> This starts to show the limitations of Schematron/XSLT. There are
> actually 3 stop codon sequences so the description is either verbose
> or nested or impossible.

Oops, typo

   <pattern is-a="DNAStopCodon" >
      <param name="CodonName" value="'UAA'"/>
      <param name="DNAString" value=" DNASequence " />
      <param name="CodonPath"
             value="U[following-sibling::A[following-sibling::A]]"/>
   </pattern>

   <pattern is-a="DNAStopCodon" >
      <param name="CodonName" value="'UGA'"/>
      <param name="DNAString" value=" DNASequence " />
      <param name="CodonPath"
             value="U[following-sibling::G[following-sibling::A]]"/>
   </pattern>

   <pattern is-a="DNAStopCodon" >
      <param name="CodonName" value="'UAG'"/>
      <param name="DNAString" value=" DNASequence " />
      <param name="CodonPath"
             value="U[following-sibling::A[following-sibling::G]]"/>
   </pattern>


> So I would like to be able to call a function like:
> DNAPROG.isStopCodon(...)

Oh, its just an example. You could certain have

     <rule
context="DNASequence/U[following-sibling::A[following-sibling::G or
following-sibling::A] or
following-sibling::G[following-sibling::A]]">
        <assert test=" something "> ....

with no abstract patterns, at the expense of losing declarative labels
(which has the side-effect of verbosity, cannot be helped.)

Cheers
Rick Jelliffe