edu.claflin.finder

Class Main

java.lang.Object

edu.claflin.finder.Main

public class Main
extends java.lang.Object

Interprets the command line arguments provided to the program.

Version:

3.2 February 4, 2016

Author:

Charles Allen Schultz II

Constructor Summary

Constructors

Constructor and Description
Main()

Method Summary

Modifier and Type	Method and Description
private static void	error() Used to process a fatal error.
static void	main(java.lang.String[] args) Command line argument processing occurs here.
private static Algorithm	parseAlgorithm(java.lang.String algorithmCode, java.util.HashMap<java.lang.String,java.lang.Boolean> config, java.util.ArrayList<Condition> conditions, java.util.Comparator<Edge> comparator) Parses an algorithm code string for returning the appropriate Algorithm object.
private static boolean[]	parseBoolean(java.lang.String booleans) Parses a boolean string for configuring the {}.
private static void	writeGraphs(java.util.ArrayList<Graph> graphs, java.lang.String output, GraphWriter writer) Writes Graph objects to memory.

Methods inherited from class java.lang.Object

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

Constructor Detail

Main

public Main()

Method Detail

main

public static void main(java.lang.String[] args)

Command line argument processing occurs here. Program usage:
java -jar SubgraphFinder.jar -v -out <booleans> -log <booleans> [ -f <FILE> | -m <MANIFEST> ] -input <TYPE> <OPTION> -output <TYPE> <OPTION> -algo <ALGO>

-f <FILE> : Supply a single file to be parsed.
-m <MANIFEST> : Supply a manifest listing several files to be parsed.

-level
{@code : A logging level.
{@code NORMAL : Shallowest logging level. Least amount of messages.}
{@code VERBOSE : Moderate logging; includes intermittent operations.}
{@code DEBUG : Highest logging granularity; logs every message.}

{@code -out :: -log }
{@code out : Logging to command prompt options.}
{@code log : Logging to file options.}

{@code : Use 't' for true and 'f' for false. The supplied arguments should}
{@code be concatenated as a single string. There are currently four (4) needed:}
{@code ALGO : Logging of Algorithm operations.}
{@code ERRR : Logging of Error informations.}
{@code GRPH : Logging of Graph operations.}
{@code INFO : Logging of General informations.}

{@code -input :: -output }
{@code input : How to process the source graphs.}
{@code output : How to output the found graphs.}

{@code : Select from one of the following options:}
{@code SIMPLE : Simple tab delimited format. (DEFUALT)}
{@code SIF : Simple Interaction Format as defined in the Cytoscape Manual.}
{@code NOA : NOA Batch Format as defined in the NOA Plugin for Cytoscape. (OUTPUT ONLY)}

{@code : Some formats require an additional parameter described below:}
{@code SIF : Default Relationship Type (i.e. \"pp\" or \"pd\")}
{@code NOA : Same as SIF.}

{@code -cfg : Some algorithms receive special configuration parameters, all of which default to false.}

{@code : Select from one of the following options:}
{@code PRESERVATIVE : Preserves edges on expansion.}

{@code -type : A subgraph type to look for.}

{@code : Select from one of the following options:}
{@code BIPARTITE : Bipartite Subgraphs.}
{@code CLIQUE : Clique Subgraphs.}
{@code DCLIQUE : Directed Clique Subgraphs.}

{@code -order : An ordering to impose}

{@code : Select from one of the following options:}
{@code EDGEWEIGHT : Order expansion based on the data attached to the edge interpretted as a number.}
{@code (Higher values are taken first.)}

{@code -undirected : Interprets a graph as being undirected.}

{@code -algo : The algorithm code indicating the method of finding BSGs to use.}

{@code : Select from one of the following options:}
{@code BFTS : Finds bipartite graphs based on a breadth first traversal search of the network.}
{@code DFTS : Finds bipartite graphs based on a depth first traversal search of the network.}
{@code BNDL : See below for instruction. (Do not self-reference. Program will exit with error.)}

{@code -algo BNDL ( ...) : Load a BUNDLE Algorithm. Processes the graph using each }
{@code of the provided Algorithms. Algorithm codes should be the same as above and delimited }
{@code using spaces. NOTE: this must be the last argument as the program assumes all following }
{@code arguments are Algorithm codes.}

Parameters:

args - the String array containing the program's startup parameters.

writeGraphs

private static void writeGraphs(java.util.ArrayList<Graph> graphs,
                                java.lang.String output,
                                GraphWriter writer)

Writes Graph objects to memory. Does so in a manner so as to promote extensibility.

Parameters:

graphs - the ArrayList object containing the graphs to write.

output - the String representing the folder in the memory to store the graphs in.

writer - the GraphWriter object to use for writing the graphs.

parseBoolean

private static boolean[] parseBoolean(java.lang.String booleans)

Parses a boolean string for configuring the {}. Converts the characters in the string into a boolean array depending on if they are 't' for true or 'f' for false.

Parameters:

booleans - the String containing the boolean pattern.

Returns:

the boolean array initialized from the String.

parseAlgorithm

private static Algorithm parseAlgorithm(java.lang.String algorithmCode,
                                        java.util.HashMap<java.lang.String,java.lang.Boolean> config,
                                        java.util.ArrayList<Condition> conditions,
                                        java.util.Comparator<Edge> comparator)

Parses an algorithm code string for returning the appropriate Algorithm object.

Parameters:

algorithmCode - the String containing the correct Algorithm code.

Returns:

the Algorithm object instantiated from the code.

error

private static void error()

Used to process a fatal error. Kills the program with a warning to the user.