statalign.postprocess.plugins.contree
Class CNetwork

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

public class CNetwork
extends java.lang.Object

The Consensus network

Author:

wood

Field Summary

java.util.ArrayList<CNetworkNode>	nodes
int	noOfTaxa
java.lang.String	outputString
java.util.ArrayList<CNetworkSplit>	splits

Constructor Summary

CNetwork(int noOfTaxa)
Constructs a new Consensus Network.

Method Summary

void	FindPositions(int noOfTaxa) Calculates positions for network nodes and edges linking them to output to the network visualiser.
void	PrintOut(int function, int noOfTaxa, TaxaMap taxa) Prints out the network in Nexus format.

Methods inherited from class java.lang.Object

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

Field Detail

outputString

public java.lang.String outputString

splits

public java.util.ArrayList<CNetworkSplit> splits

nodes

public java.util.ArrayList<CNetworkNode> nodes

noOfTaxa

public int noOfTaxa

Constructor Detail

CNetwork

public CNetwork(int noOfTaxa)

Constructs a new Consensus Network.

Parameters:

noOfTaxa - The number of taxa in the network.

Method Detail

PrintOut

public void PrintOut(int function,
                     int noOfTaxa,
                     TaxaMap taxa)
              throws java.io.IOException

Prints out the network in Nexus format. Can be read by SplitsTree 4

Parameters:

function - 1 - print as splits, 2 - print drawn network as calculated

noOfTaxa - The number of taxa in the network.

taxa - the map of taxa indices to names

Throws:

java.io.IOException

FindPositions

public void FindPositions(int noOfTaxa)

Calculates positions for network nodes and edges linking them to output to the network visualiser.

Parameters:

noOfTaxa - The number of taxa in the network