motifDataset Class Reference

Inheritance diagram for motifDataset:

List of all members.

Public Member Functions
virtual vector< vector< int > > *	classToExperiments ()=0
virtual vector< vector< int > > *	experimentsToClass ()=0
virtual string	computeClassNameForSamples (const set< int > &columnSet, double frac=1) const =0
virtual int	computeClassIndexForSamples (const set< int > &columnSet, double frac=1) const =0
virtual string	getClassNameForSample (unsigned int index) const =0
	Return the name of the class for the sample index.
virtual unsigned int	getClassIndexForSample (unsigned int index) const =0
	Return the index of the class for the sample index.
virtual string	getClassName (unsigned int index) const =0
	Return the name of the class corresponding to the index.
virtual unsigned int	getClassSize (unsigned int index) const =0
	Return the number of rows/samples in the class corresponding to the index.
virtual unsigned int	getNumClasses () const =0
	Return the number of classes.
virtual vector< string > *	probes ()=0
virtual vector< string > *	samples ()=0
virtual double	operator() (int, int)=0
virtual double	operator() (string, string)=0
virtual bool	exists (int, int)=0
virtual bool	exists (string, string)=0
virtual int	getColumnIndex (string name) const =0
virtual void	getRowAliases (string name, set< string > &aliases) const
virtual void	getRowAliases (const set< string > &names, set< string > &aliases) const
virtual void	getRowsForAlias (string otherName, set< string > &rows) const
	Return the rows that have the alias otherName.
virtual int	getRowIndex (string name) const =0
virtual string	getRowName (unsigned int index) const =0
	Return the name corresponding to a row index.
virtual bool	isAlias (string probe, string alias) const
	Return true if and only if other is an alias for probe.
virtual bool	isProbe (string id) const =0
virtual void	readProbeAliases (string aliasFile)=0
bool	getProbeInfo (string probeId, ProbeInfo &info) const
virtual void	readProbeInfo (string infoFile)=0
virtual string	getProbeURL () const
virtual void	setProbeURL (string url)
Protected Member Functions
void	_addAlias (string probe, string alias)
void	_addInfo (string probe, string symbol, string name)
Protected Attributes
map< string, set< string > >	_probesToAliases
map< string, set< string > >	_aliasesToProbes
map< string, ProbeInfo >	_probesToInfo
string	_probeURL

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Member Function Documentation

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

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

Implemented in readfile.

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

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

Implemented in readfile.

virtual int motifDataset::getColumnIndex

(

string

name

)

const [pure virtual]

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

Implemented in readfile.

bool motifDataset::getProbeInfo	(	string	probeId,
		ProbeInfo &	info
	)		const

Return the ProbeInfo for a probe.

The method returns true if and only if probeId has info stored for it.

void motifDataset::getRowAliases	(	string	name,
		set< string > &	aliases
	)		const [virtual]

Return the aliases corresponding to a row name.

Note:

If name does not have an alias, aliases is empty.

void motifDataset::getRowAliases	(	const set< string > &	names,
		set< string > &	aliases
	)		const [virtual]

Return the aliases for multiple row names.

Note:

If no name has an alias, aliases is empty.

virtual int motifDataset::getRowIndex

(

string

name

)

const [pure virtual]

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

Implemented in readfile.

virtual bool motifDataset::isProbe

(

string

id

)

const [pure virtual]

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

Note:

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

Implemented in readfile.

virtual void motifDataset::readProbeAliases

(

string

aliasFile

)

[pure 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.

Implemented in readfile.

virtual void motifDataset::readProbeInfo

(

string

infoFile

)

[pure 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.

Implemented in readfile.

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

• /home/poirel/src/c++/biorithm/xmotif/motifDataset.h
• /home/poirel/src/c++/biorithm/xmotif/motifDataset.C