- eigenvalueDecomposition(double[], int) - Method in class massbalance.MetabolicGraph
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Calculates the full eigenvalue spectrum with double precision using the Fortran method dgeev.
- eigenvalueDecomposition(float[], int) - Method in class massbalance.MetabolicGraph
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Calculates the full eigenvalue spectrum with float precision using the Fortran method sgeev.
- eigenvectorDouble(double[], int, double, boolean) - Method in class massbalance.MetabolicGraph
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Calculates the eigenvector corresponding to the largest eigenvalue of A using the
Fortran routines dnaupd and dgemv.
- eigenvectorFloat(float[], int, double, boolean) - Method in class massbalance.MetabolicGraph
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Calculates the eigenvector corresponding to the largest eigenvalue of A using the
Fortran routines snaupd and sgemv.
- equationSubstitutions(MetabolicGraph, HashMap<ArrayList<Integer>, EquivalenceClass>, HashSet<Vertex>, String, boolean) - Method in class massbalance.MetabolicGraph
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Writes each possible single and pair substitution of the reaction equations
of the original network to tab-separated files.
- Equivalence - Class in massbalance
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Class for generating, reading, and writing the mass equivalence classes required for mass balanced
randomization.
- Equivalence() - Constructor for class massbalance.Equivalence
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- EquivalenceClass - Class in massbalance
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Class representing the mass equivalence classes used for mass-balanced randomization.
- EquivalenceClass() - Constructor for class massbalance.EquivalenceClass
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Creates a new, empty equivalence class.
- EquivalenceClass(String, int[]) - Constructor for class massbalance.EquivalenceClass
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Creates a new equivalence class containing one compound with the given name and mass.
- EquivalenceClass(String, int[], String, int[]) - Constructor for class massbalance.EquivalenceClass
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Creates a new equivalence class containing a pair of compounds with the given names and masses.