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Blixem_X in the ?Method

Brian Fristensky frist at cc.umanitoba.ca
Fri Jun 4 11:17:30 EST 1999

"laminaria.EST" wrote:
> Brian Fristensky wrote :
> Whoa -- I guess I missed something. What is a ?Method object, and
> can these be defined within ACeDB or Blixem? Where are ?Method
> objects documented?
> ---------------------------------
> Hello
> What I have understood is that ?Method object correspond to the display definition. Following is a copy of the ?Method as defined in the ACEDB 4_7g model. I do not know where it is documented. If somebody knows, I am interested.
> ?Method Remark ?Text
>           // the Display information controls how the column looks.
>         Display Colour #Colour
>                 Frame_sensitive
>                 Strand_sensitive Show_up_strand #Colour
>                 Score   Score_by_offset // has priority over width, for Jean
>                         Score_by_width
>                         Score_by_histogram UNIQUE Float // baseline value
>                         Score_bounds UNIQUE Float UNIQUE Float
>                                 // limits for squashing
>                         Percent // '%' in text, + default bounds 25, 100
>                 Overlap_mode UNIQUE     Overlap           // draw on top - default
>                                         Bumpable          // bump to avoid overlap
>                                         Cluster           // one column per homol target
>                 Width UNIQUE Float
>                 Symbol UNIQUE Text      // first char only is used
>                 Right_priority UNIQUE Float // the greater the more right
>                 Max_mag UNIQUE Float    // don't show if more bases per line
>                 Min_mag UNIQUE Float    // don't show if fewer bases per line
>                 Show_text      // only put text in right-hand column if set
>         Blastn          // can calculate percent from score if blastn
>         Blixem  Blixem_X
>                 Blixem_N
>                 Blixem_P
>         Belvu
>         EMBL_dump EMBL_feature UNIQUE Text              // require this
>                   EMBL_threshold UNIQUE Float           // apply to score unless overridden
>                   EMBL_qualifier Text UNIQUE Text
>           // if 1 Text, it is the entire qualifier including '/'
>           // if 2 Texts, 1st is an sprintf format and 2nd is
>           //   an argument.  If this is "score", "note", "y1", "y2" or "target"
>           //   then use the corresponding field of the Feature or Homol line.
>           // multiple formats will be concatenated until one starts with '/'.
>         Gene_assemble   Gene_assemble_method ?Method UNIQUE Float
>                                 // Float factor to multiply score by
>                         Intron_min UNIQUE Int
>                         Exon_min UNIQUE Int
>                         Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
>                                 // base cost, cost per log bp beyond min
>                                 // Int is min for this if not Intron_min
>                         Inter_gene_cost UNIQUE Float
>         GF_parameters   GF_range UNIQUE Int
>                                 // +- range for genefinder feature calculation
>                         GF_ATG_cutoff UNIQUE Float
>                         GF_5_cutoff UNIQUE Float
>                         GF_3_cutoff UNIQUE Float
>         GFF     GFF_source UNIQUE Text
>                 GFF_feature UNIQUE Text
>         EMBL_dump_info #EMBL_dump_info // when used for controlling dump

So, this object, whose name is Method, is used for displaying output
from various
programs such as BLAST, BLIXEM, GENEFINDER etc. This raises several new

1. I get the feeling that I still don't have the entire story on
For example, in the ACeDB models.wrm file listed at


has a very different object called ?Models, so I guess that
the above object definition is specific to a particular
ACeDB-based database.

Nonetheless, this definition seems to imply that output from
various programs is being displayed by ACeDB. Presumably,
that is done by Pick_me_to_call from some other object?
Or is there a mechanism for xace to display the output?

2. At the risk of being impertinent, in my humble opinion,
it is not a good idea to call an object by the name "Method",
because the word "method" has a very precise, and important
meaning in Object-Oriented Programming.

3. On that subject, here is a probably naive question.
As an idea for the future evolution of ACeDB, is it
plausible for objects to have methods, in the OOP
sense? This could be implemented in a very limited
way, much along the lines of how 'Pick_me_to_call'
is implemented now. That is, as a way for calling
external programs, or displaying files or output from 
programs. Is it possible to get even more sophisticated,
such as interfacing with CORBA objects and their methods?
I don't think we want to see xace itself become
bloatware. Rather, I like the idea of being able to
use external objects and methods to extend functionality,
in a manner analogous to how GDE can run most types
of sequence analysis programs. 

Brian Fristensky                |  Original entry for Microsoft Windows, 
Department of Plant Science     |  in the Hitchiker's Guide to
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Winnipeg, MB R3T 2N2  CANADA    |  
frist at cc.umanitoba.ca           |  After the release of Windows NT, this
Office phone:   204-474-6085    |  was changed to "Mostly harmless".
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