[Biojava-l] calculating properties of SymbolLists

[Matthew Pocock]

Dear Gerald,

Gerald Loeffler wrote:

> Hi!
>
> I need to calculate some properties (isoelectric point, molecular
> weight, ...) of a protein sequence (which is of course a SymbolList) and
> thought about introducing a general interface for this purpose:
>
> public interface SymbolListPropertyCalculator {
>   /**
>    * calculate a property of the given symbol list and return it as an
> Object.
>    * @param sl the symbol list whose property should be calculate (may
> not be null otherwise an
>    *           IllegalArgumentException is thrown)
>    * @return the calculated property. Never returns null.
>    * @exception BioException if calculating the property was not
> possible due to mis-usage of the
>    *                         method, e.g. because the implementation
> requires that the symbol list
>    *                         be over a specific Alphabet but sl does not
> fulfill this precondition.
>    */
>   Object calculateProperty(SymbolList sl) throws BioException;
> }
>

Under what circumstances would you return something that needed to be an
Object? The properties that you have outlined are both double values. If
this interface is to be usefull for things like GUIs or configuration
scripts, then mabey:

@throws IllegalAlphabetException  if sl is over the wrong alphabet for this
metric
@throws BioException if for any reason the metric could not be calculated
double calculateProperty(SymbolList sl) throws IllegalAlphabetException,
BioException

would be more apropreate.

>
> The one could add implementations like
>
>   MolecularWeightCalculator (returns the MW in kD as a Double)
>   IsoelectricPointCalculator (requires the symbol list to be over the
> protein alphabet, return the pI as a Double)
>
> etc.
>
> 1) is this needed or is there another way of doing it in BioJava

There is definitely going to be call for this funcitonality from the protein
people.

>
> 2) does this make sense to you
> 3) in which package should this stuff go?

I would make the interface public to org.biojava.bio.sequence. These two
implementations could become public classes in sequence, but I would prefer
intances of them to be public static final properties of ProteinTools. I may
be off the wall here :-)

Matthew

>
>
>         cheers,
>         gerald
>
> --
>    Gerald.Loeffler@vienna.at _________________ Software Architect
>    http://www.imp.univie.ac.at ____ http://www.daemonstration.com
>    OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
>
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