readfile Class Reference

Inheritance diagram for readfile:

List of all members.

Public Member Functions
	readfile (set< int >, string, string)
	readfile (const readfile &in)
virtual void	readProbeAliases (string aliasFile)
virtual void	readProbeInfo (string infoFile)
void	refactor (set< int > leaveOut)
virtual bool	isProbe (string id) const
virtual vector< string > *	probes ()
virtual vector< string > *	samples ()
virtual double	operator() (int, int)
virtual double	operator() (string, string)
virtual bool	exists (int, int)
virtual bool	exists (string, string)
virtual vector< vector< int > > *	classToExperiments ()
virtual vector< vector< int > > *	experimentsToClass ()
virtual string	computeClassNameForSamples (const set< int > &columnSet, double frac=1) const
virtual int	computeClassIndexForSamples (const set< int > &columnSet, double frac=1) const
virtual string	getClassNameForSample (unsigned int index) const
	Return the name of the class for the sample index.
virtual unsigned int	getClassIndexForSample (unsigned int index) const
	Return the index of the class for the sample index.
virtual string	getClassName (unsigned int index) const
	Return the name of the class corresponding to the index.
virtual unsigned int	getClassSize (unsigned int index) const
	Return the number of rows/samples in the class corresponding to the index.
virtual unsigned int	getNumClasses () const
	Return the number of classes.
virtual int	getColumnIndex (string name) const
virtual int	getRowIndex (string name) const
virtual string	getRowName (unsigned int index) const
	Return the name corresponding to a row index.
Static Public Attributes
static const int	MISSING_VALUE = -9999999

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Member Function Documentation

int readfile::computeClassIndexForSamples	(	const set< int > &	columnSet,
		double	frac = 1
	)		const [virtual]

Compute the index of the class that at least a fraction frac of the columns/samples in columnSet belong to.

Implements motifDataset.

string readfile::computeClassNameForSamples	(	const set< int > &	columnSet,
		double	frac = 1
	)		const [virtual]

Compute the class that at least a fraction frac of the columns/samples in columnSet belong to.

Parameters:

[in]	columnSet,a	set of column/sample indices.
[in]	frac,the	fraction of columns in columnSet that must belong to the returned class.

Returns:

Any class that at least a fraction of the columns in columnSet belong to.

Warning:

The method does not check if frac lies between 0 and 1.

Implements motifDataset.

unsigned int readfile::getClassIndexForSample

(

unsigned int

index

)

const [virtual]

Return the index of the class for the sample index.

Implements motifDataset.

int readfile::getColumnIndex

(

string

name

)

const [virtual]

Return the index corresponding to a column name (-1 if the column does not exist).

Implements motifDataset.

int readfile::getRowIndex

(

string

name

)

const [virtual]

Return the index corresponding to a row name (-1 if the row does not exist).

Implements motifDataset.

bool readfile::isProbe

(

string

id

)

const [virtual]

Returns true if and only if id is a probe in the dataset.

Note:

The method will return true if id is an alias for a probe.

Implements motifDataset.

void readfile::readProbeAliases

(

string

aliasFile

)

[virtual]

Read aliases for probes/rows from aliasFile.

Each line in aliasFile should contain the name of one probe/row and one alias, separated by tabs. The mapping can be many-to-many.

Warning:

The method ignores aliases for rows/probes/genes that are not in the dataset.

Implements motifDataset.

void readfile::readProbeInfo

(

string

infoFile

)

[virtual]

Read information for probes/rows.

Each tab-separated line in infoFile should contain the name of one probe/row, one (gene) symbol, and one name/annotation for the probe. The mapping should be one-one.

Warning:

The method ignores info for rows/probes/genes that are not in the dataset.

If any probe has multiple lines, the method ignores all but the last one.

Implements motifDataset.

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

• /home/poirel/src/c++/biorithm/xmotif/readfile.h
• /home/poirel/src/c++/biorithm/xmotif/readfile.cpp