[Biojava-l] Symbol equality

[Matthew Pocock]

Hi Mark,

I don't know if there are any utility methods
available for this sort of thing. Java provides two
equivalence methods - the == operator and the
.equals() method. == checks if the two objects are
identical - do they reside in the same chunk of
memory? .equals() checks if the two objects behave the
same - have the same responses for all methods under
all circumstances. I guess comparing symbols is
another equivalence relation, but Java doesn't provide
a nice framework for plugging in equivalences.

You could look at this as a partial ordering over sets
of sequences.

A > B iff the sequence B has the same length as A, and
Ai.getSymbols().accepts(Bi), which we could write as
Ai > Bi

A == B iff A.length() == B.length() && Ai == Bi  

C = A u B iff A.length() == B.length() && Ai > Ci &&
Bi > Ci

The last one of these three comparisons says that two
sequences are in the same class iff there is at least
one sequence that is a specific case of both of them
e.g. ANY and AYN both can match to AYY.

This should all be trivial to code up. Unfortunately,
I still don't have a propper net connection. Any
takers?

Matthew

 --- "Schreiber, Mark"
<mark.schreiber@agresearch.co.nz> wrote: > Hi -
> 
> What is the best way to test for symbol equality in
> biojava.
> 
> for example one would expect that N is not
> equivalent to A, however in
> some cases it would be nice to tolerate the fact
> that sometimes N can be
> A and that A is a member of N.
> 
> So what is the best way to do a strict equality test
> ie is subsequence x
> equal to acggttg
> 
> and what is the best way to do an ambiguous equality
> test, ie is
> subsequence x a member of yynggws
> 
> thanks -
> 
> 
> Mark Schreiber
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
> 
> PH: +64 3 489 9175
> 
>  
> 
>
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