definition_parser
The model definition parser object “DefinitionParser” instantiates Models and Genes objects from XML model definitions (see Macromolecular models). The parsing consists in three phases.
Phase 1.
For each model to parse
create the Model
add this Model to the model_bank
findall genes defined in this model what are the level in the model definition.
create the CoreGene (a Gene which is not bind to a model). For each gene name there is only one instance of CoreGene
add these CoreGene in the gene_bank
Phase 2.
For each model to search
For each Gene defined in this System:
link the gene to the model. Create a ModelGene by encapsulating CoreGene from the gene_bank It can exists at each run several ModelGene for one CoreGene
If a gene has exhangeables create them (an Exchangeable inherits from ModeleGene) and add them to the current ModelGene
For instance:
Syst_1
<system inter_gene_max_space="10">
<gene name=”A” mandatory=”1” loner="1">
<exchangeables>
<gene name=”B”>
</exchangeables>
</gene>
<system>
Syst_2
<system inter_gene_max_space="15">
<gene name=”B” mandatory=”1”>
<exchangeables>
<gene name=”C”>
</exchangeables>
</gene>
<system>
Syst_3
<system inter_gene_max_space="20">
<gene name=”c” mandatory=”1” />
<system>
With the example above:
the CoreGene A, B, C will be created
the ModelGene (Syst_1, A) (Syst_1, B), (Syst_2, B), (Syst_2, C), (Syst_3, C)
The ModeleGene (Syst_1, A), (Syst_2, B) and (Syst_3, C) are directly link to their respective Models
and where (Syst_1, B) (Syst_2, C) are exchangeables and link respectively to (Syst_1, A) and (Syst_2, B)
the ModelGene has attributes defined in the model where they appear (Syst_1, B) inter_gene_max_space=”10” (Syst_2, B) inter_gene_max_space=”15”
Note
The only “full” Systems (i.e., with all corresponding Genes created) are those to detect.
