BioLegato - PCD - Language Requirements

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Look and feel

Sanity checking

Before a program is run, there need to be checks to make sure that the input given is reasonable and sufficient for running the job that has been requested. Where these criteria are not met, bioLegato should have defaults to fall back upon, and/or should abort the job, giving the user messages that describe in a meaningful way the reasons for aborting.

Sanity checking can be done internally when the "Run" button is clicked.

Sanity Checking Language

This can be accomplished by a conditions section; however, we will need the following language elements to perform the sanity checking properly:

  1. basic arithmetic: + - * /
  2. precedence: ( and ) or.... we could do polish notation
  3. comparisons: <, >, and =
  4. boolean operations: & and |

API errors

  1. file and directory permissions
    • file not found
    • directory not readable
    • permissions
  2. blank strings - forced separated (parameter: nonblank)

Conditional/Dependent variables

Changing one menu item variable can affect the display of other menu items.

Examples of implementation:

  1. greying out
  2. hiding
  3. changing the parameters based on other variables

Example of the usefulness for conditional/dependent variables: This can be useful in programs like numseq. If translation is yes, then we need:

  • reading frames
  • aa code
  • genetic code

otherwise those three items can be greyed out

Possible ideas



bioLegato can be a front end to the Seahawk API


Everything is a text document. Display the Seahawk text area in the bioLegato canvas.


Seahawk API goes to MOBY central and gets meta data about thousands of web services. That could be translated into PCD, and then directly made into menus. One thing we might do is to cache metadata, rather than getting it on the fly each time the user right-clicks.

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