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/* codatal.l - CODATA sequence lexer */
%{
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#ifdef STDC_HEADERS
# include <stdlib.h>
# include <string.h>
#endif
#include "sequence/codatay.h"
%}
%option bison-bridge
%option never-interactive
%option noinput nounput noyywrap
%x FHEAD
%x ENTAG TITAG ALTAG CTTAG ORTAG DATAG ACTAG RETAG COTAG GETAG FUTAG CXTAG
%x CLTAG KETAG FETAG SUTAG SETAG SNTAG SEQTAG ENDTAG
%x ENTAG2
aln [[:alnum:]]
alp [[:alpha:]]
asl "\\"
com ","
cpa ")"
dig [[:digit:]]
dot "."
eol "\n"
equ "="
min "-"
opa "("
sem ";"
sla "/"
spc " "
und "_"
txt .{1,80}
ennam [^# \n]{1,80}
entyp #type
enval (complete|fragments?)
acnum {alp}+{und}?{dig}+
gap {min}
bas ({alp}|{gap})
sep ({com}|{cpa}|{dot}|{equ}|{opa}|{sla}|{spc})
%%
^[A-Z]{1,10}{spc}+{min}{eol} /* Ignore empty fields made by sreformat tool */
^{spc}{eol}{spc}+P{spc}R{spc}O{spc}T{spc}E{spc}I{spc}N { BEGIN FHEAD; }
<FHEAD>{txt} ; /* Ignore file header */
<FHEAD>{eol}/{asl}{3} { BEGIN INITIAL; }
<FHEAD>{eol} ;
^{asl}{3}{eol} ; /* Ignore file trailer */
^ENTRY{spc}{10,11} { BEGIN ENTAG; return EN; }
<ENTAG>{ennam} { BEGIN ENTAG2; yylval->str = strdup(yytext); return ENNAM; }
<ENTAG>{spc}+/{eol} ; /* Trailing spaces ignored */
<ENTAG>{eol} { BEGIN INITIAL; return EOL; }
<ENTAG>. { return ERR; }
<ENTAG2>{txt} { return ENTXT; }
<ENTAG2>{eol} { BEGIN INITIAL; return EOL; }
^TITLE{spc}{10,11} { BEGIN TITAG; return TI; }
<TITAG>^{spc}{16}/{txt} { return NXT; }
<TITAG>{txt} { yylval->str = strdup(yytext); return TITXT; }
<TITAG>{eol}/{spc}{16} { return EOL; }
<TITAG>{eol} { BEGIN INITIAL; return EOL; }
^ALTERNATE_NAMES{spc} { BEGIN ALTAG; return AL; }
<ALTAG>^{spc}{16}/{txt} { return NXT; }
<ALTAG>{txt} { return TXT; }
<ALTAG>{eol}/{spc}{16} { return EOL; }
<ALTAG>{eol} { BEGIN INITIAL; return EOL; }
^CONTAINS{spc}{8} { BEGIN CTTAG; return CT; }
<CTTAG>^{spc}{16}/{txt} { return NXT; }
<CTTAG>{txt} { return TXT; }
<CTTAG>{eol}/{spc}{16} { return EOL; }
<CTTAG>{eol} { BEGIN INITIAL; return EOL; }
^ORGANISM{spc}{8} { BEGIN ORTAG; return OR; }
<ORTAG>^{spc}{3}/{txt} { return NXT; }
<ORTAG>{txt} { return TXT; }
<ORTAG>{eol}/{spc}{3} { return EOL; }
<ORTAG>{eol} { BEGIN INITIAL; return EOL; }
^DATE{spc}{12} { BEGIN DATAG; return DA; }
<DATAG>^{spc}{16}/{txt} { return NXT; }
<DATAG>{txt} { return TXT; }
<DATAG>{eol}/{spc}{16} { return EOL; }
<DATAG>{eol} { BEGIN INITIAL; return EOL; }
^ACCESSIONS{spc}{6} { BEGIN ACTAG; return AC; }
<ACTAG>^{spc}{16}/{acnum} { return NXT; }
<ACTAG>{acnum} { yylval->str = strdup(yytext); return ACNUM; }
<ACTAG>{sem}{spc} { return SEP; }
<ACTAG>{sem}/{eol} { return CNT; }
<ACTAG>{eol}/{spc}{16} { return EOL; }
<ACTAG>{eol} { BEGIN INITIAL; return EOL; }
<ACTAG>. { return ERR; }
^REFERENCE{spc}{7} { BEGIN RETAG; return RE; }
<RETAG>^{spc}{3}/{txt} { return NXT; }
<RETAG>{txt} { return TXT; }
<RETAG>{eol}/{spc}{3} { return EOL; }
<RETAG>{eol} { BEGIN INITIAL; return EOL; }
^COMMENT{spc}{9} { BEGIN COTAG; return CO; }
<COTAG>^{spc}{16}/{txt} { return NXT; }
<COTAG>{txt} { return TXT; }
<COTAG>{eol}/{spc}{16} { return EOL; }
<COTAG>{eol} { BEGIN INITIAL; return EOL; }
^GENETICS({spc}{8})? { BEGIN GETAG; return GE; }
<GETAG>^{spc}{3}/{txt} { return NXT; }
<GETAG>{txt} { return TXT; }
<GETAG>{eol}/{spc}{3} { return EOL; }
<GETAG>{eol} { BEGIN INITIAL; return EOL; }
^FUNCTION({spc}{8})? { BEGIN FUTAG; return FU; }
<FUTAG>^{spc}{3}/{txt} { return NXT; }
<FUTAG>{txt} { return TXT; }
<FUTAG>{eol}/{spc}{3} { return EOL; }
<FUTAG>{eol} { BEGIN INITIAL; return EOL; }
^COMPLEX{spc}{9} { BEGIN CXTAG; return CX; }
<CXTAG>^{spc}{3}/{txt} { return NXT; }
<CXTAG>{txt} { return TXT; }
<CXTAG>{eol}/{spc}{3} { return EOL; }
<CXTAG>{eol} { BEGIN INITIAL; return EOL; }
^CLASSIFICATION{spc}{2} { BEGIN CLTAG; return CL; }
<CLTAG>^{spc}{16}/{txt} { return NXT; }
<CLTAG>{txt} { return TXT; }
<CLTAG>{eol}/{spc}{16} { return EOL; }
<CLTAG>{eol} { BEGIN INITIAL; return EOL; }
^KEYWORDS{spc}{8} { BEGIN KETAG; return KE; }
<KETAG>^{spc}{16}/{txt} { return NXT; }
<KETAG>{txt} { return TXT; }
<KETAG>{eol}/{spc}{16} { return EOL; }
<KETAG>{eol} { BEGIN INITIAL; return EOL; }
^FEATURE/{eol} { BEGIN FETAG; return FE; }
<FETAG>^{spc}{3}/{txt} { return NXT; }
<FETAG>{txt} { return TXT; }
<FETAG>{eol}/{spc}{3} { return EOL; }
<FETAG>{eol} { BEGIN INITIAL; return EOL; }
^SUMMARY{spc}{9} { BEGIN SUTAG; return SU; }
<SUTAG>{txt} { return TXT; }
<SUTAG>{eol} { BEGIN INITIAL; return EOL; }
^SEQUENCE{spc}*/{eol} { BEGIN SETAG; return SE; }
<SETAG>{eol} { BEGIN SNTAG; return EOL; }
<SETAG>. { return ERR; }
<SNTAG>^{spc}{16,18} { return SN; }
<SNTAG>{dig}+ { return INT; }
<SNTAG>{spc}+ { return SPC; }
<SNTAG>{eol} { BEGIN SEQTAG; return EOL; }
<SNTAG>. { return ERR; }
<SEQTAG>^{spc}+ { return SEQ; }
<SEQTAG>{dig}+ { return INT; }
<SEQTAG>{bas} { yylval->str = strdup(yytext); return BAS; }
<SEQTAG>{sep}+ { return SEP; }
<SEQTAG>{eol}/{spc} { return EOL; }
<SEQTAG>{eol} { BEGIN INITIAL; return EOL; }
<SEQTAG>. { return ERR; }
^{sla}{3} { BEGIN ENDTAG; return END; }
<ENDTAG>{eol} { BEGIN INITIAL; return EOL; }
<ENDTAG>. { return ERR; }
<<EOF>> { return NUL; }
{eol} { return ERR; }
. { return ERR; }
%%
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