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#ifndef STOCKHOLM_H_INCLUDED
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#define STOCKHOLM_H_INCLUDED
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int *linetype; /* e.g. STOCKHOLM_GF_LINE; always valid */
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int *featurecode; /* all markup codes: e.g. STOCKHOLM_GF_ID;
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nonmarkup: always set to STOCKHOLM_UNPARSED */
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char **featurename; /* all unparsed markup codes: string, e.g. "ID";
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all other lines: NULL */
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int *seqidx; /* all GS, GR, GC, sequence lines: which sequence;
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int *len; /* all GR, GC, sequence lines: length of text field;
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char **text; /* all unparsed nonblank lines: rest of data
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int nseqalloc; /* current nseqs allocated for in aseqs and ainfo */
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int nlines; /* number of lines in this skel */
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int nlinealloc; /* current # of lines allocated for in this skel */
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int overall_line; /* line # in file (important in files w/ >1 ali)*/
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#define STOCKHOLM_GF_LINE 0
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#define STOCKHOLM_GS_LINE 1
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#define STOCKHOLM_GC_LINE 2
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#define STOCKHOLM_GR_LINE 3
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#define STOCKHOLM_SEQ_LINE 4
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#define STOCKHOLM_BLANK_LINE 5
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#define STOCKHOLM_COMMENT_LINE 6
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#define STOCKHOLM_UNPARSED 0
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#define STOCKHOLM_GF_ID 1
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#define STOCKHOLM_GF_AC 2
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#define STOCKHOLM_GF_DE 3
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#define STOCKHOLM_GF_AU 4
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#define STOCKHOLM_GF_GA 5
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#define STOCKHOLM_GF_NC 6
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#define STOCKHOLM_GF_TC 7
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#define STOCKHOLM_GS_WT 100
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#define STOCKHOLM_GS_AC 101
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#define STOCKHOLM_GS_DE 102
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#define STOCKHOLM_GC_CS 200
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#define STOCKHOLM_GC_RF 201
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#define STOCKHOLM_GR_SS 300
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#define STOCKHOLM_GR_SA 301
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#define SKEL_NSEQLUMP 10 /* allocate for new seqs in blocks of this size */
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#define SKEL_LUMPSIZE 100 /* allocate for new lines in skel in blocks of this size */
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#endif /*STOCKHOLM_H_INCLUDED*/
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src/squid/stockholm.h
