- main(String[]) - Static method in class massbalance.Equivalence
-
Parses the mass vectors and generates the mass equivalence classes
from the given files.
- main(String[]) - Static method in class massbalance.JMassBalance
-
GUI main application.
- main(String[]) - Static method in class massbalance.Properties
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Method for calculating graph properties.
- main(String[]) - Static method in class massbalance.Randomize
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Main method called from the command line.
- main(String[]) - Static method in class massbalance.Utilities
-
The main method can be used to call the public methods of this class
directly from the command line by executing
java -jar massbalance.jar utilities [method] [args...]
- massbalance - package massbalance
-
- massMatrix(String, boolean) - Method in class massbalance.MetabolicGraph
-
Prints a m x n matrix containing the mass vectors of the compounds in the network,
where m is the number of compounds, and n the number of considered atomic elements
(specified as ELEMENTS in the configuration file).
- matchStrings(String, String, String, double) - Static method in class massbalance.Utilities
-
- matrixSubstitutions(HashMap<ArrayList<Integer>, EquivalenceClass>, HashSet<Vertex>, String, boolean, boolean) - Method in class massbalance.MetabolicGraph
-
Writes each possible single and pair substitution of the stoichiometric matrix
of the original network to tab-separated files.
- maxDoubleClass(String) - Static method in class massbalance.Utilities
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Prints the largest pair equivalence class, including implicit pairs.
- maxExplicitDoubleClass(String) - Static method in class massbalance.Utilities
-
Prints the largest pair equivalence class, excluding implicit pairs.
- maxReactionDegree() - Method in class massbalance.MetabolicGraph
-
Returns the maximum undirected degree of a reaction in the network.
- maxReactionInDegree() - Method in class massbalance.MetabolicGraph
-
Returns the maximum in-degree of a reaction in the network.
- maxReactionOutDegree() - Method in class massbalance.MetabolicGraph
-
Returns the maximum out-degree of a reaction in the network.
- maxSingleClass(String) - Static method in class massbalance.Utilities
-
Prints the largest single equivalence class.
- MetabolicGraph - Class in massbalance
-
Objects of this class represent a metabolic network as a directed weighted bipartite graph.
- MetabolicGraph(boolean, boolean) - Constructor for class massbalance.MetabolicGraph
-
Creates an empty MetabolicGraph, a SimpleDirectedWeightedGraph.
- MetabolicGraph(String, int, boolean, boolean) - Constructor for class massbalance.MetabolicGraph
-
Creates a MetabolicGraph using numberOfCompounds as initial compounds hash capacity.