Common parameters and allowable values
	-m / --measure-mode (refers to modes defined in org.krasnow.cng.domain.Asymmetry)
		1: Nodes
		2: Euclidean distance
		3: Path distance (default)
		4: Surface area
		5: Volume
	-I / --input-dir
		Reads all swc files within this directory or under subdirectory "CNG Version" or "CNGVersion"
	-O / --output-file
		Full path and name of output file. A .csv extension will automatically be added.
* means the parameter is required
() values in parentheses is the default value

lib
	JSAP-2.1.jar
		- Contains methods for program parameter rules and extraction
	bigal.jar
		- Tools for big integer math

org.krasnow.cng.caulescence - Contains classes with main method
	AllNMCaulescenceCompare
		- Produces results for different multi-path caulescence methods
		- Parameters
			-m / --measure-mode (3)
			-I / --input-dir (C:/swcData/NM/)
			-O / --output-file (NM-caulCompare)
				
	AsymCompare
		- Produces .csv file of various types of asymmetry values for each tree
		- Parameters
			-m / --measure-mode (3)
			-I / --input-dir (C:/swcData/NM/)
			-O / --output-file (asymComparison)
		
	GenerateCaulescenceResults
		- Produces .csv file of asymmetry and caulescence values for each metric type for each tree
			-I / --input-dir (C:/swcData/NM/)
			-O / --output-file (NM-caulescence)

	RewriteSwcWithCaulescence
		- Rewrites Swc file with different node types for nodes on the caulescent path
		- Paramters
			-S / --swc-dir*
				Directory in which your targetted file resides
			-O / --output-dir*
				Directory in which your resulting file should be placed
			-N / --neuron*
				Name of the swc file without the .swc or .CNG.swc extension
			-m / --measure-mode (1)
			-a / --arbor-type (0)
				0: All
				2: Axon
				3: Dendrite (Basal for pyramidal neurons)
				4: Apical Dendrite
			--multi-branch
				1: MergeDown
				2: ByNode
				3: Selective
				4: Exhaustive
			-s / --size-mode (0)
				0: Sum
				1: Max
			-d / --dendrite (0)
				If one of several dendrites is being targetted, this parameter picks which one
			--separate (false)
				If true, each tree is placed in its own output file
			-t / --main-path-type (6)
				Sets the swc node type for main paths. If 0, each arbor type will have its 
				own type (5-axon,6-dendrite,7-apical)

	SecondaryBranchAsymmetry
		- Determines asymmetry of non-main-path nodes along with distance values

	SwcToCaulescence
		- Produces an output of caulescence at each node of an SWC file
	
org.krasnow.cng.data
	DataReader
		- Functions for reading in meta data
	DataWriter
		- Simple class for writing/appending string output to a file
	ReadSWC
		- Primary class for reading swc files into java data structures
	
org.krasnow.cng.domain
	Asymmetry
		- Holds data members associated with asymmetry measures
	BinaryTreeNode
	DistributionBean
	DoubleLinkedListNode
	LinkedQueue
	LinkedStack
	Neuron
		- Holds meta data about the neuron, as well as a soma object
	NeuronProcess
		- Holds ParentedBinaryTreeNode as tree root, as well as Neuron object for identification
	NodePair
	ParentedBinaryTreeNode
		- Extends BinaryTreeNode with a link to a parent node
	Soma
		- Contains NeuroProcess for dendrite(s), apical dendrite(s), and axon
	SwcDataNode
	SwcSecondaryData
	SwcTreeNode
		- Tree node (non-binary) that contains swc data
	TreeNode
	XYBean

org.krasnow.cng.generate
	BinaryTreeGenerator
		- Generates binary trees via several different methods

org.krasnow.cng.resources
	Constants
		- Contains references to properties files, as well as mapping an common parameter definitions
	DataProperties
	ProjectProperties
		- Helper for loading properties related to the project. Loads from resources/conf/project.properties

org.krasnow.cng.utils
	BinaryTreeUtils
		- Important utility class for caulescence, asymmetry, and other binary tree calculations
		- Includes a number of attempted multi-path algorithms.
	StringUtils
	SwcDataUtils

resources
	swcCellTypes.txt
		- Flat text file containing all cells from SWC files and their basic meta data
	ca1.txt
		- List of all CA1 cells
	ca3.txt
		
resources/conf
	data.properties
		- Contains location of meta data file relative to the resource directory
	project.properties
		- Requires a definition of the working directory