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/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
/** @file ms.h
Multiple Sequences object
Object holds multiple sequences (like an MSA) but are not necessairly aligned
@ingroup motif
*/
#ifndef MS_H
#define MS_H
#include <lists.h>
typedef struct {
double rangeLow;
double rangeHigh;
int nseqs; /**< Number of sequences */
char *alphabet; /**< Alphabet (see #DEFAULT_ALPHABET) */
int inv_alphabet[NCHARS]; /**< Inverse of 'alphabet' (maps characters to their index in 'alphabet') */
char **names; /**< Names of each sequence (2D char array) */
char **seqs; /**< Sequence data (2D char array) */
int *idx_offsets; /**< Index offset of each sequence*/
char *missing; /**< Recognized missing data characters */
int is_missing[NCHARS]; /**< Fast lookup of whether character
is missing data char */
} MS;
#endif
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