Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/clustal/symmatrix.h b/binaries/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