Maude-help mailing list

[Scott Christley <schristley AT mac.com>]

Hello,

I recently downloaded Maude, read through the tutorial and  documentation, 
and am trying to write some modules.  I wanted to do a  simple biological 
example for DNA transcription to RNA; a tricky part  is that DNA and RNA 
share the bases A, C, and G but DNA has T while  RNA has U.  So I created a 
module for nucleotides:

fmod nucleic is
 sorts Nucleotide .

 ops A C G : -> Nucleotide .
endfm


Then I wanted sequences of DNA and RNA to be lists so that I could  easily 
concatenate bases, e.g. (A T G T C C) for DNA or (A U G U C C)  for RNA.  I 
want Maude to recognize one as DNASequence and the other  as RNASequence thus 
not allow U's in DNA nor allow T's in RNA.  So I  defined these modules:


fmod DNA is
 protecting nucleic .
 sorts DNANucleotide .
 subsort Nucleotide < DNANucleotide .

 op T : -> DNANucleotide .
endfm

view DNA from TRIV to DNA is
 sort Elt to DNANucleotide .
endv

fmod DNASequence is
 protecting LIST{DNA} * (sort NeList{DNA} to DNASequence) .
endfm


fmod RNA is
 protecting nucleic .
 sorts RNANucleotide .
 subsort Nucleotide < RNANucleotide .

 op U : -> RNANucleotide .
endfm

view RNA from TRIV to RNA is
 sort Elt to RNANucleotide .
endv

fmod RNASequence is
 protecting LIST{RNA} * (sort NeList{RNA} to RNASequence) .
endfm


Lastly I make a module which is the transcription machinery, and  there is 
where the problem comes in.


fmod transcription is
 protecting DNASequence .
 protecting RNASequence .

 op translate : DNASequence -> RNASequence .

 var aSequence : DNASequence .

 eq translate(A) = A .
 eq translate(C) = C .
 eq translate(G) = G .
 eq translate(T) = U .
 eq translate(A aSequence) = A translate(aSequence) .
 eq translate(C aSequence) = C translate(aSequence) .
 eq translate(G aSequence) = G translate(aSequence) .
 eq translate(T aSequence) = U translate(aSequence) .
endfm


When I load up this module, I get advisories:


Advisory: "transcription.maude", line 7 (fmod transcription):  operator nil 
has
   been imported from both "prelude.maude", line 939 (fmod LIST) and
   "prelude.maude", line 939 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator __ has
   been imported from both "prelude.maude", line 940 (fmod LIST) and
   "prelude.maude", line 940 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator append
   has been imported from both "prelude.maude", line 948 (fmod  LIST) and
   "prelude.maude", line 948 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator head 
has
   been imported from both "prelude.maude", line 953 (fmod LIST) and
   "prelude.maude", line 953 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator tail 
has
   been imported from both "prelude.maude", line 956 (fmod LIST) and
   "prelude.maude", line 956 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator last 
has
   been imported from both "prelude.maude", line 959 (fmod LIST) and
   "prelude.maude", line 959 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator front
   has been imported from both "prelude.maude", line 962 (fmod  LIST) and
   "prelude.maude", line 962 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator occurs
   has been imported from both "prelude.maude", line 965 (fmod  LIST) and
   "prelude.maude", line 965 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator 
reverse
   has been imported from both "prelude.maude", line 969 (fmod  LIST) and
   "prelude.maude", line 969 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator 
$reverse
   has been imported from both "prelude.maude", line 973 (fmod  LIST) and
   "prelude.maude", line 973 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator size 
has
   been imported from both "prelude.maude", line 977 (fmod LIST) and
   "prelude.maude", line 977 (fmod LIST) with no common ancestor.
Advisory: "transcription.maude", line 7 (fmod transcription):  operator $size
   has been imported from both "prelude.maude", line 981 (fmod  LIST) and
   "prelude.maude", line 981 (fmod LIST) with no common ancestor.


And the reduce doesn't work:

reduce in transcription : translate(A T G T C C) .

Warning: sort declarations for constant nil do not have an unique  least sort.
reduce in transcription : translate(A T G T C C) .
rewrites: 0 in 0ms cpu (0ms real) (~ rewrites/second)
result [EmDNASequence,EmRNASequence,NucleotideSequence]: translate(A  T G T C 
C)



Can anybody tell me what I'm doing wrong?

thanks
Scott