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" <[EMAIL PROTECTED]> 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 > > > > ======================================================================= > Attention: The information contained in this message > and/or attachments > from AgResearch Limited is intended only for the > persons or entities > to which it is addressed and may contain > confidential and/or privileged > material. Any review, retransmission, dissemination > or other use of, or > taking of any action in reliance upon, this > information by persons or > entities other than the intended recipients is > prohibited by AgResearch > Limited. If you have received this message in error, > please notify the > sender immediately. > ======================================================================= > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
