Enum Class ModelField
- All Implemented Interfaces:
Serializable,Comparable<ModelField>,Constable
For more information about COBRA model fields, see the following
Supplementary
Material.
-
Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>> -
Enum Constant Summary
Enum ConstantsEnum ConstantDescriptionMatrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;Can be part of thedescription.The bound vector of metabolite concentration change rates (usually but not always all zero, i.e., steady-state): S ⋅ v = b.Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;The objective function vector for max(c' ⋅ v) for corresponding reactions.Literature references for the reactions.TODOThese are human-readable notes for reactions.Confidence score for each reaction.The csense field expresses equality constraints in the model.Human-redable information about the model, e.g., the model name.The "disabled" field comes from the reconstruction tool rBioNet.The Enzyme Commission codes for the reactions.Can be part of thedescription.Can be part of thedescription.The list of all genes in the model, where each contained gene corresponds to aAbstractSBase.getId().Can be part of thedescription.Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR).Lower reaction flux bounds for corresponding reactionsValue of charge for corresponding metabolite.Optional: if present, it must have same dimension asmets.Elemental formula for each metabolite.Optional: if present, it must have same dimension asmets.Inichi String for each corresponding metabolite.KEGG ID for each corresponding metabolite.Descriptive metabolite names, must have same dimension asmets.Pub Chem ID for each corresponding metabolite.Metabolite name abbreviation; metabolite ID; order corresponds to S matrix.Optional: if present, it must have same dimension asmets.Can be part of thedescription.Can be part of thedescription.Can be part of thedescription.Objective sense, i.e., to minimize or maximize the objective.Proteins associated with each reaction.A vector consisting of zeros and ones that translate to binary and determine if the corresponding reaction of that index is reversible (1) or not (0).Boolean rule for the corresponding reaction which defines gene-reaction relationship.TODO: description COGCell array of strings, can any value in a range of 0 to 4..E.A matrix with rows corresponding to reaction list and columns corresponding to gene list.Reaction identifiers in KEGG, but sometimes also containsecNumbers.TODO: description KEGG OrthologyDescriptive reaction names, length of this array must be identical to the number of reactions.Cell array of strings.Cell array of strings which can contain optional information on references for each specific reaction.Reaction BiGG ids.The Systems Biology Ontology Term to describe the role of a reaction.Stoichiometric matrix in sparse format.This defines groups of reactions that belong to a common reaction subsystem.Upper reaction flux bounds for corresponding reactions -
Method Summary
Modifier and TypeMethodDescriptiongetCorrectName(String query) Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be matchedgetNameForPrefix(String query) Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct field as prefix of knwon model fieldstatic ModelFieldReturns the enum constant of this class with the specified name.static ModelField[]values()Returns an array containing the constants of this enum class, in the order they are declared.
-
Enum Constant Details
-
A
Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;- See Also:
-
author
Can be part of thedescription. -
b
The bound vector of metabolite concentration change rates (usually but not always all zero, i.e., steady-state): S ⋅ v = b. Must have same dimension asmets.The mat files where the b vector isn't zero include constraints that couple the flux through the model's reactions to the BOF. These are mat files joining reconstructions of two or more species. These constraints are represented in the b and A fields.
If this cannot be expressed in SBML, then an error message would be appropriate. The SBML file would probably not result in a functional joined model though.
Data type: double array. Length must be identical to the number of reactions.
-
B
Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;- See Also:
-
c
The objective function vector for max(c' ⋅ v) for corresponding reactions. The dimension of this element must be identical to the number of reactions. Dimensions that have a zero value in this field, do not contribute to the objective function.Data type: double array. Corresponds to
FluxObjective.getCoefficient(). -
citations
Literature references for the reactions. -
coefficients
TODO -
comments
These are human-readable notes for reactions. -
confidenceScores
Confidence score for each reaction. Confidence scores must have the same dimension as the reactions. These are an optional input, but it provides additional information on the reaction content. Adding them as notes would be a good idea. -
csense
The csense field expresses equality constraints in the model. If this field is not defin object.getType();ed in the reconstruction, equality constraints are assumed when performing the optimization. Its value is aStringwhose length must equal the number of metabolites. An 'E' at index i means that in this dimension S ⋅ v = b (equality), 'G' means ≥ greater than or equal to and an 'L' denotes ≤.- See Also:
-
description
Human-redable information about the model, e.g., the model name. This field can optionally have sub-entries. -
disabled
The "disabled" field comes from the reconstruction tool rBioNet. The tool offers the option to disable certain reactions. If no reactions are disabled, then the "disabled" field in empty. -
ecNumbers
The Enzyme Commission codes for the reactions. Length must be identical to the number of reactions. -
genedate
Can be part of thedescription. -
geneindex
Can be part of thedescription. -
genes
The list of all genes in the model, where each contained gene corresponds to aAbstractSBase.getId(). Data type: cell array of string. -
genesource
Can be part of thedescription. -
grRules
Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR). Data type: cell array of strings. Example:(8639.1) or (26.1) or (314.2) or (314.1). Dimensions must be identical to the number of reactions. Corresponds toGeneProductAssociation -
lb
Lower reaction flux bounds for corresponding reactions -
metCharge
Value of charge for corresponding metabolite. Must have same dimension asmets. Data type: double array. For SBML Level < 3, it corresponds toSpecies.getCharge(). Since Level 3, it corresponds toFBCSpeciesPlugin.getCharge(). -
metCHEBIID
Optional: if present, it must have same dimension asmets. Data type: cell array of strings. Corresponds to the annotation ofSpecies -
metFormulas
Elemental formula for each metabolite. This must have same dimension asmets. Datatype: cell array of strings. Corresponds toFBCSpeciesPlugin.getChemicalFormula(). -
metHMDB
Optional: if present, it must have same dimension asmets. Data type: cell array of strings. -
metInchiString
Inichi String for each corresponding metabolite. Optional: if present, it must have same dimension asmets. Data type: cell array of strings. -
metKeggID
KEGG ID for each corresponding metabolite. Optional: if present, it must have same dimension asmets. Data type: cell array of strings. -
metNames
Descriptive metabolite names, must have same dimension asmets. Datatype: cell array of strings. Corresponds toAbstractSBase.getName() -
metPubChemID
Pub Chem ID for each corresponding metabolite. Optional: if present, it must have same dimension asmets. Data type: cell array of strings. -
mets
Metabolite name abbreviation; metabolite ID; order corresponds to S matrix. Metabolite BiGG ids (incl. compartment code). Data type: cell array of strings. Corresponds toAbstractSBase.getId(). -
metSmile
Optional: if present, it must have same dimension asmets. -
name
Can be part of thedescription. -
notes
Can be part of thedescription. -
organism
Can be part of thedescription. -
osense
Objective sense, i.e., to minimize or maximize the objective. This field can either be defined in the mat file itself or when performing an optimization function (e.g., optimizeCbModel). -
proteins
Proteins associated with each reaction. -
rev
A vector consisting of zeros and ones that translate to binary and determine if the corresponding reaction of that index is reversible (1) or not (0). Dimensions must be equal to the number of reactions. Corresponds to the valueReaction.isReversible() -
rules
Boolean rule for the corresponding reaction which defines gene-reaction relationship. -
rxnCOG
TODO: description COG -
rxnConfidenceEcoIDA
Cell array of strings, can any value in a range of 0 to 4. Length must be equal to the number of reactions. -
rxnConfidenceScores
. -
rxnsboTerm
The Systems Biology Ontology Term to describe the role of a reaction. Length must be identical to the number of reactions. Value corresponds to the attributeAbstractSBase.getSBOTerm() -
rxnGeneMat
A matrix with rows corresponding to reaction list and columns corresponding to gene list. Data type: sparse double. Size of this matrix must be number of reactions times number of genes. No counterpart in FBC v2. -
rxnKeggID
Reaction identifiers in KEGG, but sometimes also containsecNumbers. Length must be identical to the number of reactions. Entries belong to the annotation ofReaction. -
rxnNames
Descriptive reaction names, length of this array must be identical to the number of reactions. Data type: cell array of string. Corresponds to the name of aReaction. -
rxnKeggOrthology
TODO: description KEGG Orthology -
rxnECNumbers
E. C. number for each reaction- See Also:
-
rxnReferences
Cell array of strings which can contain optional information on references for each specific reaction. Example:'Na coupled transport of pyruvate, lactate, and short chain fatty acids, i.e., acetate, propionate, and butyrate mediated by SMCT1
-
rxns
Reaction BiGG ids. Corresponds to the id ofReaction. Reaction name abbreviation; reaction ID; order corresponds to S matrix. -
rxnNotes
Cell array of strings. Text notes (description) about reactions. Length must be identical to the number of reactions. -
S
Stoichiometric matrix in sparse format. -
subSystems
This defines groups of reactions that belong to a common reaction subsystem. Their number must hence be identical to the reaction count. Subsystems are listed repeatedly in the source file. If present, the size of this field must be identical to the number of reactions. Data type: cell array of strings. -
ub
Upper reaction flux bounds for corresponding reactions
-
-
Method Details
-
values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
-
valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)- Parameters:
name- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException- if this enum class has no constant with the specified nameNullPointerException- if the argument is null
-
getCorrectName
Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be matched- Parameters:
query- : Possible model field, present in model struct- Returns:
- List of matching ModelField variant names
-
getNameForPrefix
Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct field as prefix of knwon model field
-