GOEvidenceCodes Class Reference

#include <old-annotations.h>

List of all members.

Public Member Functions
	GOEvidenceCodes ()
	Default constructor, which sets weights for evidence codes based on Brett Tyler's recommendations.
MyNT	getWeight (string code) const
	Return the weight of an evidence code.
bool	hasWeight (string code) const
	Return true iff the evidence code has an associated weight.
bool	isExperimental (string code) const
void	checkEvidenceCodeWeights (const map< string, unsigned int > &ecUsageCounts, ostream &logStream)
	For every evidence code in ecUsageCounts for which the count is non-zero, check if the invocant contains a weight.
void	readEvidenceCodeWeights (string ecwFile)
	Read evidence code weights from a file.

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Detailed Description

A class for storing different GO evidence codes and numerical weights associated with them.

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Member Function Documentation

void GOEvidenceCodes::checkEvidenceCodeWeights	(	const map< string, unsigned int > &	ecUsageCounts,
		ostream &	logStream
	)

For every evidence code in ecUsageCounts for which the count is non-zero, check if the invocant contains a weight.

Parameters:

[in]	ecUsageCounts	a map from evidence codes to the number of times it occurs (in an annotation file).
[out]	logStream	Print evidence codes without weights to logStream.

MyNT GOEvidenceCodes::getWeight

(

string

code

)

const [inline]

Return the weight of an evidence code.

Parameters:

[in]

code

An evidence code.

The method returns 0 if the code does not have a weight and also print an error message.

bool GOEvidenceCodes::hasWeight

(

string

code

)

const [inline]

Return true iff the evidence code has an associated weight.

Parameters:

[in]

code

An evidence code.

bool GOEvidenceCodes::isExperimental

(

string

code

)

const [inline]

Return true if and only if the evidence code is experimental.

Experimental evidence codes are TAS, IDA, IC, NAS, IMP, IGI, IPI, and IEP.

Non-experimental evidence codes are ISS, RCA, and IEA.

void GOEvidenceCodes::readEvidenceCodeWeights

(

string

ecwFile

)

Read evidence code weights from a file.

Each line of the file should contain two values: an evidence code and its weight, separated by a tab. The method will ignore lines that start with '#'. One use of this method is to input biologist-provided weights for evidence codes. Another use of the method is to ignore some evidence codes (e.g., electronic ones) by setting their weights to 0.

Note:

The method accepts any weights that are provided in the input file.

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

• /home/poirel/src/c++/biorithm/libfun/old-annotations.h
• /home/poirel/src/c++/biorithm/libfun/old-annotations.C