massbalance

Class Utilities

java.lang.Object

massbalance.Utilities

public class Utilities
extends Object

This class contains static methods for parsing compound masses, writing graph information, and merging property files.

The public methods can be called directly from the command line by executing java -jar massbalance.jar utilities [method] [args...], where method is the method name and args... are the method arguments.

The following method arguments are supported and will be translated from the given string argument:

MetabolicGraph: pass the file name of the deserialized object.
int: pass the integer argument.
String: pass the String argument.
boolean: pass 'true' or 'false'.
ArrayList<String>: pass a list of strings as ['String1','String2',...].

An overview of the available methods is printed by executing the main class without arguments.

Author:

Georg Basler

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	sbml
static org.sbml.libsbml.SBMLDocument	sbmlDocument
static String	sbmlMessage
static Throwable	sbmlThrowable

Constructor Summary

Constructors

Constructor and Description
Utilities()

Method Summary

Methods

Modifier and Type	Method and Description
static void	appendColumns(String inputFile1, String inputFile2, String outputFile, int offset) Appends the tab-separated tokens from each line in inputFile2 to the corresponding lines in inputFile1 and prints the resulting lines to outputFile.
static void	appendDeltaG(String compoundsFile, String databaseFile, String outputFile, int hydrogenTolerance) Searches the compounds from compoundsFile in the databaseFile by case-insensitive name and sum formula, and prints the compounds with deltaG to outputFile.
static void	appendDeltaGFromKEGG(String compoundsFile, String databaseFile, String outputFile) Searches a KEGG ID in compoundsFile, matches the compound in databaseFile and appends the deltaG and uncertainties to the compounds in outputFile.
static int	appendFile(String inputFile, String outputFile) Appends the content from inputFile to the end of outputFile.
static void	appendFiles(String firstInputFile, int numberOfFiles, String outputFile) Appends the content from inputFile and the next numberOfFiles-1 inputFiles with successive index numbers to the end of outputFile.
static void	avgClassSizes(String classesFile) Prints the number of single and double mass equivalence classes and their average sizes.
static long	binomialCoefficient(long n, long k) Calculates the binomial coefficient (n over k).
static void	checkBalance(MetabolicGraph graph) Determines the mass-balance of the reactions in the given graph and prints unbalanced reactions.
static void	checkNetworks(String networkName, String inputDir, String randomization, int from, int to, String outputFile) 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.
static void	compoundAliasMap(String compoundsFile, String massesFile, String outputFile) Maps compound strings with their masses from 2 files: one contains the compound strings and aliases, the other maps the aliases to sum formulas.
static void	compoundMassesMap(String compoundsFile, String massesFile, String outputFile) Maps a list of compounds from compoundsFile to a list containing compound synonyms and masses in massesFile.
static int	countIsolatedNodes(MetabolicGraph graph) Counts the number of isolated nodes in the graph, i.e. nodes with an in-degree and out-degree of 0.
static void	countReactions(MetabolicGraph graph, boolean print) Counts the number of reactions, reversible, cyclic, zero-degree reactions, and the average and maximum reaction degrees.
static void	countReactionsWithCycles(MetabolicGraph graph) Counts the number of reactions which contain a cycle, i.e. a substrate which is also a product.
static void	createGraph(String networkFile, String outputFile, boolean reversible, boolean compartments) Creates a graph from the biocyc or flat file input directory and deserializes it to the output file name.
static void	deltaGDifferences(String databaseFile, int hydrogenTolerance) Parses the sum formulas and deltaG values from the databaseFile and determines the differences in deltaGf between compounds which have an equal sum formula up to the specified hydrogenTolerance in the number of hydrogen atoms.
static void	findTransporters(MetabolicGraph graph, ArrayList<String> compoundNames, boolean exclusive) Finds and prints all transport reactions in which the given compounds are involved.
static long	gcd(long[] values) Calculates the greatest common divisor the given values.
static org.sbml.libsbml.SBMLDocument	initSBML(String sbmlFile) Checks if there is SBML support, then validates and returns the SBMLDocument.
static void	joinLines(String inputFile1, String inputFile2, String outputFile) Searches in inputFile2 for the first string of each line in inputFile1, and joins the remaining strings in outputFile.
static void	joinSimilarSynonyms(String compoundsFile, String databaseFile, String outputFile, double maxDistance, int hydrogenTolerance) Parses the compounds file for synonyms (more than one name for a compound) and searches similar synonyms with similar sum formula in databaseFile.
static void	joinSynonyms(String inputMap, String databaseFile, String outputFile, boolean caseSensitive, int minMatch, int minAdd) Parses the inputMap file for synonyms and searches all synonyms in databaseFile.
static long	lcm(int x, int y) Returns the least common integer multiple for x and y, determined by dividing x*y by the greatest common divisors.
static double	linearDependent(double[] a, double[] b) Tests a and b for linear dependence.
static void	main(String[] args) The main method can be used to call the public methods of this class directly from the command line by executing java -jar massbalance.jar utilities [method] [args...]
static void	matchStrings(String templateFile, String databaseFile, String outputFile, double maxDistance)
static void	maxDoubleClass(String classesFile) Prints the largest pair equivalence class, including implicit pairs.
static void	maxExplicitDoubleClass(String classesFile) Prints the largest pair equivalence class, excluding implicit pairs.
static void	maxSingleClass(String classesFile) Prints the largest single equivalence class.
static double	parseCoefficient(String s) 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.
static int[]	parseInChIString(String name, String InChI, BufferedWriter infoWriter) Parses an InChI string and returns an int[ELEMENTS.length] containing the mass vector.
static int[]	parseMass(String massString, BufferedWriter infoWriter) Parses a string of format CXHYNZ..., where C,H,N are chemical elements followed by the number of atoms X,Y,Z.
static ArrayList<String>	parseTokens(String input, String delimiter, boolean lowercase) Parses the input string and returns a list of tokens separated by delimiter.
static void	printCoefficients(MetabolicGraph graph) Prints the stoichiometric coefficients of the given graph, i.e., its edge weights.
static void	printCompartmentInfo(MetabolicGraph graph) Prints the number of compounds, reactions, and transporters associated with each compartment.
static void	printCompoundIndices(MetabolicGraph graph, ArrayList<String> compounds) Prints the indices in the sorted lists of compounds from the given compounds list.
static void	printDeadEnds(MetabolicGraph graph, String output)
static void	printEquivalenceClass(String classesFile, String compound) Prints the equivalence classes in which the given compound is contained.
static void	printExampleReactions(String networkFile) Prints some example reactions of the graph with in- and out-degree smaller than 4.
static void	printExternalCompoundIndices(MetabolicGraph graph) Prints the sorted stoichiometric matrix indices of all compounds in a compartment starting with "ext", "ex", or "e".
static void	printHubCompounds(MetabolicGraph graph, int number) Prints the number of compounds given by number with largest degree.
static void	printLargeCoefficients(MetabolicGraph graph, int min) Print all reactions in the given graph that have a coefficient at least as large as min.
static void	printMappedIndices(MetabolicGraph graph, String mappingFile, String indexFile) 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.
static void	printMass(MetabolicGraph graph, String compoundString)
static void	printMasses(String compoundsFile, String networkFile, String infoFile) Print all compounds with masses and the largest integer factorization.
static void	printMaxCoefficient(MetabolicGraph graph) Searches for the largest coefficient in the network and prints the corresponding reaction.
static void	printMaxDeltaGr(MetabolicGraph graph, boolean reversible, boolean excludeTransprorters) Searches for the largest deltaGr in the network and prints the corresponding reaction.
static void	printPathway(MetabolicGraph graph) 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.
static void	printReaction(MetabolicGraph graph, String reaction, boolean printMass, boolean printDeltaG) Prints the reaction equation from the given graph.
static void	printReaction(MetabolicGraph graph, Vertex reaction, boolean printMass, boolean printDeltaG) Prints the equation of the given reaction.
static void	printReactionIndices(MetabolicGraph graph, ArrayList<String> reactions) Prints the indices in the sorted lists of reactions from the given reaction list.
static void	printReactions(MetabolicGraph graph) Prints all reaction equations of the given graph.
static void	printReactions(MetabolicGraph graph, ArrayList<String> reactions) Prints the reaction equations from the given graph.
static void	printSmallDegreeReactions(MetabolicGraph graph) Prints all reactions with in-degree+out-degree < 3 in the graph.
static void	printTCACycleReactions(MetabolicGraph graph) Prints reactions containing TCA cycle intermediaries from ecoli, satisfying additional conditions.
static void	reachable(ArrayList<String> substrateNames, ArrayList<String> productNames, MetabolicGraph graph)
static void	select(String inputFile, String outputFile, boolean append) Writes every tenth element from every line of the input file to the output file.
static void	summary(MetabolicGraph graph) Print the summary statistics for the given graph: - number of compounds and those containing only CHNOPS - number of reactions, unbalanced and unannotated reactions - reversibility of the graph, number of vertices and edges - sizes of connected and strongly connected components
static void	testGraphs(String inputDir, String version, boolean massbalance, int from, int to) Tests the serialized graphs in the given directory of the given species version.
static void	validateSBML(org.sbml.libsbml.SBMLDocument sbmlDoc) Performs an internal consistency check of the SBML Document.
static void	writeBioCycWeights(String compoundsDir, String outputPath) Prints the molecular weights of all compounds in the given biocyc directory.
static void	writeCompartments(String reactionsFile) Prints all compartments in the given network.
static void	writeLines(String inputFile, int from, int to) Prints the lines in the given from-to range of the given inputFile.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sbml

public static boolean sbml

sbmlMessage

public static String sbmlMessage

sbmlThrowable

public static Throwable sbmlThrowable

sbmlDocument

public static org.sbml.libsbml.SBMLDocument sbmlDocument

Constructor Detail

Utilities

public Utilities()

Method Detail

main

public static void main(String[] args)

The main method can be used to call the public methods of this class directly from the command line by executing
java -jar massbalance.jar utilities [method] [args...]
where method is the method name and args... are the method arguments. The following method arguments are supported and will be translated from the given string argument:

MetabolicGraph: pass the file name of the deserialized object.
int: pass the integer argument.
String: pass the String argument.
boolean: pass 'true' or 'false'.
ArrayList<String>: pass a list of strings as ['String1','String2',...].

An overview of the available methods is printed by executing the main class without arguments.

select

public static void select(String inputFile,
          String outputFile,
          boolean append)
                   throws IOException

Writes every tenth element from every line of the input file to the output file.

Parameters:

inputFile -

outputFile -

Throws:

IOException

writeLines

public static void writeLines(String inputFile,
              int from,
              int to)
                       throws IOException

Prints the lines in the given from-to range of the given inputFile.

Parameters:

inputFile -

from -

to -

Throws:

IOException

appendFile

public static int appendFile(String inputFile,
             String outputFile)
                      throws IOException

Appends the content from inputFile to the end of outputFile. Careful when applying to files with unfinished lines: remove the unfinished line before.

Parameters:

inputFile -

outputFile -

Returns:

number of lines in the output file

Throws:

IOException

appendFiles

public static void appendFiles(String firstInputFile,
               int numberOfFiles,
               String outputFile)
                        throws IOException

Appends the content from inputFile and the next numberOfFiles-1 inputFiles with successive index numbers to the end of outputFile. E.g., "in.1.file 3 outFile" appends the contents of "in.1.file", "in.2.file", and "in.3.file", to "outFile". Index ranges are also supported if the file name contains a dash, e.g. "in.0-9.file 3 outFile" appends the contents of "in.0-9.file", "in.10-19.file", and "in.20-29.file" to "outFile". Careful when applying to files with unfinished lines: remove the unfinished line before.

Parameters:

firstInputFile -

numberOfFiles -

outputFile -

Throws:

IOException

appendColumns

public static void appendColumns(String inputFile1,
                 String inputFile2,
                 String outputFile,
                 int offset)
                          throws IOException

Appends the tab-separated tokens from each line in inputFile2 to the corresponding lines in inputFile1 and prints the resulting lines to outputFile. Lines starting with '#' are skipped. In addition, if offset<0, the inputFile1 is skipped by -offset lines, if offset>0, inputFile2 is skipped by offset lines.

Parameters:

inputFile1 -

inputFile2 -

outputFile -

offset -

Throws:

IOException

joinLines

public static void joinLines(String inputFile1,
             String inputFile2,
             String outputFile)
                      throws IOException

Searches in inputFile2 for the first string of each line in inputFile1, and joins the remaining strings in outputFile.

Parameters:

inputFile1 -

inputFile2 -

outputFile -

Throws:

IOException

maxSingleClass

public static void maxSingleClass(String classesFile)
                           throws IOException,
                                  InterruptedException

Prints the largest single equivalence class.

Parameters:

classesFile -

Throws:

IOException

InterruptedException

maxExplicitDoubleClass

public static void maxExplicitDoubleClass(String classesFile)
                                   throws IOException,
                                          InterruptedException

Prints the largest pair equivalence class, excluding implicit pairs.

Parameters:

classesFile -

Throws:

IOException

InterruptedException

maxDoubleClass

public static void maxDoubleClass(String classesFile)
                           throws IOException,
                                  InterruptedException

Prints the largest pair equivalence class, including implicit pairs.

Parameters:

classesFile -

Throws:

IOException

InterruptedException

printEquivalenceClass

public static void printEquivalenceClass(String classesFile,
                         String compound)
                                  throws IOException,
                                         InterruptedException

Prints the equivalence classes in which the given compound is contained.

Parameters:

compound -

Throws:

IOException

InterruptedException

avgClassSizes

public static void avgClassSizes(String classesFile)
                          throws IOException,
                                 InterruptedException

Prints the number of single and double mass equivalence classes and their average sizes.

Parameters:

classesFile -

Throws:

IOException

InterruptedException

writeCompartments

public static void writeCompartments(String reactionsFile)
                              throws IOException

Prints all compartments in the given network.

Parameters:

reactionsFile -

Throws:

IOException

printCompartmentInfo

public static void printCompartmentInfo(MetabolicGraph graph)

Prints the number of compounds, reactions, and transporters associated with each compartment.

Parameters:

graph -

testGraphs

public static void testGraphs(String inputDir,
              String version,
              boolean massbalance,
              int from,
              int to)
                       throws IOException,
                              ClassNotFoundException

Tests the serialized graphs in the given directory of the given species version. If massbalance==true massbalance randomized files are tested, otherwise switch randomized files.

Parameters:

inputDir -

version -

massbalance -

Throws:

IOException

ClassNotFoundException

createGraph

public static void createGraph(String networkFile,
               String outputFile,
               boolean reversible,
               boolean compartments)
                        throws IOException,
                               ClassNotFoundException

Creates a graph from the biocyc or flat file input directory and deserializes it to the output file name.

Parameters:

networkFile -

outputFile -

reversible -

compartments -

Throws:

IOException

ClassNotFoundException

checkNetworks

public static void checkNetworks(String networkName,
                 String inputDir,
                 String randomization,
                 int from,
                 int to,
                 String outputFile)
                          throws IOException,
                                 ClassNotFoundException

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.

Parameters:

networkName -

inputDir -

randomization -

from -

to -

Throws:

IOException

ClassNotFoundException

countIsolatedNodes

public static int countIsolatedNodes(MetabolicGraph graph)

Counts the number of isolated nodes in the graph, i.e. nodes with an in-degree and out-degree of 0.

Parameters:

graph -

countReactionsWithCycles

public static void countReactionsWithCycles(MetabolicGraph graph)

Counts the number of reactions which contain a cycle, i.e. a substrate which is also a product.

Parameters:

graph -

checkBalance

public static void checkBalance(MetabolicGraph graph)

Determines the mass-balance of the reactions in the given graph and prints unbalanced reactions.

Parameters:

graph -

countReactions

public static void countReactions(MetabolicGraph graph,
                  boolean print)
                           throws IOException

Counts the number of reactions, reversible, cyclic, zero-degree reactions, and the average and maximum reaction degrees.

Parameters:

graph -

print -

Throws:

IOException

printReactionIndices

public static void printReactionIndices(MetabolicGraph graph,
                        ArrayList<String> reactions)
                                 throws IOException,
                                        ClassNotFoundException

Prints the indices in the sorted lists of reactions from the given reaction list.

Parameters:

graph -

reactions -

Throws:

IOException

ClassNotFoundException

printCompoundIndices

public static void printCompoundIndices(MetabolicGraph graph,
                        ArrayList<String> compounds)
                                 throws IOException,
                                        ClassNotFoundException

Prints the indices in the sorted lists of compounds from the given compounds list.

Parameters:

graph -

compounds -

Throws:

IOException

ClassNotFoundException

findTransporters

public static void findTransporters(MetabolicGraph graph,
                    ArrayList<String> compoundNames,
                    boolean exclusive)
                             throws IOException,
                                    ClassNotFoundException

Finds and prints all transport reactions in which the given compounds are involved. If exclusive==true, than only transporters which exclusively carry the given compound (in- and out-degree is 1) are printed.

Parameters:

graph -

compoundNames -

exclusive -

Throws:

IOException

ClassNotFoundException

printExternalCompoundIndices

public static void printExternalCompoundIndices(MetabolicGraph graph)

Prints the sorted stoichiometric matrix indices of all compounds in a compartment starting with "ext", "ex", or "e".

Parameters:

graph -

summary

public static void summary(MetabolicGraph graph)

Print the summary statistics for the given graph: - number of compounds and those containing only CHNOPS - number of reactions, unbalanced and unannotated reactions - reversibility of the graph, number of vertices and edges - sizes of connected and strongly connected components

Parameters:

graph -

printExampleReactions

public static void printExampleReactions(String networkFile)
                                  throws IOException

Prints some example reactions of the graph with in- and out-degree smaller than 4.

Parameters:

networkFile -

Throws:

IOException

printCoefficients

public static void printCoefficients(MetabolicGraph graph)

Prints the stoichiometric coefficients of the given graph, i.e., its edge weights.

Parameters:

graph -

printMasses

public static void printMasses(String compoundsFile,
               String networkFile,
               String infoFile)
                        throws IOException

Print all compounds with masses and the largest integer factorization.

Parameters:

compoundsFile -

networkFile -

infoFile -

Throws:

IOException

printLargeCoefficients

public static void printLargeCoefficients(MetabolicGraph graph,
                          int min)

Print all reactions in the given graph that have a coefficient at least as large as min. Reactions with more than one large coefficient are repeatedly printed.

Parameters:

graph -

min -

printMaxCoefficient

public static void printMaxCoefficient(MetabolicGraph graph)

Searches for the largest coefficient in the network and prints the corresponding reaction.

Parameters:

graph -

printMaxDeltaGr

public static void printMaxDeltaGr(MetabolicGraph graph,
                   boolean reversible,
                   boolean excludeTransprorters)

Searches for the largest deltaGr in the network and prints the corresponding reaction. If reversible==true, then the deltaGr of reversible reactions is 0, otherwise, the maximum is determined for each direction independently. If excludeTransporters, transport reactions as well as import/export reactions are skipped.

Parameters:

graph -

printMass

public static void printMass(MetabolicGraph graph,
             String compoundString)

printReactions

public static void printReactions(MetabolicGraph graph)

Prints all reaction equations of the given graph.

Parameters:

graph -

printDeadEnds

public static void printDeadEnds(MetabolicGraph graph,
                 String output)
                          throws IOException

Throws:

IOException

printReaction

public static void printReaction(MetabolicGraph graph,
                 Vertex reaction,
                 boolean printMass,
                 boolean printDeltaG)

Prints the equation of the given reaction.

Parameters:

graph -

reaction -

printReaction

public static void printReaction(MetabolicGraph graph,
                 String reaction,
                 boolean printMass,
                 boolean printDeltaG)

Prints the reaction equation from the given graph.

Parameters:

graph -

reaction -

printReactions

public static void printReactions(MetabolicGraph graph,
                  ArrayList<String> reactions)

Prints the reaction equations from the given graph.

Parameters:

graph -

reactions -

printSmallDegreeReactions

public static void printSmallDegreeReactions(MetabolicGraph graph)

Prints all reactions with in-degree+out-degree < 3 in the graph.

Parameters:

graph -

printHubCompounds

public static void printHubCompounds(MetabolicGraph graph,
                     int number)

Prints the number of compounds given by number with largest degree.

Parameters:

graph -

number -

printPathway

public static void printPathway(MetabolicGraph graph)

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.

Parameters:

graph -

printTCACycleReactions

public static void printTCACycleReactions(MetabolicGraph graph)

Prints reactions containing TCA cycle intermediaries from ecoli, satisfying additional conditions.

Parameters:

graph -

parseInChIString

public static int[] parseInChIString(String name,
                     String InChI,
                     BufferedWriter infoWriter)
                              throws IOException

Parses an InChI string and returns an int[ELEMENTS.length] containing the mass vector.

Parameters:

InChI -

Returns:

Chemical formula string.

Throws:

IOException

parseMass

public static int[] parseMass(String massString,
              BufferedWriter infoWriter)
                       throws IOException

Parses a string of format CXHYNZ..., where C,H,N are chemical elements followed by the number of atoms X,Y,Z. The elements need to be in a specific order. Dots '.' are treated as 1. Returns an int[ELEMENTS.length] containing the mass vector.

Parameters:

massString -

Returns:

The mass vector.

Throws:

IOException

parseCoefficient

public static double parseCoefficient(String s)

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.

Parameters:

s -

Returns:

The stoichiometric coefficient, or -1 if the string is not a stoichiometric coefficient.

gcd

public static long gcd(long[] values)

Calculates the greatest common divisor the given values.

Parameters:

values -

Returns:

The greatest common divisor.

lcm

public static long lcm(int x,
       int y)

Returns the least common integer multiple for x and y, determined by dividing x*y by the greatest common divisors.

Parameters:

x -

y -

Returns:

The least common integer multiple of x and y.

binomialCoefficient

public static long binomialCoefficient(long n,
                       long k)

Calculates the binomial coefficient (n over k).

Parameters:

n -

k -

Returns:

The binomial coefficient.

linearDependent

public static double linearDependent(double[] a,
                     double[] b)

Tests a and b for linear dependence.

Parameters:

a -

b -

Returns:

The factor f=b/a, or 0, if the vectors are linearly independent.

printMappedIndices

public static void printMappedIndices(MetabolicGraph graph,
                      String mappingFile,
                      String indexFile)
                               throws IOException

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.

Parameters:

graph -

mappingFile -

indexFile -

Throws:

IOException

compoundAliasMap

public static void compoundAliasMap(String compoundsFile,
                    String massesFile,
                    String outputFile)
                             throws IOException

Maps compound strings with their masses from 2 files: one contains the compound strings and aliases, the other maps the aliases to sum formulas. Writes a table of compound names and corresponding mass strings.

Parameters:

compoundsFile -

massesFile -

outputFile -

Throws:

IOException

appendDeltaG

public static void appendDeltaG(String compoundsFile,
                String databaseFile,
                String outputFile,
                int hydrogenTolerance)
                         throws IOException

Searches the compounds from compoundsFile in the databaseFile by case-insensitive name and sum formula, and prints the compounds with deltaG to outputFile. A difference in hydrogen atoms is tolerated as specified by hydrogenTolerance. Used to append the deltaG values from the KEGG compounds to the compounds file of a network.

Parameters:

compoundsFile -

databaseFile -

outputFile -

hydrogenTolerance -

Throws:

IOException

appendDeltaGFromKEGG

public static void appendDeltaGFromKEGG(String compoundsFile,
                        String databaseFile,
                        String outputFile)
                                 throws IOException

Searches a KEGG ID in compoundsFile, matches the compound in databaseFile and appends the deltaG and uncertainties to the compounds in outputFile. Used to append the deltaG values from the KEGG compounds to the compounds file of a network, matching by ID.

Parameters:

compoundsFile -

databaseFile -

outputFile -

Throws:

IOException

deltaGDifferences

public static void deltaGDifferences(String databaseFile,
                     int hydrogenTolerance)
                              throws IOException

Parses the sum formulas and deltaG values from the databaseFile and determines the differences in deltaGf between compounds which have an equal sum formula up to the specified hydrogenTolerance in the number of hydrogen atoms.

Parameters:

databaseFile -

hydrogenTolerance -

Throws:

IOException

parseTokens

public static ArrayList<String> parseTokens(String input,
                            String delimiter,
                            boolean lowercase)

Parses the input string and returns a list of tokens separated by delimiter. If lowercase==true, all characters are converted to lower-case.

Parameters:

input -

delimiter -

lowercase -

Returns:

ArrayList containing the parsed tokens.

joinSynonyms

public static void joinSynonyms(String inputMap,
                String databaseFile,
                String outputFile,
                boolean caseSensitive,
                int minMatch,
                int minAdd)
                         throws IOException

Parses the inputMap file for synonyms and searches all synonyms in databaseFile. If a synonym matches, the database line is appended by the name from inputMap and written to outputFile. Used to add new compound synonyms from a mapping file of a network to the database, which can then be used by appendDeltaG to add the deltaG values to the compounds list.

Parameters:

inputMap -

databaseFile -

outputFile -

Throws:

IOException

joinSimilarSynonyms

public static void joinSimilarSynonyms(String compoundsFile,
                       String databaseFile,
                       String outputFile,
                       double maxDistance,
                       int hydrogenTolerance)
                                throws IOException

Parses the compounds file for synonyms (more than one name for a compound) and searches similar synonyms with similar sum formula in databaseFile. The names and sum formulas of the compounds file are collected, and then compared with the names and sum formulas in the database file. The distance between names from the compounds file and names from the database file is determined by the edit distance (Levenshtein distance) divided by the length of the larger name. If the distance is below maxDistance, and the sum formulas equal up to a difference of the number of hydrogen atoms specified by hydrogenTolerance, then all synonyms of the compound are added to the corresponding line in the database file. The output is written to outputFile. Used to add new compound synonyms from a compounds file of a network to a KEGG database file with synonyms, which can then be used by appendDeltaG to add the deltaG values to the compounds.

Parameters:

compoundsFile -

databaseFile -

outputFile -

maxDistance -

hydrogenTolerance -

Throws:

IOException

matchStrings

public static void matchStrings(String templateFile,
                String databaseFile,
                String outputFile,
                double maxDistance)
                         throws IOException

Throws:

IOException

compoundMassesMap

public static void compoundMassesMap(String compoundsFile,
                     String massesFile,
                     String outputFile)
                              throws IOException

Maps a list of compounds from compoundsFile to a list containing compound synonyms and masses in massesFile. There may be several tab-separated synonyms before the mass. The outputFile contains a list of the compounds with found masses.

Parameters:

compoundsFile -

massesFile -

outputFile -

Throws:

IOException

reachable

public static void reachable(ArrayList<String> substrateNames,
             ArrayList<String> productNames,
             MetabolicGraph graph)
                      throws IOException

Throws:

IOException

initSBML

public static org.sbml.libsbml.SBMLDocument initSBML(String sbmlFile)

Checks if there is SBML support, then validates and returns the SBMLDocument. Terminates if there is no SBML support, or if the document contains fatal errors (see validateSBML(SBMLDocument)). For some reason, the SBML Model is not stored properly as static variable. Therefore, we store the SBMLDocument, which avoids multiple validations.

Parameters:

sbmlFile -

Returns:

The SBMLDocument.

validateSBML

public static void validateSBML(org.sbml.libsbml.SBMLDocument sbmlDoc)

Performs an internal consistency check of the SBML Document. Terminates if a fatal error exists, prints out any errors and the number of warnings.

Parameters:

sbmlDoc -

writeBioCycWeights

public static void writeBioCycWeights(String compoundsDir,
                      String outputPath)
                               throws IOException

Prints the molecular weights of all compounds in the given biocyc directory.

Parameters:

compoundsDir -

outputPath -

Throws:

IOException