Algo Class Reference

Structure search algorithm related utility functions. More...

#include <algo/Algo.h>

Public Member Functions
ytGraph *	Algo_readGraph (char *file, char *type, ytKeyValues *args, ytData *data, ytGraph *G)
	Reads a graph from a file with respect to the specified data.
void	Algo_setNetworkProperties (Score *score, ytNetwork *network, const char *filename)
	Calculates the node and edge properties and sets to the ytNetwork instance.
ytGraph *	Algo_readGraphData (char *file, char *type, ytKeyValues *args, ytData *data, int fill, ytGraph *g)
	Reads a graph from file with respect to specified data.

Detailed Description

Structure search algorithm related utility functions.

Member Function Documentation

Algo_readGraph()

ytGraph * Algo_readGraph	(	char *	file,
		char *	type,
		ytKeyValues *	args,
		ytData *	data,
		ytGraph *	G )

Reads a graph from a file with respect to the specified data.

This can be used only for reading a constrain graph.

Node IDs are converted based on the specified data.

Available types and their arguments

parents

The file is a TAB seperated text file. Each row corresponds to a node name. This returns a graph with edges that are connected from nodes in a file to all the other nodes in data. This is mainly designed to read a constain file where only listed nodes can be parents.
Arguments:
col=n : Column position of the nodes in the TAB separated file. The first column is n=0.

no_parents

The file is a TAB separated text file. Each row corresponds to a node name. This returns a graph with edges that are connected from node NOT in a file to all the other nodes in data. Arguments:
col=n : Column position of the nodes in the TAB separated file. The first column is n=0.

other arbitrary file formats listed in Network File Formats

The following argument is available in addition to the type specified arguments.
not_found=restrict : By default, nodes not found in the read graph are connected to all the other nodes. This is to not restrict edges for nodes not found in the file for generating the constrain file. If this is specified, such edge are not connected. Therefore they are restricted.

Parameters

file	File name to read.
type	One of parents, no_parents, or arbitrary file format names. See Network File Formats for the avaiable network file formats.
args	Type specific arguments.
G	ytGraph instance to merge. NULL acceptable. If specified, the read graph and G are merged and returned. The specified instance will be deleted.

Returns

Algo_readGraphData()

ytGraph * Algo_readGraphData	(	char *	file,
		char *	type,
		ytKeyValues *	args,
		ytData *	data,
		int	fill,
		ytGraph *	g )

Reads a graph from file with respect to specified data.

Parameters

file	file name of the network file to read.
type	type of network file. NULL can be acceptable. If so, tries to determine the type by the file name suffix.
args	file type specific arguments.
data	data set defining node sets for the returning graph.
fill	Specify a non zero value if you want to fill edges from or to variables that exists in the given data set but does not in the given network file. This is maily used for preparing a constraint graph.

Algo_setNetworkProperties()

void Algo_setNetworkProperties	(	Score *	score,
		ytNetwork *	network,
		const char *	filename )

Calculates the node and edge properties and sets to the ytNetwork instance.

If filename is non-NULL, input data matrix, target data matrix, partial residual matrix, and log likelihood matrix are output into the specified file with suffixes .X, .Y, PR.Y, and LL.

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

• algo/Algo.c