- actionPerformed(ActionEvent) - Method in class massbalance.JMassBalance
-
Event handling for this ActionListener.
- addAllCompounds(ArrayList<String>, ArrayList<int[]>) - Method in class massbalance.EquivalenceClass
-
Adds a set of compounds and their corresponding mass vectors
to the mass equivalence class.
- addAllPairs(ArrayList<String>, ArrayList<int[]>) - Method in class massbalance.EquivalenceClass
-
Adds a set of compound pairs and their corresponding mass vectors
to the mass equivalence class.
- addCompound(String, int[]) - Method in class massbalance.EquivalenceClass
-
Adds a compound name and its mass to the mass equivalence class.
- addEdge(Vertex, Vertex) - Method in class massbalance.MetabolicGraph
-
Adds an edge to connect source and target.
- addEdge(Vertex, Vertex, DefaultWeightedEdge) - Method in class massbalance.MetabolicGraph
-
Adds the edge to connect source and target.
- addPair(String, int[], String, int[]) - Method in class massbalance.EquivalenceClass
-
Adds a pair of compound names and masses to the mass equivalence class.
- addVertex(Vertex) - Method in class massbalance.MetabolicGraph
-
Adds the vertex to the graph and creates an entry in the compounds or
reactions HashMap.
- adjacencyMatrix(String) - Method in class massbalance.MetabolicGraph
-
Deprecated.
- appendColumns(String, String, String, int) - Static method in class massbalance.Utilities
-
Appends the tab-separated tokens from each line in inputFile2 to the corresponding
lines in inputFile1 and prints the resulting lines to outputFile.
- appendDeltaG(String, String, String, int) - Static method in class massbalance.Utilities
-
Searches the compounds from compoundsFile in the databaseFile by case-insensitive name and sum formula,
and prints the compounds with deltaG to outputFile.
- appendDeltaGFromKEGG(String, String, String) - Static method in class massbalance.Utilities
-
Searches a KEGG ID in compoundsFile, matches the compound in databaseFile and appends
the deltaG and uncertainties to the compounds in outputFile.
- appendFile(String, String) - Static method in class massbalance.Utilities
-
Appends the content from inputFile to the end of outputFile.
- appendFiles(String, int, String) - Static method in class massbalance.Utilities
-
Appends the content from inputFile and the next numberOfFiles-1 inputFiles with
successive index numbers to the end of outputFile.
- assortativities() - Method in class massbalance.MetabolicGraph
-
Calculates two assortativity coefficients on the directed MM-network: the pearson
correlation coefficient of (1) the compound in-degrees and the average in-degrees of
predecessors, (2) the compound out-degrees and the average out-degrees of successors.
- assortativities_old() - Method in class massbalance.MetabolicGraph
-
Deprecated.
- averageReactionDegree() - Method in class massbalance.MetabolicGraph
-
Determines the average reaction degree, i.e., the average of the
in-degrees plus the out-degrees.
- avgClassSizes(String) - Static method in class massbalance.Utilities
-
Prints the number of single and double mass equivalence classes and their average sizes.