net.maizegenetics.taxa.tree

Class SimpleNode

net.maizegenetics.taxa.tree.SimpleNode

All Implemented Interfaces:

AttributeNode, Node

public class SimpleNode
implements AttributeNode

data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree

Constructor Detail

SimpleNode

public SimpleNode()

constructor default node

SimpleNode

public SimpleNode(java.lang.String name,
                  double branchLength)

SimpleNode

protected SimpleNode(Node[] children,
                     double branchLength)

Constructor

Parameters:

children -

branchLength -

Throws:

IllegalArgumentException - if only one child!

SimpleNode

protected SimpleNode(Node[] children)

SimpleNode

public SimpleNode(Node n)

constructor used to clone a node and all children

SimpleNode

public SimpleNode(Node n,
                  boolean keepIds)

SimpleNode

public SimpleNode(Node n,
                  LabelMapping lm)

Method Detail

reset

public void reset()

init

protected void init(Node n)

init

protected void init(Node n,
                    boolean keepId)

Initialized node instance variables based on given Node. children are ignored.

init

protected void init(Node n,
                    boolean keepId,
                    LabelMapping lm)

Initialized node instance variables based on given Node. children are ignored.

Parameters:

lm - - may be null

getParent

public Node getParent()

Returns the parent node of this node.

setParent

public void setParent(Node node)

Set the parent node of this node.

removeParent

public void removeParent()

removes parent.

getSequenceString

public java.lang.String getSequenceString()

Returns the sequence at this node, in the form of a String.

getSequence

public kotlin.Array[] getSequence()

Returns the sequence at this node, in the form of an array of bytes.

setSequence

public void setSequence(kotlin.Array[] s)

Sets the sequence at this node, in the form of an array of bytes.

getBranchLength

public double getBranchLength()

Get the length of the branch attaching this node to its parent.

setBranchLength

public void setBranchLength(double value)

Set the length of the branch attaching this node to its parent.

getBranchLengthSE

public double getBranchLengthSE()

Get the length SE of the branch attaching this node to its parent.

setBranchLengthSE

public void setBranchLengthSE(double value)

Set the length SE of the branch attaching this node to its parent.

getNodeHeight

public double getNodeHeight()

Get the height of this node relative to the most recent node.

setNodeHeight

public void setNodeHeight(double value)

Set the height of this node relative to the most recent node.

setNodeHeight

public void setNodeHeight(double value,
                          boolean adjustChildBranchLengths)

Set the height of this node relative to the most recent node.

Parameters:

adjustChildBranchLengths - if true

getIdentifier

public Taxon getIdentifier()

Returns the identifier for this node.

setIdentifier

public void setIdentifier(Taxon id)

Set identifier for this node.

setNumber

public void setNumber(int n)

getNumber

public int getNumber()

getChild

public Node getChild(int n)

get child node

Parameters:

n - number of child

Returns:

org.jetbrains.dokka.NodeRenderContent@4b6fb76: child node

setChild

public void setChild(int n,
                     Node node)

set child node

Parameters:

n - number

hasChildren

public boolean hasChildren()

check whether this node is an internal node

Returns:

org.jetbrains.dokka.NodeRenderContent@5814dfea: result (true or false)

isLeaf

public boolean isLeaf()

check whether this node is an external node

Returns:

org.jetbrains.dokka.NodeRenderContent@60043238: result (true or false)

isRoot

public boolean isRoot()

check whether this node is a root node

Returns:

org.jetbrains.dokka.NodeRenderContent@73cb3979: result (true or false)

addChild

public void addChild(Node n)

add new child node

Parameters:

n - new child node

insertChild

public void insertChild(Node n,
                        int pos)

add new child node (insertion at a specific position)

Parameters:

n - new child node + @param pos position

removeChild

public Node removeChild(int n)

remove child

Parameters:

n - number of child to be removed

lengths2HeightsContemp

public void lengths2HeightsContemp()

determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.

setAttribute

public void setAttribute(java.lang.String name,
                         java.lang.Object value)

Sets a named attribute to the given value.

Parameters:

name - the name of the attribute

value - the value to set the attribute

getAttribute

public java.lang.Object getAttribute(java.lang.String name)

Parameters:

name - the name of the attribute.

Returns:

org.jetbrains.dokka.NodeRenderContent@4095013d: the attribute with the given name or null if it doesn't exist.

getAttributeNames

public java.util.Enumeration getAttributeNames()

Returns:

org.jetbrains.dokka.NodeRenderContent@3e007d4a: an enumeration of the attributes that this node has or null if the node has no attributes.

getChildCount

public int getChildCount()

Returns the number of children this node has.

toString

public java.lang.String toString()