Re: [sbml-arrays] Arrays and inheriting dimensions

[Sarah K. <ske...@ca...>]

So I think what got decided was:

1. A child object inherits the dimensions of its parent implicitly. This 
include listOf children that would not normally be dimensioned.

So assuming the compartment Cell and species A also have dimension '0' 
of size n
the speciesReference in the reaction below inherits dimension '0' of 
size n without the need to explicitly declare it.

       <reaction id="r" reversible="false" fast="false" compartment="Cell">
         <arrays:listOfDimensions
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
           <arrays:dimension arrays:id="d0" arrays:size="n" 
arrays:arrayDimension="0"/>
         </arrays:listOfDimensions>
         <arrays:listOfIndices
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
           <arrays:index arrays:arrayDimension="0" 
arrays:referencedAttribute="compartment">
             <math xmlns="http://www.w3.org/1998/Math/MathML">
               <ci> d0 </ci>
             </math>
           </arrays:index>
         </arrays:listOfIndices>
         <listOfReactants metaid="_msr">
           <speciesReference constant="true" species="A" 
stoichiometry="1" id="sr1">
             <arrays:listOfIndices
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
               <arrays:index arrays:referencedAttribute="species" 
arrays:arrayDimension="0">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                   <ci> d0 </ci>
                 </math>
               </arrays:index>
             </arrays:listOfIndices>
           </speciesReference>

and you would expect when flattened to get (assume n = 2)

       <reaction id="r_0" reversible="false" fast="false" 
compartment="Cell_0">
         <listOfReactants  metaid="_msr_0">
           <speciesReference constant="true" species="A_0" 
stoichiometry="1" id="sr1_0">
           </speciesReference>
...
       <reaction id="r_1" reversible="false" fast="false" 
compartment="Cell_1">
         <listOfReactants  metaid="_msr_1">
           <speciesReference constant="true" species="A_1" 
stoichiometry="1" id="sr1_1">
           </speciesReference>
...




2. If any child object adds dimensions of its own then it MUST also 
declare the inherited dimensions from the parent.

So my species reference claims to have two dimensions in the one 
dimension reaction so has to redeclare the dimension d0 that it inherits 
and then add another

       <reaction id="r" reversible="false" fast="false" compartment="Cell">
         <arrays:listOfDimensions
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
           <arrays:dimension arrays:id="d0" arrays:size="n" 
arrays:arrayDimension="0"/>
         </arrays:listOfDimensions>
         <arrays:listOfIndices
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
           <arrays:index arrays:arrayDimension="0" 
arrays:referencedAttribute="compartment">
             <math xmlns="http://www.w3.org/1998/Math/MathML">
               <ci> d0 </ci>
             </math>
           </arrays:index>
         </arrays:listOfIndices>
         <listOfReactants metaid="_msr">
           <speciesReference constant="true" species="A" 
stoichiometry="1" id="sr1">
         <arrays:listOfDimensions
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
           <arrays:dimension arrays:id="d0" arrays:size="n" 
arrays:arrayDimension="0"/>
           <arrays:dimension arrays:id="d1" arrays:size="n" 
arrays:arrayDimension="1"/>
         </arrays:listOfDimensions>
             <arrays:listOfIndices
 
xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
               <arrays:index arrays:referencedAttribute="species" 
arrays:arrayDimension="0">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                   <ci> d0 </ci>
                 </math>
               </arrays:index>
               <arrays:index arrays:referencedAttribute="id" 
arrays:arrayDimension="1">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                   <ci> d1 </ci>
                 </math>
               </arrays:index>
             </arrays:listOfIndices>
           </speciesReference>

and you would expect when flattened to get (assume n = 2) I think ????

       <reaction id="r_0" reversible="false" fast="false" 
compartment="Cell_0">
         <listOfReactants  metaid="_msr_0">
           <speciesReference constant="true" species="A_0" 
stoichiometry="1" id="sr1_0_0">
           <speciesReference constant="true" species="A_0" 
stoichiometry="1" id="sr1_0_1">
           </speciesReference>
...
       <reaction id="r_1" reversible="false" fast="false" 
compartment="Cell_1">
         <listOfReactants  metaid="_msr_1">
           <speciesReference constant="true" species="A_1" 
stoichiometry="1" id="sr1_1_0">
           <speciesReference constant="true" species="A_1" 
stoichiometry="1" id="sr1_1_1">
           </speciesReference>
...


Before I change my flattening code any more it would be great if someone 
would confirm my recollection and my interpretation :-)

Sarah