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[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / clustal / symmatrix.h

diff --git a/website/archive/binaries/mac/src/clustalo/src/clustal/symmatrix.h b/website/archive/binaries/mac/src/clustalo/src/clustal/symmatrix.h
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--- a/website/archive/binaries/mac/src/clustalo/src/clustal/symmatrix.h
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-/*********************************************************************
- * 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 216 2011-03-19 10:11:53Z 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
-
-
-/**
- * @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);
-
-extern int
-SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p);
-
-#endif