/usr/include/clustalo/squid/stockholm.h is in libclustalo-dev 1.2.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | #ifndef STOCKHOLM_H_INCLUDED
#define STOCKHOLM_H_INCLUDED
#include "gki.h"
typedef struct {
int *linetype; /* e.g. STOCKHOLM_GF_LINE; always valid */
int *featurecode; /* all markup codes: e.g. STOCKHOLM_GF_ID;
nonmarkup: always set to STOCKHOLM_UNPARSED */
char **featurename; /* all unparsed markup codes: string, e.g. "ID";
all other lines: NULL */
int *seqidx; /* all GS, GR, GC, sequence lines: which sequence;
other lines: 0 */
int *len; /* all GR, GC, sequence lines: length of text field;
other lines: 0 */
char **text; /* all unparsed nonblank lines: rest of data
other lines: NULL */
int nseqalloc; /* current nseqs allocated for in aseqs and ainfo */
int nlines; /* number of lines in this skel */
int nlinealloc; /* current # of lines allocated for in this skel */
int overall_line; /* line # in file (important in files w/ >1 ali)*/
} alifile_skeleton;
#define STOCKHOLM_GF_LINE 0
#define STOCKHOLM_GS_LINE 1
#define STOCKHOLM_GC_LINE 2
#define STOCKHOLM_GR_LINE 3
#define STOCKHOLM_SEQ_LINE 4
#define STOCKHOLM_BLANK_LINE 5
#define STOCKHOLM_COMMENT_LINE 6
#define STOCKHOLM_UNPARSED 0
#define STOCKHOLM_GF_ID 1
#define STOCKHOLM_GF_AC 2
#define STOCKHOLM_GF_DE 3
#define STOCKHOLM_GF_AU 4
#define STOCKHOLM_GF_GA 5
#define STOCKHOLM_GF_NC 6
#define STOCKHOLM_GF_TC 7
#define STOCKHOLM_GS_WT 100
#define STOCKHOLM_GS_AC 101
#define STOCKHOLM_GS_DE 102
#define STOCKHOLM_GC_CS 200
#define STOCKHOLM_GC_RF 201
#define STOCKHOLM_GR_SS 300
#define STOCKHOLM_GR_SA 301
#define SKEL_NSEQLUMP 10 /* allocate for new seqs in blocks of this size */
#define SKEL_LUMPSIZE 100 /* allocate for new lines in skel in blocks of this size */
#endif /*STOCKHOLM_H_INCLUDED*/
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