- parseArgs(String[]) - Method in class massbalance.Properties
-
- parseArgs(String[]) - Method in class massbalance.Randomize
-
- parseCoefficient(String) - Static method in class massbalance.Utilities
-
Parses a string and returns the stoichiometric coefficient, or -1 if
the string is not a stoichiometric coefficient, i.e., a double number
enclosed by DELIMITER_COEFFICIENT_START and DELIMITER_COEFFICIENT_END.
- parseInChIString(String, String, BufferedWriter) - Static method in class massbalance.Utilities
-
Parses an InChI string and returns an int[ELEMENTS.length] containing the mass vector.
- parseMass(String, BufferedWriter) - Static method in class massbalance.Utilities
-
Parses a string of format CXHYNZ..., where C,H,N are chemical elements followed by the
number of atoms X,Y,Z.
- parseTokens(String, String, boolean) - Static method in class massbalance.Utilities
-
Parses the input string and returns a list of tokens separated by delimiter.
- predecessorsOf(Vertex) - Method in class massbalance.MetabolicGraph
-
Returns the set containing all second predecessor vertices.
- printCoefficients(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints the stoichiometric coefficients of the given graph,
i.e., its edge weights.
- printCompartmentInfo(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints the number of compounds, reactions, and transporters associated with each compartment.
- printCompoundIndices(MetabolicGraph, ArrayList<String>) - Static method in class massbalance.Utilities
-
Prints the indices in the sorted lists of compounds from the given compounds list.
- printDeadEnds(MetabolicGraph, String) - Static method in class massbalance.Utilities
-
- printEquivalenceClass(String, String) - Static method in class massbalance.Utilities
-
Prints the equivalence classes in which the given compound is contained.
- printExampleReactions(String) - Static method in class massbalance.Utilities
-
Prints some example reactions of the graph with in- and out-degree smaller than 4.
- printExternalCompoundIndices(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints the sorted stoichiometric matrix indices of all compounds in a compartment
starting with "ext", "ex", or "e".
- printHubCompounds(MetabolicGraph, int) - Static method in class massbalance.Utilities
-
Prints the number of compounds given by number with largest degree.
- printLargeCoefficients(MetabolicGraph, int) - Static method in class massbalance.Utilities
-
Print all reactions in the given graph that have a coefficient at least as large as min.
- printMappedIndices(MetabolicGraph, String, String) - Static method in class massbalance.Utilities
-
Maps the compound names given in indexFile to the pair of corresponding names given in mappingFile,
and prints the indices of the mapped compounds in the sorted stoichiometric matrix.
- printMass(MetabolicGraph, String) - Static method in class massbalance.Utilities
-
- printMasses(String, String, String) - Static method in class massbalance.Utilities
-
Print all compounds with masses and the largest integer factorization.
- printMaxCoefficient(MetabolicGraph) - Static method in class massbalance.Utilities
-
Searches for the largest coefficient in the network and prints the
corresponding reaction.
- printMaxDeltaGr(MetabolicGraph, boolean, boolean) - Static method in class massbalance.Utilities
-
Searches for the largest deltaGr in the network and prints the
corresponding reaction.
- printPathway(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints a particular type of pathway, if present:
A -> B+D
B+D -> C
where D is a cofactor (has a large degree), and B not.
- printReaction(MetabolicGraph, Vertex, boolean, boolean) - Static method in class massbalance.Utilities
-
Prints the equation of the given reaction.
- printReaction(MetabolicGraph, String, boolean, boolean) - Static method in class massbalance.Utilities
-
Prints the reaction equation from the given graph.
- printReactionIndices(MetabolicGraph, ArrayList<String>) - Static method in class massbalance.Utilities
-
Prints the indices in the sorted lists of reactions from the given reaction list.
- printReactions(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints all reaction equations of the given graph.
- printReactions(MetabolicGraph, ArrayList<String>) - Static method in class massbalance.Utilities
-
Prints the reaction equations from the given graph.
- printSmallDegreeReactions(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints all reactions with in-degree+out-degree < 3 in the graph.
- printTCACycleReactions(MetabolicGraph) - Static method in class massbalance.Utilities
-
Prints reactions containing TCA cycle intermediaries from ecoli, satisfying
additional conditions.
- Properties - Class in massbalance
-
Class for parsing, graph creation and calculating properties of randomized networks.
- Properties() - Constructor for class massbalance.Properties
-