[Biojava-l] Anotatable Symbol

[Mike Jones]

I think the interface idea sounds good but doesn't that seem like a lot of extra
classes if you
would make one for each property type. I would need at least 2 for residue
masses
(mon and iso topic masses). Maybe it could be more generic like:



public interface SymbolProperty {
  FiniteAlphabet getAlphabet();
  Object getValue(Symbol s, String type) throws IllegalSymbolException, throws
UnknownTypeException;
}

Also why would I want to return a FiniteAlphabet for each SymbolProperty?

I would like to get a better look at the AlphabetIndex
source. Since I am behind a pretty serious fire wall here I can't use cvs to get
the latest source.
Do you have a zipped archive containing the code.

Matthew Pocock wrote:

> Hi Mike.
>
> There are several ways to do this without breaking anything we have at the
> moment. Firstly, you could add a method to ProteinTools
>
> double getResidueMass(Symbol s) throws IllegalSymbolException
>
> You could store the mass information in a format similar to
> resources/org/biojava/bio/seq/TranslationTables.xml (which is loaded by
> RNATools). The proplem with this is that you would have many
> getResidueMassByBla methods. Alternatively, you could write a new interface
> like this:
>
> public interface SymbolProperty {
>   FiniteAlphabet getAlphabet();
>   double getValue(Symbol s) throws IllegalSymbolException;
> }
>
> You could then have ProteinTools provide several well-known versions - mass,
> charge, size etc. and load the data from a SymbolProperty.xml resource. It
> also leaves the door open to things like DNA physical properties.
>
> Another way to do this is to add the data to AlphabetManager.xml directly.
> You would have to modify the DTD so that the description element could have
> <key type="java.lang.String">mass<value
> type="java.lang.Double">90.3</value></key> style children, and then extend
> the symbolForXML code to handle this. The description elements should
> probably move to being <key type="java.lang.String"><value
> type="java.lang.String">The description goes in here</value></key>
>
> My money is on the interface option, as it lets you plug in new physical
> properties without having to have access to AlphabetManager.xml, including
> parameterising algorithms at run-time - TranslationTables ended up being
> great for this. The down-side for heavily computational algorithms is that
> you will have to perform some type of search within the implementations to
> find the value associated with a symbol. The issue of how to optimaly
> implement this search is nicely solved with the AlphabetIndex interface
> (just in), so it may not be that bad in practice. I have a feeling that the
> overhead of finding a particular key within an annotation bundle will be
> higher than the cost of looking up a double based upon the amino-acid, as
> hash-codes have to be calculated, and lots of functions and members are
> fetched to traverse the hash table.
>
> What do other people think?
>
> Mike Jones wrote:
>
> > I am starting to work on a package for biojava that can be used for MS
> > experimental data. Initially for proteins. So I need a way to annotate
> > amino acids with their atomic mass. I would appreciate the help of those
> > who have done such things. Can I just modify the AlphabetManager.xml.
> > Say add a new Alphabet
> >
> > I would rather not rewrite each symbol but if I were this is how it
> > would look.
> > <alphabet name="RESIDUE_MASS" parent="PROTEIN">
> >     <symbol name="s">
> >             <short>S</short>
> >             <long>SER</long>
> >             <mono-mass>87.03203</mono-mass>
> >             <avg-mass>87.0782</avg-mass>
> >     </symbol>
> >
> > ...
> >
> > To do this though I imagine I would have to modify
> > AlphabetManager.symbolFromXML.
> >
> > Please let me know if I am missing something or if any body has any
> > ideas.
> >
> > _______________________________________________
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>
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