model syntax:

Danielle et Jean Thierry-Mieg mieg at kaa.crbm.cnrs-mop.fr
Sat Feb 3 10:51:48 EST 1996


3 sort of problems were reported:

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1) Model error: non-tag ?Journal in column in model ?Paper

//------------------------------------------------------------------
?Journal Paper ?Paper XREF Journal

//------------------------------------------------------------------
?Paper   Reference Title UNIQUE ?Text
                   Journal UNIQUE ?Journal XREF Paper
                                  Unpublished
 
Journal does, in fact appear as a tag in tags.wrm.

###########################################################################

First of all, tags.wrm can be removed before constructing
a new database,
the file must stay if the database was constructed before 3.3
but really this does not apply to ace4 databases

also the construction:

  Journal UNIQUE ?Journal XREF Paper
                                  Unpublished
is not legal
in a given column one should not mix up tags and class objects

the corerect model should say

?Paper Reference Title UNIQUE ?Text
                 J UNIQUE  Journal ?Journal XREF Paper
                           Unpublished

in fact it is closer to real life


###########################################################################

2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample
//------------------------------------------------------------------
?DNA_Sample Genomic ?Species Strain Text
            
###########################################################################

This is indeed illegal
only basic or constructed types may appear to the right of a pointer


you should say

?DNA_Sample Genomic ?Species #St

#St Strain Text

or you can have

?DNA_Sample Genomic ?Species ?Strain

###########################################################################
3) Model error: In model ?Library, tag Paper XREF's to tag Library
             in class ?Paper
             can't find tag Library in model ?Paper

//------------------------------------------------------------------
?Library  Name Text // Full name
          Description ?Text // Description of material included
          Laboratory ?Laboratory
          Author ?Author
          Paper ?Paper XREF Library
          Experiment ?Experiment XREF Library REPEAT
          Donor_Species ?Species
                        Strain Text
          Library_Type UNIQUE cDNA
                              Genomic UNIQUE sheared
                                             Restriction_Enzyme Text
          Vector ?Vector
                 Restriction_Site Text Text
          Host_Strain ?Bacterial_Stock


very true: you are trying to XREF to a non existing tag
this is clearly a bug


#####################################

The fatsest way to edit the models is to open emacs
edit the models file

and in a separate window to start tace and issue the command
read_model

this is much better for that task than using xace

####################################

ace 4 models support DateType , look in the session object to see
the date foramt

correect dates are for example

now
today
1996
1992-01-25
1995-01-25_18:11:37

..

in addition the coming 4.2 supports COORD modificator inside 
sequence models to indicate numbers which may slide when an 
insertion is made

say i insert a base in 200
then internally the code will edit every COORD > 200 to
increase by 1

there is no esxternal interface yet for this thing but it
is used by our sequence manipulation tools

Jean




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