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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
points:

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

http://probe.nalusda.gov:8000/acedocs/models/models.html

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. 


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