statalign.postprocess.plugins.contree
Class CTMain

java.lang.Object
  statalign.postprocess.plugins.contree.CTMain

public class CTMain
extends java.lang.Object

The main thread for calculating consensus trees and networks. Note that networks is dependent on the initial tree...

Author:

wood, eiriksson

Constructor Summary

CTMain()
Initialise the class

Method Summary

void	addNewTree(TreeNode root) Add a new tree to the hash table
void	addTestSplit(java.util.BitSet partition) FOR TESTING ONLY Add a single split to the hash table
void	addTestTree(java.util.ArrayList<java.util.BitSet> splits) FOR TESTING ONLY Add a tree to the hash table
CTree	constructMajorityTree() Constructs the majorityTree.
CNetwork	constructNetwork(CTree tree) Constructs the network beginning with the consensus tree and then calls the network drawing function to calculate positions
void	CopyNode(java.util.ArrayList<CNetworkNode> nodesToCopy, CNetworkSplit splitToAdd, CNetwork network, java.util.ArrayList<CNetworkEdge> incompatibleEdges) Copy the list of nodes that need copying when adding a new split into a network.
double	getResPercentage()
long	getSeed()
void	InitialiseNetworkTester(int noOfTestTaxa, int noOfTestSamples) FOR TESTING ONLY Function called to initialise the Network Tester hash table & rest of CTMain
void	initialize(TreeNode root, int noOfSamples) Initialise a CTMain before usage with a first tree, going through and setting up the hash table etc.
static void	main(java.lang.String[] args)
void	printConfig() Print some configuration information
void	printDetails(CTree tree, CNetwork network) FOR TESTING ONLY Print details from the network - call after it has been constructed!
static java.lang.String[]	readTreesFromFile(java.lang.String fileName, int n)
void	setResPercentage(double resPercentage)
void	setSeed(long seed)
CNetworkNode	TaxonRefToNode(int taxonRef, CNetwork network) Find the taxon node in the network.
void	updateInterestThreshold() Simply update our interest threshold

Methods inherited from class java.lang.Object

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

Constructor Detail

CTMain

public CTMain()

Initialise the class

Method Detail

printConfig

public void printConfig()

Print some configuration information

initialize

public void initialize(TreeNode root,
                       int noOfSamples)

Initialise a CTMain before usage with a first tree, going through and setting up the hash table etc.

Parameters:

root - Root of the initial tree to initialise with

noOfSamples - Current number of samples taken

updateInterestThreshold

public void updateInterestThreshold()

Simply update our interest threshold

addNewTree

public void addNewTree(TreeNode root)

Add a new tree to the hash table

Parameters:

root - Root of new tree to add

constructMajorityTree

public CTree constructMajorityTree()

Constructs the majorityTree. Used to make Network so remember to call this first!

constructNetwork

public CNetwork constructNetwork(CTree tree)

Constructs the network beginning with the consensus tree and then calls the network drawing function to calculate positions

Parameters:

tree - Consensus tree already calculated

CopyNode

public void CopyNode(java.util.ArrayList<CNetworkNode> nodesToCopy,
                     CNetworkSplit splitToAdd,
                     CNetwork network,
                     java.util.ArrayList<CNetworkEdge> incompatibleEdges)

Copy the list of nodes that need copying when adding a new split into a network.

Parameters:

nodesToCopy - ArrayList of nodes in the network that need to be copied

network - Network we are working in

incompatibleEdges - Edges that are in the path that joins up the nodes that are being copied

splitToAdd - Split that we are currently adding in by copying these nodes

TaxonRefToNode

public CNetworkNode TaxonRefToNode(int taxonRef,
                                   CNetwork network)

Find the taxon node in the network.

Parameters:

network - The network to find the taxon in

taxonRef - Integer representation of taxon in the TaxaMap

readTreesFromFile

public static java.lang.String[] readTreesFromFile(java.lang.String fileName,
                                                   int n)
                                            throws java.io.IOException

Throws:

java.io.IOException

main

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

Throws:

java.io.IOException

getResPercentage

public double getResPercentage()

setResPercentage

public void setResPercentage(double resPercentage)

getSeed

public long getSeed()

setSeed

public void setSeed(long seed)

InitialiseNetworkTester

public void InitialiseNetworkTester(int noOfTestTaxa,
                                    int noOfTestSamples)

FOR TESTING ONLY Function called to initialise the Network Tester hash table & rest of CTMain

Parameters:

noOfTestTaxa - Number of taxa

noOfTestSamples - number of trees input

addTestTree

public void addTestTree(java.util.ArrayList<java.util.BitSet> splits)

FOR TESTING ONLY Add a tree to the hash table

Parameters:

splits - Tree to add consisting of an arraylist of BitSet splits

addTestSplit

public void addTestSplit(java.util.BitSet partition)

FOR TESTING ONLY Add a single split to the hash table

Parameters:

partition - BitSet split to add

printDetails

public void printDetails(CTree tree,
                         CNetwork network)

FOR TESTING ONLY Print details from the network - call after it has been constructed!

Parameters:

tree - Standard consensus tree

network - The network