statalign.postprocess.plugins.contree
Class CNetworkNode

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

public class CNetworkNode
extends java.lang.Object

Nodes in the consensus network Also includes a substantial amount of code that draws the edges from the node.

Author:

wood

Field Summary

double	angleDirection
double	angleWidth
boolean	consideration
CNetworkNode	CopiedToNode
boolean	drawn
java.util.ArrayList<CNetworkEdge>	joins
int	outputNumber
java.util.ArrayList<CNetworkPath>	paths
java.lang.String	Taxaname
double	xPos
double	yPos

Constructor Summary

CNetworkNode()
Initialise the node

Method Summary

void	AddToPaths(CNetworkPath pathToAdd, java.util.ArrayList<CNetworkNode> nodesToClearUp) Add a path to the node path list..
java.util.ArrayList<CNetworkNode>	DrawEdges(int noOfTaxa) Function to draw the network i.e. find x and y co-ordinates for nodes.
CNetworkNode	findFirstNonSubset(CNetworkSplit addSplit, java.util.ArrayList<CNetworkNode> consideredNodes, boolean zeroSide, int noOfTaxa) Recursive function used to find node at which we can add a split compatible with the network Goes up from first node and finds where edges joining are no longer subset of specified side of split we want to add
double	FindWeighting(CNetworkEdge compEdge, int noOfTaxa) Finds the weighting of this this node using the joins that join to it.
void	ListToAdd(CNetworkEdge neighbourLink, boolean start, java.util.ArrayList<CNetworkEdge> ListToAddTo) Function returns joined up ArrayList if must be joined in a certain order...
double	returnAngle(double inputAngle) Return an angle that is in the range 0 to 2*pi....

Methods inherited from class java.lang.Object

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

Field Detail

joins

public java.util.ArrayList<CNetworkEdge> joins

Taxaname

public java.lang.String Taxaname

outputNumber

public int outputNumber

CopiedToNode

public CNetworkNode CopiedToNode

paths

public java.util.ArrayList<CNetworkPath> paths

consideration

public boolean consideration

drawn

public boolean drawn

angleDirection

public double angleDirection

angleWidth

public double angleWidth

xPos

public double xPos

yPos

public double yPos

Constructor Detail

CNetworkNode

public CNetworkNode()

Initialise the node

Method Detail

AddToPaths

public void AddToPaths(CNetworkPath pathToAdd,
                       java.util.ArrayList<CNetworkNode> nodesToClearUp)

Add a path to the node path list..

Parameters:

pathToAdd - Path to add to this node's list

nodesToClearUp - List of nodes to remove paths from at end of adding split

findFirstNonSubset

public CNetworkNode findFirstNonSubset(CNetworkSplit addSplit,
                                       java.util.ArrayList<CNetworkNode> consideredNodes,
                                       boolean zeroSide,
                                       int noOfTaxa)

Recursive function used to find node at which we can add a split compatible with the network Goes up from first node and finds where edges joining are no longer subset of specified side of split we want to add

Parameters:

addSplit - Split that we are adding

consideredNodes - Nodes that we have so far considered

zeroSide - True if looking on zero side of split, otherwise false. Try to choose side with fewer taxa to improve efficiency.

noOfTaxa - Number of taxa

DrawEdges

public java.util.ArrayList<CNetworkNode> DrawEdges(int noOfTaxa)

Function to draw the network i.e. find x and y co-ordinates for nodes.

Parameters:

noOfTaxa - Number of taxa

FindWeighting

public double FindWeighting(CNetworkEdge compEdge,
                            int noOfTaxa)

Finds the weighting of this this node using the joins that join to it. Based on: a) returning "1" if it is a taxon. b) return the number of linked taxon in this direction by finding which node is a subset of this split

Parameters:

compEdge - Edge that we want to find the weighting for

noOfTaxa - Number of taxa

ListToAdd

public void ListToAdd(CNetworkEdge neighbourLink,
                      boolean start,
                      java.util.ArrayList<CNetworkEdge> ListToAddTo)

Function returns joined up ArrayList if must be joined in a certain order... Used for stitching together neighbours Runs recursively!

Parameters:

neighbourLink -

start - begin from start if true, begin from end if false

ListToAddTo -

returnAngle

public double returnAngle(double inputAngle)

Return an angle that is in the range 0 to 2*pi....

Parameters:

inputAngle - Any input angle