cs195z.support
Class PDataSet

java.lang.Object
  cs195z.support.PDataSet

public class PDataSet
extends Object

Generates an nds4 LinkedBinaryTree[PSpeciesNode] selected from the available ones. Note that your project should work for any dataset of PSpeciesNode, regardless of the ZCharacter sequence of the leaves (although your input is guaranteed to a binary tree with species as leaves...)

Author:

apstewar - nobody else would do such busy work

Nested Class Summary

static class

PDataSet.AvailableDataSets The data sets we have access to.

Constructor Summary

PDataSet(PDataSet.AvailableDataSets s)
PDataSet preloads the desired data set from the AvailableDataSets.

Method Summary

double[][]	getFelsensteinMatrix()
int[][]	getSankoffMatrix()
int	getSequenceLength()
HashMap<ZCharacter,Integer>	getStateIndices()
net.datastructures.LinkedBinaryTree<PSpeciesNode>	getTree()

Methods inherited from class java.lang.Object

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

Constructor Detail

PDataSet

public PDataSet(PDataSet.AvailableDataSets s)

PDataSet preloads the desired data set from the AvailableDataSets. Use the getter methods after to get the requisite data.

Parameters:

s -

Method Detail

getTree

public net.datastructures.LinkedBinaryTree<PSpeciesNode> getTree()

getStateIndices

public HashMap<ZCharacter,Integer> getStateIndices()

getSankoffMatrix

public int[][] getSankoffMatrix()

getFelsensteinMatrix

public double[][] getFelsensteinMatrix()

getSequenceLength

public int getSequenceLength()