!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
!    $Source: /kappa1/srs4_0/odd/RCS/embl.sdl,v $
!    $Revision: 1.13 $
!    $Date: 1995/01/11 17:26:28 $
!    $Author: etzold $
!
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


#library /id=%EMBL_DB 
    /group=@SEQUENCE_LIBS /name=EMBL /logicname=EM, EMBL 
    /format=@EMBL_FORMAT /cachesize=2048 /maxIndexSizeKb=3200
    /oddfile="embl.sdl"
{
    #file /name=est 
    #file /name=patent
    #file /name=fun 
    #file /name=inv 
    #file /name=mam 
    #file /name=org 
    #file /name=phg 
    #file /name=pln 
    #file /name=pri 
    #file /name=pro 
    #file /name=rod 
    #file /name=syn 
    #file /name=unc 
    #file /name=vrl 
    #file /name=vrt 
    #file /name=sts 
}       

!names of the files in GCG format
!{
!    #file /name=em_fun /logicname=EM_FUN
!    #file /name=em_in /logicname=EM_IN
!    #file /name=em_om /logicname=EM_OM
!    #file /name=em_or /logicname=EM_OR
!    #file /name=em_ph /logicname=EM_PH
!    #file /name=em_pl /logicname=EM_PL
!    #file /name=em_pr /logicname=EM_PR
!    #file /name=em_ba /logicname=EM_BA
!    #file /name=em_ro /logicname=EM_RO
!    #file /name=em_sy /logicname=EM_SY
!    #file /name=em_un /logicname=EM_UN
!    #file /name=em_vi /logicname=EM_VI
!    #file /name=em_ov /logicname=EM_OV
!    #file /name=em_sts /logicname=EM_STS
!    #file /name=em_pat /logicname=EM_PAT
!    #file /name=em_est /logicname=EM_EST
!}       



#libformat /id=%EMBL_FORMAT /parser=@EMBL_PARSER
    /file_type=@EMBLREF_FILE, @EMBLSEQ_FILE 
!GCG format 
!    /file_type=@GCGREF_FILE, @GCGSEQ_FILE 
    /featureExpression=@EMBL_FEATURE_EXPRESSION
{
    !ID-field
    #field /gblid=%EMBL_ID_FIELD 
           /itype=ID /ftype=@DF_ID /idtype=@SRSxSEQID
           /begstr="ID  " /find=id /maxlines=1
           /relIndexSize=0.95
    !accession
    #field /gblid=%EMBL_ACC_FIELD
           /itype=key /ftype=@DF_ACCESSION /idtype=@SRSxSEQID
           /find=accession /begstr="AC   " /nextstr="AC   " 
           /relIndexSize=1
    !date
    #field /itype=num /ftype=@DF_DATE /idtype=@SRSxSEQID
           /find=date /begstr="DT   " /nextstr="DT   " 
    !keywords    
    #field /itype=key /ftype=@DF_KEYWORDS /idtype=@SRSxSEQID
           /find=keywords /begstr="KW   " /nextstr="KW   " 
           /relIndexSize=0.34
    !definiton
    #field /itype=key /ftype=@DF_DEFINITION /idtype=@SRSxSEQID
           /find=definition /begstr="DE   " /nextstr="DE   " 
           /relIndexSize=0.61
    !organism
    #field /itype=key /ftype=@DF_ORGANISM /idtype=@SRSxSEQID
           /find=emtaxons /begstr="OS   ", "OG   "
           /nextstr="OC   ", "OS   ", "OG   " 
           /relIndexSize=0.1
    !reference number
    #field /itype=show /ftype=@DF_REFNUMBER /idtype=@SRSxSEQID
           /begstr="RN   " /nextstr="RN   " 
    !authors
    #field /itype=key /ftype=@DF_AUTHORS /idtype=@SRSxSEQID
           /find=authors /begstr="RA   " /nextstr="RA   " 
           /relIndexSize=0.6
    !title
    #field /itype=key /ftype=@DF_TITLE /idtype=@SRSxSEQID
           /find=definition /begstr="RT   " /nextstr="RT   " 
           /relIndexSize=0.25
    !features
    #field /gblid=%EMBL_FEATURES_FIELD 
        /itype=key /ftype=@DF_FEATURES /idtype=@SRSxSFTID
           /begstr="FT   " /nextstr="FT   " /next1str="FT        " 
           /find=feature         
           /relIndexSize=0.29
    !link        
    #field /gblid=%EMBL_DR_FIELD 
           /itype=link /ftype=@DF_LINK /idtype=@SRSxLINKID
           /begstr="DR   " /nextstr="DR EXIT "
           /find=embllink         
    !reference
    #field /gblid=%EMBL_REF_FIELD
           /itype=key /ftype=@DF_REF /idtype=@SRSxSEQID /suppress_error=yes
           /find=reference /begstr="RL   " /nextstr="RL   "!/maxlines=1
           /relIndexSize=0.13
    !comment
    #field /itype=key /ftype=@DF_COMMENT /idtype=@SRSxSEQID
           /find=comment /begstr="CC   " /nextstr="CC   "
           /relIndexSize=0.1

    !sequence length
    #field /itype=num /ftype=@DF_SEQLENGTH /idtype=@SRSxSEQID
           /find="" 
    #readlink/id=%EMBL_EPD_REF /link=@EMBL_EPD_LINK

}



#library /id=%EMBLNEW_DB 
    /group=@SEQUENCE_LIBS
    /name=EMNEW /format=@EMNEW_FORMAT /logicname=EMBL_NEW 
    /cachesize=2024 /oddfile="embl.sdl"
{
    #file /id=0  /name=emnew
}



#libformat /id=%EMNEW_FORMAT /parser=@EMBL_PARSER
    /file_type=@EMBLREF_FILE, @EMBLSEQ_FILE 
!    /file_type=@GCGREF_FILE, @GCGSEQ_FILE
    /featureExpression=@EMBL_FEATURE_EXPRESSION
{
    !ID-field
    #field /gblid=%EMNEW_ID_FIELD 
           /itype=ID /ftype=@DF_ID /idtype=@SRSxSEQID
           /begstr="ID  " /find=id /maxlines=1
    !accession
    #field /gblid=%EMNEW_ACC_FIELD
           /itype=key /ftype=@DF_ACCESSION /idtype=@SRSxSEQID
           /find=accession /begstr="AC   " /nextstr="AC   " 
    !date
    #field /itype=show /ftype=@DF_DATE /idtype=@SRSxSEQID
           /find=accession /begstr="DT   " /nextstr="DT   " 
    !keywords    
    #field /itype=key /ftype=@DF_KEYWORDS /idtype=@SRSxSEQID
           /find=keywords /begstr="KW   " /nextstr="KW   " 
           /relIndexSize=0.34
    !definiton
    #field /itype=key /ftype=@DF_DEFINITION /idtype=@SRSxSEQID
           /find=definition /begstr="DE   " /nextstr="DE   " 
           /relIndexSize=0.6
    !organism
    #field /itype=key /ftype=@DF_ORGANISM /idtype=@SRSxSEQID
           /find=emtaxons /begstr="OS   ", "OG   "
           /nextstr="OC   ", "OS   ", "OG   " 
           /relIndexSize=0.1
    !authors
    #field /itype=key /ftype=@DF_AUTHORS /idtype=@SRSxSEQID
           /find=authors /begstr="RA   " /nextstr="RA   " 
           /relIndexSize=0.6
    !title
    #field /itype=key /ftype=@DF_TITLE /idtype=@SRSxSEQID
           /find=definition /begstr="RT   " /nextstr="RT   " 
           /relIndexSize=0.3
    !features
    #field /gblid=%EMNEW_FEATURES_FIELD 
           /itype=key /ftype=@DF_FEATURES /idtype=@SRSxSFTID
           /begstr="FT   " /nextstr="FT   " /next1str="FT        " 
           /find=feature         
           /relIndexSize=0.3
    !link        
    #field /itype=link /ftype=@DF_LINK /idtype=@SRSxLINKID
           !/link=@EMBL_EPD_LINK
           /begstr="DR   " /nextstr="DR EXIT "
           /find=embllink         
    !reference number
    #field /itype=show /ftype=@DF_REFNUMBER /idtype=@SRSxSEQID
        /begstr="RN   " /nextstr="RN   " 
    !reference
    #field 
           /itype=key /ftype=@DF_REF /idtype=@SRSxSEQID /suppress_error=yes
           /find=reference /begstr="RL   " /nextstr="RL   "!/maxlines=1
           /relIndexSize=0.2
    !comment
    #field /itype=key /ftype=@DF_COMMENT /idtype=@SRSxSEQID
           /find=comment /begstr="CC   " /nextstr="CC   "
           /relIndexSize=0.1
    !sequence length
    #field /itype=num /ftype=@DF_SEQLENGTH /idtype=@SRSxSEQID
           /find="" 
}



#link /id=%EMBL_EPD_LINK
      /lib1=@EMBL_DB /lib2=@EPD_DB 
      /field1=@EMBL_ID_FIELD /field2=@EPD_ID_FIELD
      /idtype1=@SRSxSEQID /idtype2=@ENTRY_ID

!#link /id=%EMBL_GENBANK_LINK
!      /lib1=@EMBL_DB /lib2=@GENBANK_DB /type=index
!      /field1=@EMBL_ACC_FIELD /field2=@GENBANK_ACC_FIELD
!      /idtype1=@SRSxSEQID /idtype2=@SRSxSEQID

#link /id=%EMNEW_EMBL_LINK
      /lib1=@EMBLNEW_DB /lib2=@EMBL_DB /type=index
      /field1=@EMNEW_ACC_FIELD /field2=@EMBL_ACC_FIELD
      /idtype1=@SRSxSEQID /idtype2=@SRSxSEQID

#filetype /ID=%EMBLREF_FILE 
          /typename="dat" /maxline=90 /exitstr="  "
#filetype /ID=%EMBLSEQ_FILE 
          /begstr="SQ   " /advance=1 
          /seqtype=embl ! SLBxEMBL, dgg addition
          /typename="dat" /maxline=90 /exitstr="//"

#srsfield /id=%DF_REFNUMBER
    /shortname="RFN" /name="RefNumber" /itype=show

ASSIGN %%EM_SFT_KEY      2
ASSIGN %%EM_SFT_FSTKEY   1
ASSIGN %%EM_SFT_OPEN    20
ASSIGN %%EM_SFT_BEG     21
ASSIGN %%EM_SFT_END     22
ASSIGN %%EM_SFT_COMPL   23
ASSIGN %%EM_SFT_OP      30


#PARSER /id=%EMBL_PARSER /newline="\n" /ignore=" "
        /convert=upper /#BNF = 
 name       = ~A-Z0-9$_\-~;
 noword     = ~\-;.()[=,/]'\"~;
 word       = ~\-,;.()[=/] '\\\"~ <not>;    
 cword      = ~',;.()[=/] \\\"~ <not>;    
 id         = name <wrt>;
 key        = word;
 accnr      = ^A-Z^ ~0-9~;
 accession  = accnr <wrt c=1> ';' [accession];
 definition = { noword  | key <new> };
 taxon      = ~;.(),~ <new spanlf not>;
 taxons     = { taxon | ~;.~ };
 trivial    = '(' { ~);,(~ <new spanlf not> | ~;,~ | trivial } ')';
 emtax      = ~;.()~ <new not> [ '(' ~;.()~ <new not> ')'];
 emtaxons   =  { emtax | ~.;~ };
 keyword    = ~;.~ <new not>;
 keywords   = [keyword { ';' keyword }] ['.'];
!
 authors    = author { ',' author} [';']; 
 author     = ~A-Z'\-~ <wrt> {?initials | (~ ~<noskip app> ~A-Z'\-~ <app>) };
 initials   = ~ ~<noskip> ','<load app> 
              ~A-Z\-~<app> '.'<app> {~A-Z\-~<app>'.'<app>};
!
!literature reference
!
 num        = ~0-9~ <wrt>;
 year       = '(' num ')';
 page       = num '-';
 reference  = ? ref | {~ ~ <not>};
 ref        = ~A-Za-z .\-_~ <wrt c=@JNL> ~0-9~ <wrt c=@VOL> ':' 
               ~0-9~ <wrt c=@PP> '-' <app c=@PP> ~0-9~
               '(' ~0-9~ <wrt c=@YEAR> ')';
!
!date
!
date       = ?credate | ~@~ <not>;
credate    = ~0-9A-Z\-~ <wrt> '(REL.'<nocase> ~0-9~ ',' 'CREATED)' <nocase>;
!
!parsing feature tables
!
  feature    = ffirstword [location]  
               { qualifier };
  ffirstword <wrt c=@EM_SFT_FSTKEY> = ~a-zA-Z0-9_\-'~;
  location   = ~/~ <not spanlf>;
  qualifier  =  ecnumber | citation | qual;
  ecnumber   = '/EC_NUMBER=' <wrt nocase c=@EM_SFT_KEY>'\"' 
               ~0123456789.\-~ <wrt c=2> '\"';
  qual       = '/'<wrt c=@EM_SFT_KEY> ~/a-zA-Z0-9\-_~<app c=@EM_SFT_KEY>  ['='
               ( '\"' {fwordquot} '\"' | ~/~ <not>)];
  fwordquot  = inparenth | fsepquot | fword;
  fsepquot   = ~\-;:.()[=,/]'~;
  fword      = ~\-,;.:()[=/] '\\\"~ <c=@EM_SFT_KEY wrt not>;
  inparenth  = '(' ~)"~ <spanlf not> [')'];
  citation   = '/CITATION='<wrt nocase c=@EM_SFT_KEY> ( ('[' ~]~ <not> ']' ) |
               ('(' ~)~<spanlf not> ')') );

!
 comment    = {  (~\-A-Z0-9~ <not>)  |  (~\-A-Z0-9~ <wrt>) };
 locus      = name <wrt>;
!
!--------EMBL links -----------------------------------------------------------
 epdlink    = 'EPD;' ~0-9~ <wrt c=@EMBL_EPD_REF>;
 embllink     = 'SWISS-PROT' | 'TFD' | 'FLYBASE' | epdlink.