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java.lang.Objectsbrt.shell.text.fba.PalssonRxnNodeParser
public class PalssonRxnNodeParser
This class is used to make a direct translation from SBML 'reaction' nodes into Systems Biology Research Tool objects. The names of reactions or chemical species are not checked or processed in any way during this translation. This class works for SBML files downloaded directly from Palsson's website.
Field Summary | |
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static java.lang.String |
RXN_NODE_NAME
The name of the nodes parsed by this class ('reaction'). |
Constructor Summary | |
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PalssonRxnNodeParser()
Constructs a new SBML reaction node parser. |
Method Summary | |
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Or<And<java.lang.String>> |
getCatalysts(org.w3c.dom.Node reactionNode,
java.lang.String prefix)
Returns the boolean logic rules for the catalysts of the provided reaction node. |
Interval |
getFluxBounds(org.w3c.dom.Node reactionNode)
Returns the flux bounds of the provided reaction node. |
double |
getFluxValue(org.w3c.dom.Node reactionNode)
Returns the flux value of the provided reaction node. |
Or<And<java.lang.String>> |
getGenes(org.w3c.dom.Node reactionNode)
Calls getCatalysts(Node, String) with " GENE_ASSOCIATION: "
as the prefix . |
double |
getLowerBound(org.w3c.dom.Node reactionNode)
Returns the lower flux bound of the provided reaction node. |
LinearComb<java.lang.String> |
getProducts(org.w3c.dom.Node reactionNode)
Returns the products of the provided reaction node. |
Or<And<java.lang.String>> |
getProteins(org.w3c.dom.Node reactionNode)
Calls getCatalysts(Node, String) with " PROTEIN_ASSOCIATION: "
as the prefix . |
LinearComb<java.lang.String> |
getReactants(org.w3c.dom.Node reactionNode)
Returns the reactants of the provided reaction node. |
java.lang.String |
getRxnId(org.w3c.dom.Node reactionNode)
Returns the reaction ID of the provided reaction node. |
double |
getUpperBound(org.w3c.dom.Node reactionNode)
Returns the upper flux bound of the provided reaction node. |
boolean |
isReversible(org.w3c.dom.Node reactionNode)
Indicates if the reaction in the provided reaction node is reversible. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String RXN_NODE_NAME
Constructor Detail |
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public PalssonRxnNodeParser()
Method Detail |
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public java.lang.String getRxnId(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose ID is to be returned.
public Interval getFluxBounds(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose flux bounds are to be returned.
public double getLowerBound(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose lower flux bound is to be returned.
public double getUpperBound(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose upper flux bound is to be returned.
public double getFluxValue(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose flux value are to be returned.
public LinearComb<java.lang.String> getReactants(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose reactants are to be returned.
public LinearComb<java.lang.String> getProducts(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose products are to be returned.
public boolean isReversible(org.w3c.dom.Node reactionNode)
reactionNode
- the reaction node whose reversibility is to be determined.
true
if the reaction node indicates a reversible reaction;
false
if the reaction node indicates an irreversible reaction.public Or<And<java.lang.String>> getGenes(org.w3c.dom.Node reactionNode)
GENE_ASSOCIATION:
"
as the prefix
.
reactionNode
- the reaction node for which the genes are to be returned.
public Or<And<java.lang.String>> getProteins(org.w3c.dom.Node reactionNode)
PROTEIN_ASSOCIATION:
"
as the prefix
.
reactionNode
- the reaction node for which the proteins are to be returned.
public Or<And<java.lang.String>> getCatalysts(org.w3c.dom.Node reactionNode, java.lang.String prefix)
reactionNode
- the reaction node for which the catalysts are to be returned.prefix
- the string used to denote these catalysts in the SBML file.
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