Biolegato current development

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bioLegato

This section should soon get replaced with a separate bioinformatics.org project on bioLegato.

• How should we display selections in bioLegato? First, let's eliminate graying out of the sequences when the cursor is out of the sequence window. Keep the background white at all times. We also need alternatives for telling the user what is selected:
  • active selection: white text and blue background
  • selections that are inactive: black on gray background

• Import Free Format (FSAP) - full path is used as name; should be base name.
• For programs with no GDE Help file, create a dummy help file saying that no help is available.
• Long term: New format to generate bioLegato menu items eg. PISE, EMBOSS ACD?
• Long term: biolegato probably needs an object ontology. Can we leverage the ontology used by MOBY/Seahawk?
• for the 'birch' instance of biolegato, how should bioLegato handle the File and Edit menus? That is, if these menus are excluded from the menulist file, should the also be omitted from bioLegato?

Forking bioLegato and GDE

BIRCH is now at the point where further development is limited by the need for backward compatability with GDE. We need to begin the process of forking bioLegato and GDE. GDE will continue to be distributed with BIRCH for the immediate future as an unsupported legacy application.

Nomenclature of commands for biolegato

foreach program in (bldna, blprotein, bldata, blmarker, bltree)

# ----- Convert an existing local/dat/GDE directory into a local/dat/biolegato
# ----- directory. This is only called in an update, not in a new install


if local/dat/bldna exists

     do nothing

else

   if local/dat/GDE exists

      # Make a copy of the existing GDE directory and use it to create
      # a new biolegato directory

      # Restructure the biolegato directory so that it only contains
      # the contents of the existing makemenus directory, minus the 
      # GDE-HELP-DIR-xxx-xxx etc.

What has to be done by hand:

• Change calls to gde, mgde, tgde in to calls to either bldna or blprotein, blmarker, and bltree. This must be done in both
  • .item files
  • scripts in $BIRCH/local/script
• local GDE item files will be added both to bldna and blprotein, on the theory that it is easier to remove items than to add them. It is up to each local BIRCH administrator to remove protein items from bldna and dna items from blprotein.