Mercurial > repos > clustalomega > clustalomega
comparison clustalomega/clustal-omega-1.0.2/src/squid/stockholm.h @ 1:bc707542e5de
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author | clustalomega |
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date | Thu, 21 Jul 2011 13:35:08 -0400 |
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0:ff1768533a07 | 1:bc707542e5de |
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1 #ifndef STOCKHOLM_H_INCLUDED | |
2 #define STOCKHOLM_H_INCLUDED | |
3 | |
4 #include "gki.h" | |
5 | |
6 typedef struct { | |
7 int *linetype; /* e.g. STOCKHOLM_GF_LINE; always valid */ | |
8 int *featurecode; /* all markup codes: e.g. STOCKHOLM_GF_ID; | |
9 nonmarkup: always set to STOCKHOLM_UNPARSED */ | |
10 char **featurename; /* all unparsed markup codes: string, e.g. "ID"; | |
11 all other lines: NULL */ | |
12 int *seqidx; /* all GS, GR, GC, sequence lines: which sequence; | |
13 other lines: 0 */ | |
14 int *len; /* all GR, GC, sequence lines: length of text field; | |
15 other lines: 0 */ | |
16 char **text; /* all unparsed nonblank lines: rest of data | |
17 other lines: NULL */ | |
18 int nseqalloc; /* current nseqs allocated for in aseqs and ainfo */ | |
19 int nlines; /* number of lines in this skel */ | |
20 int nlinealloc; /* current # of lines allocated for in this skel */ | |
21 int overall_line; /* line # in file (important in files w/ >1 ali)*/ | |
22 } alifile_skeleton; | |
23 | |
24 #define STOCKHOLM_GF_LINE 0 | |
25 #define STOCKHOLM_GS_LINE 1 | |
26 #define STOCKHOLM_GC_LINE 2 | |
27 #define STOCKHOLM_GR_LINE 3 | |
28 #define STOCKHOLM_SEQ_LINE 4 | |
29 #define STOCKHOLM_BLANK_LINE 5 | |
30 #define STOCKHOLM_COMMENT_LINE 6 | |
31 | |
32 #define STOCKHOLM_UNPARSED 0 | |
33 #define STOCKHOLM_GF_ID 1 | |
34 #define STOCKHOLM_GF_AC 2 | |
35 #define STOCKHOLM_GF_DE 3 | |
36 #define STOCKHOLM_GF_AU 4 | |
37 #define STOCKHOLM_GF_GA 5 | |
38 #define STOCKHOLM_GF_NC 6 | |
39 #define STOCKHOLM_GF_TC 7 | |
40 #define STOCKHOLM_GS_WT 100 | |
41 #define STOCKHOLM_GS_AC 101 | |
42 #define STOCKHOLM_GS_DE 102 | |
43 #define STOCKHOLM_GC_CS 200 | |
44 #define STOCKHOLM_GC_RF 201 | |
45 #define STOCKHOLM_GR_SS 300 | |
46 #define STOCKHOLM_GR_SA 301 | |
47 | |
48 #define SKEL_NSEQLUMP 10 /* allocate for new seqs in blocks of this size */ | |
49 #define SKEL_LUMPSIZE 100 /* allocate for new lines in skel in blocks of this size */ | |
50 | |
51 #endif /*STOCKHOLM_H_INCLUDED*/ |