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[Scott Christley <schristley AT mac.com>]

Thanks, I ended up changing the two conditional rules which use a contains() 
operator that checks for existence, and yes I intend to use search to explore 
alternative possibilities.  After experimenting I answered the question 
myself, it would appear that a general non-conditional rule does match.

If you are interested, here is the code I have.  After loading the maude 
file, do a rewrite:

rewrite altMucusModel .

you will get the result:

rewrite in MUCUS_MODEL : altMucusModel .
rewrites: 11 in 0ms cpu (0ms real) (11000000 rewrites/second)
result specification: spec(BKR(emptyStatement), MS(NM(variable(muc2-mRNA), 
ODE(hillFunction(variable(muc2-gene)) linearFunction(variable(muc2-mRNA))))))

So the thing to note is ODE() which contains two terms.  This is the result 
that I want, one term from a [transcribe] rule and another term from a 
[decay] rule.

If you look in the MAPPING system module, you will see the rules for 
[transcribe] and [decay].  If you comment out the two conditional rules, then 
uncomment the two non-conditional rules, this is the answer from the rewrite:

rewrite in MUCUS_MODEL : altMucusModel .
rewrites: 4 in 0ms cpu (0ms real) (4000000 rewrites/second)
result specification: spec(BKR(emptyStatement), MS(NM(variable(muc2-mRNA), 
ODE(hillFunction(variable(muc2-gene))))
        NM(variable(muc2-mRNA), ODE(linearFunction(variable(muc2-mRNA))))))

Which is not what I want, because it creates two separate ODE() sections, not 
a combined one.

thanks
Scott

Attachment: biomodel.maude
Description: Binary data

On Feb 7, 2011, at 2:15 PM, Steven Eker wrote:

> WIthout the signature, it's hard to know what you are trying to do or what 
> a 
> given pattern will match. Always post complete modules.
> 
> If you are just manipulating data in a functional way (instead of changing 
> state with alternative possibilities that might have to be explored using 
> search or model checking) you are much better off using equations - they 
> are 
> _much_ faster and allow common subexpression evaluation (with rules, common 
> subexpressions might evaluate differently in each occurrence).
> 
> Steven
> 
> On Monday 07 February 2011 10:32:03 am Scott Christley wrote:
>> Hello,
>> 
>> I'm writing some rules where I want to add items to a "list" of things.  In
>> the case of when the "list" is empty then I want to create the list (kind
>> of like an initial condition or tail-end of recursion).  Otherwise when
>> the list is already there then I just want to add to it.  So I'm writing
>> two rules, one non-conditional rule for when the list is not there, and
>> another conditional rule for when the list is there.  But I'm worried that
>> one rule (the non-conditional rule) is too general and always matches.
>> 
>> For example I have these two rules, where I match a "foo" in the first
>> part, then I add "bar" to a list of results for "foo".  The first
>> non-conditional rule creates the first "result" while the second
>> conditional rule adds "bar" to the existing list of results.
>> 
>> 
>> rl [test] : test( X foo, answers(Y) )
>>   => test( X, answers(Y result(foo, bar)) ) .
>> 
>> 
>> crl [test] : test( X foo, answers(Y result(Z, W)) )
>>    => test( X, answers(Y result(Z, add(W, bar))) )
>>    if Z = foo .
>> 
>> 
>> 
>> My concern is that it seems that the non-conditional rule will always
>> match.  Is this true?  Or will a conditional rule which matches always
>> override a more general rule?
>> 
>> What is the correct way to write such rules?  I can think of one change by
>> changing the non-conditional rule into a conditional rule that checks for
>> non-existence, something like this:
>> 
>> 
>> crl [test] : test( X foo, answers(Y) )
>>    => test( X, answers(Y result(foo, bar)) ) .
>>    if not(contains(foo, Y)) .
>> 
>> 
>> thanks
>> Scott
>> 
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