- gcd(long[]) - Static method in class massbalance.Utilities
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Calculates the greatest common divisor the given values.
- getCompartment() - Method in class massbalance.Vertex
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Returns the compartment of the compound vertex.
- getCompartments(Vertex) - Method in class massbalance.MetabolicGraph
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Returns the map of compartment strings and the substrates/products of the reaction which belong to
the compartment.
- getCompartments() - Method in class massbalance.MetabolicGraph
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Returns a map of compartment strings and vertex sets.
- getCompound(String, String) - Method in class massbalance.MetabolicGraph
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Returns the compound vertex with the specified name and compartment.
- getCompounds() - Method in class massbalance.MetabolicGraph
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Returns an immutable collection of the compound vertices.
- getDeltaGDifference(Vertex, int, Vertex, Vertex, int[]) - Method in class massbalance.MetabolicGraph
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Calculates the difference in deltaG of the reaction after substituting compound
by substitute on the given side, without modifying the network.
- getDeltaGDifference(Vertex, int, Vertex, Vertex, Vertex, Vertex, int[]) - Method in class massbalance.MetabolicGraph
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Calculates the difference in deltaG of the reaction after substituting compound1
and compound1 by substitute1 and substitute2 on the given side.
- getDeltaGf() - Method in class massbalance.Vertex
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Returns the deltaGf of a compound.
- getDeltaGn() - Method in class massbalance.MetabolicGraph
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Calculates the sum of deltaGr over all reactions.
- getDeltaGr(Vertex, boolean) - Method in class massbalance.MetabolicGraph
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Calculates the deltaGr of a reaction by summing over the negative deltaGf of
substrates and the positive deltaGf of products, multiplied by the stoichiometric
coefficients.
- getDoubleMass(int) - Method in class massbalance.EquivalenceClass
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Returns the double mass vector at the given index.
- getDoubleName(int) - Method in class massbalance.EquivalenceClass
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Returns the double compound name at the given index.
- getExplicitDoubleMasses() - Method in class massbalance.EquivalenceClass
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Returns the set of all explicit double compound masses in the class.
- getExplicitDoubleNames() - Method in class massbalance.EquivalenceClass
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Returns the set of all explicit double compound names in the class.
- getMass(int) - Method in class massbalance.EquivalenceClass
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Returns the single mass vector at the given index.
- getMass() - Method in class massbalance.Vertex
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Returns the mass vector (sum formula) of the compound vertex.
- getMasses(HashMap<ArrayList<Integer>, EquivalenceClass>) - Static method in class massbalance.Equivalence
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Extracts the compound names and masses from the equivalence classes and returns them
in a hash map.
- getMasses() - Method in class massbalance.EquivalenceClass
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Returns the set of all single compound masses in the class.
- getName(int) - Method in class massbalance.EquivalenceClass
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Returns the single compound name at the given index.
- getName() - Method in class massbalance.Vertex
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- getNames() - Method in class massbalance.EquivalenceClass
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Returns the set of all single compound names in the class.
- getPairs() - Method in class massbalance.EquivalenceClass
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Returns a hash map of all pairs of compound names and masses in the class,
including the implicit pairs from single compound equivalences.
- getReaction(String) - Method in class massbalance.MetabolicGraph
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Returns the reaction vertex with the specified name.
- getReactionEquation(MetabolicGraph, Vertex) - Method in class massbalance.MetabolicGraph
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Returns the equation of the given reaction in the given graph as String.
- getReactionNames() - Method in class massbalance.MetabolicGraph
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Returns the set of reactions names in the graph.
- getReactions() - Method in class massbalance.MetabolicGraph
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Returns an immutable collection of the reaction vertices.
- getRxnLocation() - Method in class massbalance.Vertex
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Gets the reaction location.
- getTransitionDegree(HashMap<ArrayList<Integer>, EquivalenceClass>, HashSet<Vertex>) - Method in class massbalance.MetabolicGraph
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Calculates the number of possible substitutions for all reactions, i.e., the
degree of the node representing this graph in the transition graph Sigma_G.
- getType() - Method in class massbalance.Vertex
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Returns the type of the vertex: either Vertex.COMPOUND or Vertex.REACTION.