- randomize(MetabolicGraph, HashMap<ArrayList<Integer>, EquivalenceClass>, HashSet<Vertex>, float, boolean, float, String, String, boolean, String) - Method in class massbalance.MetabolicGraph
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Performs mass balanced randomization on the graph by perturbing single compounds and pairs.
- Randomize - Class in massbalance
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Main class for randomizing a MetabolicGraph using the pre-calculated mass equivalence classes.
- Randomize() - Constructor for class massbalance.Randomize
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- randomScopeSizes(int[], String, String, boolean) - Method in class massbalance.MetabolicGraph
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Calculates random scopes for the given seed sizes and writes the scope sizes of each seed size
to a separate file.
- reachable(ArrayList<String>, ArrayList<String>, MetabolicGraph) - Static method in class massbalance.Utilities
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- reactionCentralities(MetabolicGraph, double, boolean, boolean) - Method in class massbalance.MetabolicGraph
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Calculates the global propagation of the local reaction centralities.
- reactionDegrees(String, boolean) - Method in class massbalance.MetabolicGraph
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Prints a tab-separated list of reaction in-degrees and reaction out-degrees.
- readClasses(String) - Static method in class massbalance.Equivalence
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Reads the equivalence classes from the classesFile and creates a hash map of the normalized mass vector as key
and the EquivalenceClass as value.
- readDeltaG(String, String) - Method in class massbalance.MetabolicGraph
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Reads the deltaGf of compounds from a tab-separated file and stores the values
with the compound vertices.
- removeEdge(Vertex, Vertex) - Method in class massbalance.MetabolicGraph
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Removes the edge connecting source and target.
- removeEdge(DefaultWeightedEdge) - Method in class massbalance.MetabolicGraph
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Removes the edge.
- removeVertex(Vertex) - Method in class massbalance.MetabolicGraph
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Removes the vertex from the graph and removes the entry from the
compounds or reactions HashMap.
- reversedReaction() - Method in class massbalance.Vertex
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Returns the reversed part of a reversible reaction vertex.
- run() - Method in class massbalance.Properties
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- run() - Method in class massbalance.Randomize
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Runs the randomization.