fern.tools

Class NetworkTools

java.lang.Object

fern.tools.NetworkTools

public class NetworkTools
extends Object

Contains various helper methods dealing with the Network interface.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
NetworkTools()

Method Summary

Modifier and Type	Method and Description
static boolean	areEqual(Network a, Network b) Gets whether or not the two given networks contain the same species, the same reactions and yield the same propensities when the amounts of each reactant are respectively 1, 5, 10, 100.
static void	dumpMathTree(MathTree tree) Dumps the MathTree to stdout.
static void	dumpMathTree(MathTree tree, Writer writer) Dumps the math tree to the given Writer.
static void	dumpNetwork(Network net) Dumps the network to stdout.
static void	dumpNetwork(Network net, Writer writer) Dumps the network to the given Writer.
static double	getConstantBySettingReactantsToStoich(Network net, int r) Gets the reaction rate constant by setting the reactant amounts to the stoichiometric coefficient.
static String[]	getReactionNames(Network net, int[] reaction) Transforms the reaction indices in the given array to the corresponding names.
static String	getReactionNameWithAmounts(Network net, int... reactions) Gets a string representation of the given reactions and the amounts of each participating species in parentheses.
static int[]	getReactionsOf(Network net, String[] speciesName) Gets the reaction whose products / reactants are in speciesName
static int[]	getSpeciesIndices(Network net, String[] speciesName) Transforms the species names in the given array to the corresponding indices.
static String[]	getSpeciesNames(Network net, int[] species) Transforms the species indices in the given array to the corresponding names.
static String	getSpeciesNameWithAmount(Network net, int... species) Gets the species names together with its actual amount in parentheses
static Network	loadNetwork(File file) Loads a network from file identifying the type (FernML/SBML).
static void	useActualAmountAsInitialAmount(Network net) Copies the actual amount of the species in the network to its initial amount.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NetworkTools

public NetworkTools()

Method Detail

getConstantBySettingReactantsToStoich

public static double getConstantBySettingReactantsToStoich(Network net,
                                                           int r)

Gets the reaction rate constant by setting the reactant amounts to the stoichiometric coefficient.

Parameters:

net - network

r - reaction index

Returns:

reaction rate constant

areEqual

public static boolean areEqual(Network a,
                               Network b)

Gets whether or not the two given networks contain the same species, the same reactions and yield the same propensities when the amounts of each reactant are respectively 1, 5, 10, 100.

Parameters:

a - first network

b - first network

Returns:

whether or not a and b are equal

loadNetwork

public static Network loadNetwork(File file)
                           throws IOException,
                                  org.jdom.JDOMException,
                                  FeatureNotSupportedException,
                                  ClassNotFoundException

Loads a network from file identifying the type (FernML/SBML).

Parameters:

file - network file

Returns:

network object

Throws:

org.jdom.JDOMException

IOException

FeatureNotSupportedException

ClassNotFoundException

getSpeciesNameWithAmount

public static String getSpeciesNameWithAmount(Network net,
                                              int... species)

Gets the species names together with its actual amount in parentheses

Parameters:

net - network

species - species indices

Returns:

species name with amount

getReactionNameWithAmounts

public static String getReactionNameWithAmounts(Network net,
                                                int... reactions)

Gets a string representation of the given reactions and the amounts of each participating species in parentheses.

Parameters:

net - network

reactions - reaction indices

Returns:

reaction string representation with amounts of participating species

getReactionNames

public static String[] getReactionNames(Network net,
                                        int[] reaction)

Transforms the reaction indices in the given array to the corresponding names.

Parameters:

net - the network

reaction - reaction indices

Returns:

names of the reactions

getSpeciesNames

public static String[] getSpeciesNames(Network net,
                                       int[] species)

Transforms the species indices in the given array to the corresponding names.

Parameters:

net - the network

species - species indices

Returns:

names of the species

getSpeciesIndices

public static int[] getSpeciesIndices(Network net,
                                      String[] speciesName)

Transforms the species names in the given array to the corresponding indices.

Parameters:

net - the network

speciesName - species names

Returns:

indices of the species

getReactionsOf

public static int[] getReactionsOf(Network net,
                                   String[] speciesName)

Gets the reaction whose products / reactants are in speciesName

Parameters:

net - network

speciesName - names of species

Returns:

reaction indices

dumpNetwork

public static void dumpNetwork(Network net)

Dumps the network to stdout.

Parameters:

net - network

dumpNetwork

public static void dumpNetwork(Network net,
                               Writer writer)
                        throws IOException

Dumps the network to the given Writer.

Parameters:

net - network

Throws:

IOException

dumpMathTree

public static void dumpMathTree(MathTree tree)

Dumps the MathTree to stdout.

Parameters:

tree - mathtree

dumpMathTree

public static void dumpMathTree(MathTree tree,
                                Writer writer)
                         throws IOException

Dumps the math tree to the given Writer.

Parameters:

tree - mathtree

Throws:

IOException

useActualAmountAsInitialAmount

public static void useActualAmountAsInitialAmount(Network net)

Copies the actual amount of the species in the network to its initial amount.

Parameters:

net - network.