6 *****************************************************************************
8 * Copyright (c) 2004, Luke Sheneman
11 * Redistribution and use in source and binary forms, with or without
12 * modification, are permitted provided that the following conditions
15 * + Redistributions of source code must retain the above copyright
16 * notice, this list of conditions and the following disclaimer.
17 * + Redistributions in binary form must reproduce the above copyright
18 * notice, this list of conditions and the following disclaimer in
19 * the documentation and/or other materials provided with the
21 * + The names of its contributors may not be used to endorse or promote
22 * products derived from this software without specific prior
25 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
26 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
27 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
28 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
29 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
30 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
31 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
32 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
33 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
34 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
35 * POSSIBILITY OF SUCH DAMAGE.
37 *****************************************************************************
42 * sheneman@cs.uidaho.edu
47 #ifndef _INC_NJ_FASTA_H_
48 #define _INC_NJ_FASTA_H_ 1
56 #define NJ_INITIAL_BUFFER_SIZE 512
57 #define NJ_INITIAL_NSEQS 64
59 #define NJ_FASTA_MODE_TITLE 100
60 #define NJ_FASTA_MODE_SEQUENCE 101
61 #define NJ_FASTA_MODE_NEWLINE 102
62 #define NJ_FASTA_MODE_UNKNOWN 103
65 typedef struct _STRUCT_NJ_ALIGNMENT {
78 NJ_read_fasta(NJ_ARGS *nj_args);
81 NJ_print_alignment(NJ_alignment *alignment);
84 NJ_free_alignment(NJ_alignment *alignment);
87 NJ_taxaname_unique(NJ_alignment *alignment);
93 #endif /* _INC_NJ_FASTA_H_ */