- characteristicPathLength() - Method in class massbalance.MetabolicGraph
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Implementation of Floyd-Warshall's algorithm for computing all shortest paths in
a directed graph.
- checkBalance(MetabolicGraph) - Static method in class massbalance.Utilities
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Determines the mass-balance of the reactions in the given graph and prints
unbalanced reactions.
- checkNetworks(String, String, String, int, int, String) - Static method in class massbalance.Utilities
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Checks certain properties of the original network and the given range of randomized networks,
e.g. the number of isolated compound nodes or the number of reactions containing a cycle.
- clone() - Method in class massbalance.MetabolicGraph
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Creates an identical copy of the graph: reversibility is copied, vertices are
copied with names, mass and reversible reactions, edges are copied with weights.
- clone() - Method in class massbalance.Vertex
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- clusteringCoefficientUndirected() - Method in class massbalance.MetabolicGraph
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Determines the undirected clustering coefficient in the corresponding
metabolite-metabolite network, i.e., the clustering coefficient in
the mm-network, where all edges are considered undirected.
- compare(MetabolicGraph) - Method in class massbalance.MetabolicGraph
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Compares this MetabolicGraph to the given MetabolicGraph.
- compare(MetabolicGraph, MetabolicGraph) - Static method in class massbalance.Properties
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Compares two graph objects for equality.
- compare(Vertex) - Method in class massbalance.Vertex
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Compares the member variables of this vertex to the member variables of the given vertex.
- compare(Vertex, Vertex) - Method in class massbalance.VertexComparator
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Compound vertices are compared their name and compartment,
reaction vertices by their name and reversibility.
- compareClasses(HashMap<ArrayList<Integer>, EquivalenceClass>, HashMap<ArrayList<Integer>, EquivalenceClass>) - Static method in class massbalance.Equivalence
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Compares two sets of equivalence classes for equality of the contained compounds.
- compareEdges(MetabolicGraph) - Method in class massbalance.MetabolicGraph
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Compares the edges of this MetabolicGraph to the edges of the given MetabolicGraph.
- compoundAliasMap(String, String, String) - Static method in class massbalance.Utilities
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Maps compound strings with their masses from 2 files: one contains the compound strings and
aliases, the other maps the aliases to sum formulas.
- compoundDeadEnds(String) - Method in class massbalance.MetabolicGraph
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Prints the dead-end compounds to a file.
- compoundDegrees(String, boolean) - Method in class massbalance.MetabolicGraph
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Prints a tab-separated list of compound degrees.
- compoundInOutDegrees(String, boolean, boolean) - Method in class massbalance.MetabolicGraph
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Prints a tab-separated list of compound in- or out-degrees.
- compoundMassesMap(String, String, String) - Static method in class massbalance.Utilities
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Maps a list of compounds from compoundsFile to a list containing compound synonyms and masses in massesFile.
- connectedComponents(boolean) - Method in class massbalance.MetabolicGraph
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Determines the sizes of all connected components in the graph by expanding
the transitive closure until every compound was visited.
- consistency(HashMap<ArrayList<Integer>, EquivalenceClass>, int, boolean) - Static method in class massbalance.Equivalence
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Performs a consistency check of the equivalence classes.
- correlation(int[], float, float[], float) - Method in class massbalance.MetabolicGraph
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Calculates the empirical pearson correlation of x and y with given
means meanX and meanY.
- countIsolatedNodes(MetabolicGraph) - Static method in class massbalance.Utilities
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Counts the number of isolated nodes in the graph, i.e. nodes with an in-degree and out-degree of 0.
- countReactions(MetabolicGraph, boolean) - Static method in class massbalance.Utilities
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Counts the number of reactions, reversible, cyclic, zero-degree reactions, and the average
and maximum reaction degrees.
- countReactionsWithCycles(MetabolicGraph) - Static method in class massbalance.Utilities
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Counts the number of reactions which contain a cycle, i.e. a substrate which is also a product.
- createBiocycGraph(String, String, String, HashMap<String, int[]>, boolean, boolean, boolean, boolean, boolean) - Static method in class massbalance.Properties
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Parses a BioCyc flat file and creates a MetabolicGraph with weights according to the stoichiometric
coefficients.
- createClasses(HashMap<String, int[]>) - Static method in class massbalance.Equivalence
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Generates the mass equivalence classes from a given map of compound names and mass vectors.
- createGraph(String, String, String, HashMap<String, int[]>, boolean, boolean, boolean, boolean, boolean) - Static method in class massbalance.Properties
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Creates a MetabolicGraph object from a tab-delimited network file.
- createGraph(String, String, boolean, boolean) - Static method in class massbalance.Utilities
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Creates a graph from the biocyc or flat file input directory and deserializes it to the output file name.
- createSBMLGraph(String, String, HashMap<String, int[]>, boolean, boolean, boolean, boolean, boolean) - Static method in class massbalance.Properties
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Parses an SBML file and creates a MetabolicGraph with weights according to the stoichiometric
coefficients. if reversible==true, for every reaction a reversed reaction is added which converts
the products into the substrates.
- cycleCount(List<Set<Vertex>>, int, boolean, boolean) - Method in class massbalance.MetabolicGraph
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Given a set of strongly connected components, returns the number of n-cycles.