public class GPRParser
extends java.lang.Object
GeneProductAssociation
used in SBML level 3.
The conversion modify directly the arguments so clone them beforehand if needed. The SBML level is not changed so
that's also something that need to be done before calling the method parseGPR(Reaction, String, boolean)
Constructor | Description |
---|---|
GPRParser() |
Modifier and Type | Method | Description |
---|---|---|
static GeneProductAssociation |
parseGPR(Reaction r,
java.lang.String geneReactionRule,
boolean omitGenericTerms) |
Parses a gene association string as used in COBRA in SBML level 2 into a
GeneProductAssociation
used in SBML level 3. |
static GeneProductAssociation |
parseGPR(Reaction r,
java.lang.String geneReactionRule,
boolean omitGenericTerms,
boolean displayWarning) |
Parses a gene association string as used in COBRA in SBML level 2 into a
GeneProductAssociation
used in SBML level 3. |
public static GeneProductAssociation parseGPR(Reaction r, java.lang.String geneReactionRule, boolean omitGenericTerms)
GeneProductAssociation
used in SBML level 3.r
- the Reaction
geneReactionRule
- the gene associationomitGenericTerms
- boolean to indicate if we should set SBO term for the operators and and or.GeneProductAssociation
instance representing the given gene association string.public static GeneProductAssociation parseGPR(Reaction r, java.lang.String geneReactionRule, boolean omitGenericTerms, boolean displayWarning)
GeneProductAssociation
used in SBML level 3.r
- the Reaction
geneReactionRule
- the gene associationomitGenericTerms
- boolean to indicate if we should set SBO term for the operators and and or.displayWarning
- boolean to indicates if we should display a warning to the user
when a GeneProduct
is not found for the given identifierGeneProductAssociation
instance representing the given gene association string.