	the interaction energy object used for computation
columns	the order and list of columns to be printed
colSep	the column separator to be used in CSV output
printHeader	whether or not to print header information = col names
listSep	if multiple entries have to be printed per column, this separator is used between values

~OutputHandlerCsv()

virtual IntaRNA::OutputHandlerCsv::~OutputHandlerCsv ( )

virtual

destruction

Member Function Documentation

add()

virtual void IntaRNA::OutputHandlerCsv::add ( const Interaction &  interaction )

virtual

Write a given RNA-RNA interaction in simple text format to the output stream.

Parameters

interaction

the interaction to output

Implements IntaRNA::OutputHandler.

getColType2string()

const std::map< OutputHandlerCsv::ColType, std::string > & IntaRNA::OutputHandlerCsv::getColType2string ( )

inlinestatic

Access to the mapping of ColTypes to according strings

getHeader()

std::string IntaRNA::OutputHandlerCsv::getHeader ( const ColTypeList &  colTypes, const std::string &  colSep  )

inlinestatic

Generates the header line for a given list of columns

Parameters

colTypes	the list of column types to consider
colSep	the column separator to be used

Returns

the header line of the CSV output

initColType2string()

static void IntaRNA::OutputHandlerCsv::initColType2string ( )

inlinestaticprotected

initializes the mapping of ColType elements to respective strings

list2string()

std::string IntaRNA::OutputHandlerCsv::list2string ( const ColTypeList &  colTypes, const std::string &  sep  )

inlinestatic

Converts a list of Coltypes to their string representation.

Parameters

colTypes	the list to convert
sep	the separator to use

Returns

the string representation of the list

needBPs()

bool IntaRNA::OutputHandlerCsv::needBPs ( const ColTypeList &  colTypes )

inlinestatic

Checks whether or not interaction base pairs are needed to generate all colTypes

Parameters

colTypes

the list of column types to consider

Returns

true if one of the colTypes requires Zall computation; false otherwise.

needsZall()

bool IntaRNA::OutputHandlerCsv::needsZall ( const ColTypeList &  colTypes )

inlinestatic

Checks whether or not Zall needs to be computed to generate all colTypes

Parameters

colTypes

the list of column types to consider

Returns

true if one of the colTypes requires Zall computation; false otherwise.

string2list()

OutputHandlerCsv::ColTypeList IntaRNA::OutputHandlerCsv::string2list ( const std::string &  listString )

inlinestatic

Converts string representation of a list of Coltypes to the respective list.

If the provided string encoding is empty or equals '*', all available columns are returned

Parameters

listString

the string representation of the list

Returns

the parsed list

Exceptions

std::runtime_error

in case of parsing problems

Member Data Documentation

colSep

std::string IntaRNA::OutputHandlerCsv::colSep

protected

the column separator to be used

colType2string

std::map<ColType,std::string> IntaRNA::OutputHandlerCsv::colType2string

staticprotected

mapping of ColTypes to according strings

colTypeNumericSort

const ColTypeList IntaRNA::OutputHandlerCsv::colTypeNumericSort

static

list of ColTypes that have to be sorted numerically

columns

const std::list< ColType > IntaRNA::OutputHandlerCsv::columns

protected

the sequence of columns to be reported

energy

const InteractionEnergy& IntaRNA::OutputHandlerCsv::energy

protected

the interaction energy function used for interaction computation

listSep

std::string IntaRNA::OutputHandlerCsv::listSep

protected

the list separator to be used within single columns

notAvailable

const std::string IntaRNA::OutputHandlerCsv::notAvailable

static

string to encode not available values

out

std::ostream& IntaRNA::OutputHandlerCsv::out

protected

the output stream to write to

Z

Z_type IntaRNA::OutputHandler::Z

protected

overall partition function (if set)

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

• src/IntaRNA/OutputHandlerCsv.h