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