/usr/include/clustalo/clustal/symmatrix.h is in libclustalo-dev 1.2.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | /*********************************************************************
* Clustal Omega - Multiple sequence alignment
*
* Copyright (C) 2010 University College Dublin
*
* Clustal-Omega is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation; either version 2 of the
* License, or (at your option) any later version.
*
* This file is part of Clustal-Omega.
*
********************************************************************/
/*
* RCS $Id: symmatrix.h 288 2013-07-29 13:15:50Z andreas $
*/
/**
* Functions for symmetric (square) matrices including diagonal.
*
* Supports the notion of non-square sub-matrices of a symmetric
* matrix, i.e. where |rows|<|cols| and the corresponding full matrix
* would be |cols|x|cols|
*
* Instead of making this one big chunk of memory we keep pointers to
* pointers, so that we can easily realloc (the project where this file
* originated from needed this for growing a "seed" matrix).
*
* FIXME Allocating one big chunk of memory is probably
* much faster and also easier to maintain.
*
*
*/
#ifndef CLUSTALO_SYMMATRIX_H
#define CLUSTALO_SYMMATRIX_H
/* ugly, but necessary for cross-checking of names in distmat and
* mseq */
#include "seq.h"
/**
* @brief symmetric matrix structure
*/
typedef struct {
int nrows; /**< number of rows */
int ncols; /**< number of columns */
/**
* stored data
*
* @note indices range: [i][j-i] i<=j. use getvalue() and
* setvalue() instead of accessing directly
*
* @see SymMatrixGetValue(), SymMatrixSetValue()
*/
double **data;
} symmatrix_t;
extern int
NewSymMatrix(symmatrix_t **symmat, const int nrows, const int ncols);
extern void
SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value);
extern double
SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j);
extern void
SymMatrixGetValueP(double **value, symmatrix_t *symmat, const int i, const int j);
extern void
FreeSymMatrix(symmatrix_t **symmat);
extern void
SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID);
extern int
SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p, mseq_t *prMSeq);
#endif
|