minimal ACEDB classes.wrm file

Detlef Wolf D.Wolf at dkfz-heidelberg.de
Sat Aug 27 11:14:48 EST 1994


If you want to add many classes (150) to an ACEDB database,
then read this
else skip it.

---------------------------
probably this comes a bit late now, since Jean will
release a code that does not need this anymore.
But for the time being:

Starting from the code as of 94-07-14 for ACEDB 3.1 from the
Montpellier workshop (this most probably also applies to ACEDB 3.3),
I wanted to add a lot of classes to ACEDB, so I had to leave out
some of the old ones.  Since I needed a contiguous space of class
numbers I had to recompile.  But which user-defined classes are
needed by the code?

All classes used in ACEDB source code:
perl -ne '/(_V\w+)/ && print $1,"\n"' w?/*.c w?/*.h | sort | uniq

Then I form the intersection with the classes in the 
orginal classes.wrm file.

The tags file I keep, because many tags are used and
new tags are cheap.

The options.wrm is adapted to classes.wrm

Thus having minimal {classes,tags,options}.wrm files
for compiling, I use the "newspec" script from Otto that
auguments the {classes,tags,options}.wrm with everything
necessary for the current models.wrm

I append all classes, options and newspec files, so you can use them.
tags.wrm is from the distribution.
Detlef

-----------------------------------------------------------
-----------------------------------------------------------
/* minimal version Fri Aug 26 12:10:40 WET DST 1994  dok256 */
  /* wspec/classes.wrm
     
     This file is read at compile and at execution time.

     It holds the enumaration of the application dependent classes.
     Classes necessary to the kernel are defined in a second file 
     wspec/sysclasses.wrm, which should not be touched except in
     consultation with us.

     You can add new classes at will, but if you suppress one or 
     renumber it, you must recompile and reconstruct the database 
     from ace files.

     Class properties, formerly defined in this file, are
     now in wspec/options.wrm.  If there is no entry there then
     classes are type B (tree), hidden, with display method TREE.

     Each #define line corresponds to a class. We require strlen(name) < 32.
     There must be no repetitions of class numbers.
     The total number of classes cannot exceed 255.
     The total number of display types cannot exceed 64.
     
     For now we allocate 0-100 for system classes
			 101-199 for application classes
			 200-255 for subtypes 
	The subytypes will not need class numbers when the ?Model
	class works fully.
  */

/* def  _VClass_name  Class_number */

#define _V2_point_data 101
#define _VAllele 102
#define _VChrom_Band 103
#define _VClone 104
#define _VClone_Grid 105
#define _VContig 106
#define _VDNA 107
#define _VDf_Dup_data 108
#define _VGene_Class 109
#define _VInterval 110
#define _VLocus 111
#define _VMap 112
#define _VMethod 113
#define _VMotif 114
#define _VMultiMap 115
#define _VMulti_pt_data 116
#define _VPaper 117
#define _VPeptide 118
#define _VPool 119
#define _VProbe 120
#define _VRestriction 121
#define _VSequence 122
#define _VgMap 123
#define _VpMap 124
#define _VvMap 125

/*  --------- end of needed classes ----------- */


-----------------------------------------------------------
/* minimal version Fri Aug 26 12:10:40 WET DST 1994  dok256 */
  /* wspec/options.wrm
     
     This file is read only at execution time

     It holds the class definitions necessary to the applications.
     The kernel classes are defined in  wspec/sysoptions.wrm
     which can serve as a model when editing this one.

     You can freely edit this file without recompiling
     but it must remain consistent with the other wspec files
     and you must never change the type (A, B, X) of a class
     unless you reconstruct the database from ace files.

     Line starting with _VClassName are parsed, they are expected
     to contain a la Unix a set of -Option parameters.
     Class names must match their enumeration in wspec/classes.wrm
	
     The order in which classes appear here will be used in displays.
	
     Options names can be abbreviated, recognized options are
     -Hidden    : this class will not be listed in the acedb Main Window.
     -Visible   : this class will be listed in the acedb Main Window.
     -Array     : this class is of type A, (Array or tuple).
     -Btree     : this class is of type B, it must be further defined in models.wrm
     -XREF      : Auto cross referencing Hidden B system class. Do not use.
     -Display  displayType : The preferred display type of the class,
		             as enumerated in wspec/disptype.wrm
     -Title  Tag : Tag must be a tag name listed in wspec/tags.wrm (or systags)
	           If present in some object of that class, the text following it
                   will be used preferentially when referring to that object.
     -Symbol Tag : Tag must be a tag name listed in wspec/tags.wrm (or systags)
	           If present in some object of that class, the text
		   or key following it will be used preferentially
                   when referring to that object in Maps.
     -Rename otherName : Other name will show in lists, old and new
                         name will be recognized in ace files and queries, old
                         is used in the code. In case some newName
			 matches some old name, the new name takes precedence.
     -CaseSensitive : The names in this class will be case sensitive.
                      Never undo this option once it has been used.
     -Sybase : Experimental external storage in sybase.
     -Known : Prevents indirect creation of new object in ace files
              You can't enter a new object in this class directly
              but not by quoting it in another object.

     Classes default as -B -H -D TREE
     A classes further default as -H -D ZERO


     Displays:
	Every display type needs a display function.
     Parsers:
        Special code must be provided for A Classes
     Dumps:
        Special code must be provided to dump A classes
     
     These routines must be registered in file wspec/quovadis.h before
     recompilation.
  */


// _VAA                -A -H  
_VChrom_Band      -V  -D VMAP
_VClone          -V -D PMAP
_VContig             -V -D PMAP
_VDNA                 -A -V -D FMAP
// _VFragment -V -D VMAP
// _VGDB_id    -V -Protected
_VLocus            -V -D VMAP 
_VMap     -V -D VMAP  
_VMotif    -V 
_VMultiMap -V -D DtMULTIMAP
_VPaper           -V -T Title 
_VProbe            -V -T Name
// _VSTS -V -D VMAP
_VSequence       -V -D FMAP      -T  Title 
// _VYAC   -V -D DtPmapFingerprint
_VgMap		     -A -H -D GMAP
_VpMap		     -A -H -D PMAP
_VvMap		     -A -H -D VMAP

/* ------------ minimal version ends here ----------------- */




-----------------------------------------------------------
#!/usr/local/bin/gawk -f 
#          ^
#          use nawk or gawk, but NOT awk 
#
# filename: newspec
# by Otto Ritter, DKFZ, Germany [o.ritter at dkfz-heidelberg.de] 
#    created     Nov  3 93
#    last modif  Apr 23 94 SGI
# purpose; parse models.wrm and generate new {tags|classes|options}
# syntax: setenv ACEDB <dirpath>; newspec 
#         -- no command line arguments
# Fri Aug 26 12:49:58 WET DST 1994  dok256  -- classes are no tags
########################################################################

BEGIN { 

### check the environment & backup some files
if ( ENVIRON["ACEDB"] == "") { 
   print "newspec error:: ACEDB variable not defined." ; exit 1 }
path = ( ENVIRON["ACEDB"] "/wspec/" )
print "echo newspec :: " path "models.wrm"

if ( system("cd " path  "; \cp tags.wrm tags.wrm.bak") != 0 ) { 
   print "newspec error:: cannot backup tags.wrn" ; exit 1 }
if ( system("cd " path  "; \cp  classes.wrm classes.wrm.bak") != 0 ) { 
   print "newspec error:: cannot backup classes.wrn" ; exit 1 }

### now we are working in $ACEDB/wspec
      logfile = path "newspec.log"

### parse sys files first
      print "// newspec.log\n" > logfile

       ff = (path "sysclass.wrm")
       while ((getline < ff ) >0) 
             if ($1=="#define") class[tolower($2)] = $2;
       close(ff); 

       ff = (path "classes.wrm")
       while ((getline < ff ) >0) 
              if ($1=="#define"){ if (tolower($2) in class) { 
                 printf "## warning: %s both in sysclass.wrm and classes.wrm ", tolower($2) ;} 
              else class[tolower($2)] = $2; ClassNr =$3+1; } 
       close(ff); 

       ff = (path "systags.wrm")
       while ((getline < ff ) >0) 
             if ($1=="#define")   tag[tolower($2)] = $2;
       close(ff); 

       ff = (path "tags.wrm")
       while ((getline < ff ) >0) 
              if ($1=="#define") {  if (tolower($2) in tag ) {
                 printf "## warning: %s both in systags.wrm and tags.wrm", tolower(tg); }
              else tag[tolower($2)] = $2; TagNr = $3+1; }
       close(ff); 

       ff = (path "options.wrm")
       while ((getline < ff ) >0) 
             if (substr($1,1,2) =="_V") in_options[$1] = 1;
       close(ff); 

if (ClassNr < 110 ) ClassNr =  110
if (  TagNr < 1000) TagNr   = 1000


### parse models.wrm
ff = (path "models.wrm")
while ((getline < ff ) > 0 ){ 
    gsub("#","?"); 
    gsub(/\/\/.*$/,""); 
    gsub(/@.*$/,""); 
    for (i=1;i<=NF;i++) {
        if (substr($i,1,1) == "?" ) {  # classname
              cl = "_V" substr($i,2) ; 
        if (tolower(cl) in class) { 
              if ( class[tolower(cl)] != cl ) print "## warning: case mismatch ", cl, class[tolower(cl)]  ;  }
        else {class[tolower(cl)] = cl; 
              print ("#define",cl,ClassNr++) >> (path "classes.wrm"); 
              newclass = newclass SUBSEP cl;}
        if (!(cl in in_options) && !(cl in newoptions)) {print cl " -V" >> "options.wrm"; newoptions[cl] = ++nopt; };
        continue;  # detlef thinks classes are no tags
      } # classname
        tg = "_" $i;                  # tag name
        gsub(/\?/,"",tg);
        if ( tolower(tg) in tag ) { 
              if ( tag[tolower(tg)] != tg ) print "case mismatch ", tg, tag[tolower(tg)] ; }
        else { tag[tolower(tg)] = tg; 
               print ("#define",tg,TagNr++) >> (path "tags.wrm"); 
               newtag = newtag SUBSEP tg; }
     }#for
} #while 
close(ff); 

### generate report 
{ 
  
  ncl = split(newclass,arr,SUBSEP);
  print "======== added classes ======" > logfile 
  for ( x in arr ) print arr[x] > logfile 

  ntg = split(newtag,arr,SUBSEP);
  print "\n======== added tags  =========" > logfile 
  for ( x in arr ) print arr[x] > logfile 

  print "\n======== added options ======" > logfile 
  for (x in newoptions) print x, "-V" > logfile

  printf "## newspec added:\n%i to %s\n%i to %s\n%i to %s\nsee the logfile %s\n\n", ncl,"classess.wrm",\
          ntg, "tags.wrm", nopt,"options.wrm",  logfile  ; 

} 

exit 0

}#BEGIN  


{} # empty main





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