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+/* MOD2DENSE.H - Interface to module for handling dense mod2 matrices. */
+
+/* Copyright (c) 1995-2012 by Radford M. Neal.
+ *
+ * Permission is granted for anyone to copy, use, modify, and distribute
+ * these programs and accompanying documents for any purpose, provided
+ * this copyright notice is retained and prominently displayed, and note
+ * is made of any changes made to these programs.  These programs and
+ * documents are distributed without any warranty, express or implied.
+ * As the programs were written for research purposes only, they have not
+ * been tested to the degree that would be advisable in any important
+ * application.  All use of these programs is entirely at the user's own
+ * risk.
+ */
+
+
+/* This module implements operations on matrices of mod2 elements (bits,
+   with addition and multiplication being done modulo 2).  The matrices
+   are stored with consecutive bits of a column packed into words, and 
+   the procedures are implemented where possible using bit operations 
+   on these words.  This is an appropriate representation when the matrices 
+   are dense (ie, 0s and 1s are about equally frequent). 
+  
+   All procedures in this module display an error message on standard 
+   error and terminate the program if passed an invalid argument (indicative
+   of a programming error), or if memory cannot be allocated.  Errors from 
+   invalid contents of a file result in an error code being returned to the 
+   caller, with no message being printed by this module. 
+*/
+
+
+#include <stdint.h>		/* Has the definition of uint32_t used below */
+
+/* PACKING OF BITS INTO WORDS.  Bits are packed into 32-bit words, with
+   the low-order bit coming first. */
+
+typedef uint32_t mod2word;	/* Data type that holds packed bits. If uint32_t
+		 		   doesn't exist, change it to unsigned long */
+
+#define mod2_wordsize 32	/* Number of bits that fit in a mod2word. Can't
+				   be increased without changing intio module */
+
+#define mod2_wordsize_shift 5	/* Amount to shift by to divide by wordsize */
+#define mod2_wordsize_mask 0x1f /* What to AND with to produce mod wordsize */
+
+/* Extract the i'th bit of a mod2word. */
+
+#define mod2_getbit(w,i) (((w)>>(i))&1) 
+
+/* Make a word like w, but with the i'th bit set to 1 (if it wasn't already). */
+
+#define mod2_setbit1(w,i) ((w)|(1<<(i))) 
+
+/* Make a word like w, but with the i'th bit set to 0 (if it wasn't already). */
+
+#define mod2_setbit0(w,i) ((w)&(~(1<<(i)))) 
+
+
+/* STRUCTURE REPRESENTING A DENSE MATRIX.  These structures are dynamically
+   allocated using mod2dense_allocate (or by other procedures that call
+   mod2dense_allocate).  They should be freed with mod2dense_free when no 
+   longer required. 
+
+   Direct access to this structure should be avoided except in low-level
+   routines.  Use the macros and procedures defined below instead. */
+
+typedef struct 
+{
+  int n_rows;		/* Number of rows in the matrix */
+  int n_cols;		/* Number of columns in the matrix */
+
+  int n_words;		/* Number of words used to store a column of bits */
+
+  mod2word **col;	/* Pointer to array of pointers to columns */
+
+  mod2word *bits;	/* Pointer to storage block for bits in this matrix 
+                           (pieces of this block are pointed to from col) */
+} mod2dense;
+
+
+/* MACROS. */
+
+#define mod2dense_rows(m) ((m)->n_rows)  /* Get the number of rows or columns */
+#define mod2dense_cols(m) ((m)->n_cols)  /* in a matrix                       */
+
+
+/* PROCEDURES. */
+
+mod2dense *mod2dense_allocate (int, int);
+void mod2dense_free           (mod2dense *);
+
+void mod2dense_clear    (mod2dense *);
+void mod2dense_copy     (mod2dense *, mod2dense *);
+void mod2dense_copyrows (mod2dense*, mod2dense *, int *);
+void mod2dense_copycols (mod2dense*, mod2dense *, int *);
+
+void mod2dense_print      (FILE *, mod2dense *);
+int  mod2dense_write      (FILE *, mod2dense *);
+mod2dense *mod2dense_read (FILE *);
+
+int  mod2dense_get (mod2dense *, int, int);
+void mod2dense_set (mod2dense *, int, int, int);
+int  mod2dense_flip(mod2dense *, int, int);
+
+void mod2dense_transpose (mod2dense *, mod2dense *);
+void mod2dense_add       (mod2dense *, mod2dense *, mod2dense *);
+void mod2dense_multiply  (mod2dense *, mod2dense *, mod2dense *);
+
+int mod2dense_equal (mod2dense *, mod2dense *);
+
+int mod2dense_invert          (mod2dense *, mod2dense *);
+int mod2dense_forcibly_invert (mod2dense *, mod2dense *, int *, int *);
+int mod2dense_invert_selected (mod2dense *, mod2dense *, int *, int *);