GraphAlignment/src/GraphAlignment.h File Reference

Graph alignment module. More...

#include "R.h"
#include "Rinternals.h"
#include "Rdefines.h"
#include "R_ext/Rdynload.h"
#include "GA_message.h"
#include "GA_vector.h"
#include "GA_matrix.h"

Go to the source code of this file.

Typedefs
typedef enum GADirectedMode_Impl	GADirectedMode
Enumerations
enum	GADirectedMode_Impl { GA_DIRECTED_ENABLED = 1, GA_DIRECTED_DISABLED = 0 }
Functions
void	R_init_GraphAlignment (DllInfo *info)
void	R_unload_GraphAlignment (DllInfo *info)
void	GA_msg_R (const char *text, GAMessageLevel level)
GAVectorInt *	GA_linear_assignment_solve (GAMatrixInt *costMatrix)
GAMatrixReal *	GA_encode_directed_graph (GAMatrixReal *matrix, GAVectorInt *p)
SEXP	GA_encode_directed_graph_R (SEXP matrix, SEXP p)
SEXP	GA_linear_assignment_solve_R (SEXP costMatrix)
GADirectedMode	GA_directed_mode_from_R (SEXP robj)
GAMatrixReal *	GA_compute_M (GAMatrixReal *na, GAMatrixReal *nb, GAMatrixReal *r, GAVectorInt *p, GAMatrixReal *linkScore, GAMatrixReal *selfLinkScore, GAVectorReal *nodeScore1, GAVectorReal *nodeScore2, GAVectorReal *lookupLink, GAVectorReal *lookupNode, GAClampMode clamp)
SEXP	GA_compute_M_R (SEXP a, SEXP b, SEXP r, SEXP p, SEXP linkScore, SEXP selfLinkScore, SEXP nodeScore1, SEXP nodeScore2, SEXP lookupLink, SEXP lookupNode, SEXP clamp)

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Detailed Description

Graph alignment module.

This module provides various functions used by the graph alignment R package, such as the wrapper for the linear assignment problem solver and the function which computes the score matrix M.

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Typedef Documentation

typedef enum GADirectedMode_Impl GADirectedMode

Directed mode.

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Enumeration Type Documentation

enum GADirectedMode_Impl

Directed mode (implementation).

The directed mode specifies whether input matrices should be treated as adjacency matrices of directed graphs.

Enumerator:

GA_DIRECTED_ENABLED	Directed mode: enabled.
GA_DIRECTED_DISABLED	Directed mode: disabled.

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Function Documentation

GAMatrixReal* GA_compute_M	(	GAMatrixReal *	na,
		GAMatrixReal *	nb,
		GAMatrixReal *	r,
		GAVectorInt *	p,
		GAMatrixReal *	linkScore,
		GAMatrixReal *	selfLinkScore,
		GAVectorReal *	nodeScore1,
		GAVectorReal *	nodeScore2,
		GAVectorReal *	lookupLink,
		GAVectorReal *	lookupNode,
		GAClampMode	clamp
	)

Compute score matrix.

Compute the complete score matrix M. The matrix which is returned will be referenced and should be destroyed by using GA_matrix_destroy_real() when it is not needed anymore.

Parameters:

	na	adjacency matrix for network A
	nb	adjacency matrix for network B
	r	node similarity matrix
	p	permutation vector
	linkScore	link score matrix
	selfLinkScore	self link score matrix
	nodeScore1	node score matrix (1)
	nodeScore2	node score matrix (2)
	lookupLink	link bin lookup table
	lookupNode	node bin lookup table
	clamp	clamp mode for bin lookups

Returns:

the score matrix M

See also:

GA_get_bin_number()

SEXP GA_compute_M_R	(	SEXP	a,
		SEXP	b,
		SEXP	r,
		SEXP	p,
		SEXP	linkScore,
		SEXP	selfLinkScore,
		SEXP	nodeScore1,
		SEXP	nodeScore2,
		SEXP	lookupLink,
		SEXP	lookupNode,
		SEXP	clamp
	)

Compute score matrix (R).

Compute the complete score matrix M.

Parameters:

	a	adjacency matrix for network A
	b	adjacency matrix for network B
	r	node similarity matrix
	p	permutation vector
	linkScore	link score matrix
	selfLinkScore	self link score matrix
	nodeScore1	node score matrix (1)
	nodeScore2	node score matrix (2)
	lookupLink	link bin lookup table
	lookupNode	node bin lookup table
	clamp	clamp mode for bin lookups

Returns:

the score matrix M

GADirectedMode GA_directed_mode_from_R

(

SEXP

robj

)

Get directed mode from R object (real).

Get the directed mode corresponding to the value of the specified R object.

Parameters:

robj

R object

Returns:

directed mode

GAMatrixReal* GA_encode_directed_graph	(	GAMatrixReal *	matrix,
		GAVectorInt *	p
	)

Encode directed graph.

Encode an adjacency matrix for a directed graph into a symmetric matrix.

This is done by setting entries (i, j) and (j, i) of the target matrix m' to 1 if entry m[i, j] = 1 and i > j and to -1 if m[i, j] = 1 and j > i. A permutation will be applied to i, j if specified as an argument.

The matrix which is returned will be referenced and should be destroyed by using GA_matrix_destroy_real() when it is not needed anymore.

Parameters:

	matrix	matrix
	p	permutation vector

Returns:

symmetric matrix

SEXP GA_encode_directed_graph_R	(	SEXP	matrix,
		SEXP	p
	)

Encode directed graph (R).

Encode an adjacency matrix for a directed graph into a symmetric matrix.

Parameters:

	matrix	matrix
	p	permutation vector

Returns:

symmetric matrix

GAVectorInt* GA_linear_assignment_solve

(

GAMatrixInt *

costMatrix

)

Solve linear assignment problem.

Solve the linear assignment problem specified by the cost matrix. The solution returned is a vector of columns assigned to rows. The vector which is returned will be referenced and should be destroyed by using GA_vector_destroy_int() when it is not needed anymore.

Parameters:

costMatrix

cost matrix

Returns:

Solution of the linear assignment problem

SEXP GA_linear_assignment_solve_R

(

SEXP

costMatrix

)

Solve linear assignment problem (R).

Solve the linear assignment problem specified by the cost matrix. The solution returned is a vector of rows assigned to columns.

Parameters:

costMatrix

cost matrix

Returns:

Solution of the linear assignment problem

void GA_msg_R	(	const char *	text,
		GAMessageLevel	level
	)

Report a message.

Report a message using the appropriate R functions.

Parameters:

	text	text of the message
	level	message level

void R_init_GraphAlignment

(

DllInfo *

info

)

Module initialization hook.

Hook function for module initialization.

Parameters:

info

dynamic link library info

void R_unload_GraphAlignment

(

DllInfo *

info

)

Module unloading hook.

Hook function for module unloading.

Parameters:

info

dynamic link library info

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