sbrt.shell.proc.fba
Class PalssonRxnNodeParser

java.lang.Object
  extended by sbrt.shell.proc.fba.PalssonRxnNodeParser

public class PalssonRxnNodeParser
extends java.lang.Object

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.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Field Summary
static java.lang.String RXN_NODE_NAME
          The name of the nodes parsed by this class ('reaction').
 
Constructor Summary
PalssonRxnNodeParser()
          Constructs a new SBML reaction node parser.
 
Method Summary
 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

RXN_NODE_NAME

public static final java.lang.String RXN_NODE_NAME
The name of the nodes parsed by this class ('reaction').

See Also:
Constant Field Values
Constructor Detail

PalssonRxnNodeParser

public PalssonRxnNodeParser()
Constructs a new SBML reaction node parser.

Method Detail

getRxnId

public java.lang.String getRxnId(org.w3c.dom.Node reactionNode)
Returns the reaction ID of the provided reaction node.

Parameters:
reactionNode - the reaction node whose ID is to be returned.
Returns:
the reaction ID of the provided reaction node.

getFluxBounds

public Interval getFluxBounds(org.w3c.dom.Node reactionNode)
Returns the flux bounds of the provided reaction node.

Parameters:
reactionNode - the reaction node whose flux bounds are to be returned.
Returns:
the flux bounds of the provided reaction node.

getLowerBound

public double getLowerBound(org.w3c.dom.Node reactionNode)
Returns the lower flux bound of the provided reaction node.

Parameters:
reactionNode - the reaction node whose lower flux bound is to be returned.
Returns:
the lower flux bound of the provided reaction node.

getUpperBound

public double getUpperBound(org.w3c.dom.Node reactionNode)
Returns the upper flux bound of the provided reaction node.

Parameters:
reactionNode - the reaction node whose upper flux bound is to be returned.
Returns:
the upper flux bound of the provided reaction node.

getFluxValue

public double getFluxValue(org.w3c.dom.Node reactionNode)
Returns the flux value of the provided reaction node.

Parameters:
reactionNode - the reaction node whose flux value are to be returned.
Returns:
the flux value of the provided reaction node.

getReactants

public LinearComb<java.lang.String> getReactants(org.w3c.dom.Node reactionNode)
Returns the reactants of the provided reaction node.

Parameters:
reactionNode - the reaction node whose reactants are to be returned.
Returns:
the reactants of the provided reaction node.

getProducts

public LinearComb<java.lang.String> getProducts(org.w3c.dom.Node reactionNode)
Returns the products of the provided reaction node.

Parameters:
reactionNode - the reaction node whose products are to be returned.
Returns:
the products of the provided reaction node.

isReversible

public boolean isReversible(org.w3c.dom.Node reactionNode)
Indicates if the reaction in the provided reaction node is reversible.

Parameters:
reactionNode - the reaction node whose reversibility is to be determined.
Returns:
true if the reaction node indicates a reversible reaction; false if the reaction node indicates an irreversible reaction.

getGenes

public Or<And<java.lang.String>> getGenes(org.w3c.dom.Node reactionNode)
Calls getCatalysts(Node, String) with "GENE_ASSOCIATION:" as the prefix.

Parameters:
reactionNode - the reaction node for which the genes are to be returned.
Returns:
the boolean logic rules for the genes of the provided reaction node.

getProteins

public Or<And<java.lang.String>> getProteins(org.w3c.dom.Node reactionNode)
Calls getCatalysts(Node, String) with "PROTEIN_ASSOCIATION:" as the prefix.

Parameters:
reactionNode - the reaction node for which the proteins are to be returned.
Returns:
the boolean logic rules for the proteins of the provided reaction node.

getCatalysts

public 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.

Parameters:
reactionNode - the reaction node for which the catalysts are to be returned.
prefix - the string used to denote these catalysts in the SBML file.
Returns:
the boolean logic rules for the catalysts of the provided reaction node.