PhyloNode (com.hfg API Documentation)

java.lang.Object
- com.hfg.bio.phylogeny.PhyloNode

```
public class PhyloNode
extends Object
```
Object representation of a node in a Newick format phylogenetic tree. Does not work with negative distance values.

Constructor Summary

Constructors
Constructor and Description

PhyloNode()

Constructors
Constructor and Description
`PhyloNode()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`addEdge(Edge<PhyloNode> inEdge)`
`void`	`addEdge(PhyloNode in2ndNode, Float inDistance)`
`void`	`clearAttributes()`
`Float`	`distanceTo(PhyloNode inNode2)` Calculates the distance between two nodes in the tree.
`Double`	`getAngle()`
`Object`	`getAttribute(String inName)`
`Collection<String>`	`getAttributeNames()`
`List<PhyloNode>`	`getChildNodes()`
`Color`	`getColor()`
`Float`	`getDistanceFromRoot()`
`List<Edge<PhyloNode>>`	`getEdges()`
`String`	`getId()`
`String`	`getLabel()`
`List<Edge<PhyloNode>>`	`getLeafFacingEdges()` Returns the leaf-facing edges.
`protected Integer`	`getLineIndex()`
`Float`	`getMaxDistanceToLeaf()`
`Edge<PhyloNode>`	`getParentEdge()` Returns the root-facing edge.
`PhyloNode`	`getParentNode()`
`int`	`getSubnodeCount()`
`String`	`getTooltip()`
`protected Integer`	`getVericalLineEndIndex()`
`protected Integer`	`getVericalLineStartIndex()`
`boolean`	`hasAttribute(String inName)`
`boolean`	`hasAttributes()`
`boolean`	`isLeaf()`
`void`	`makeRoot()`
`void`	`orderEdgesByLeafCount()`
`Object`	`removeAttribute(String inName)`
`protected boolean`	`removeEdge(Edge<PhyloNode> inEdge)`
`protected boolean`	`removeEdgeFrom(PhyloNode inNode)`
`PhyloNode`	`setAngle(Double inAngleInRadians)`
`void`	`setAttribute(String inName, Object inValue)`
`PhyloNode`	`setColor(Color inValue)`
`PhyloNode`	`setId(int inValue)`
`PhyloNode`	`setId(String inValue)`
`PhyloNode`	`setLabel(String inValue)`
`protected void`	`setLineIndex(int inValue)`
`protected void`	`setRootDirection(Edge<PhyloNode> inEdge)`
`PhyloNode`	`setTooltip(String inValue)`
`protected void`	`setVerticalLineEndIndex(int inValue)`
`protected void`	`setVerticalLineStartIndex(int inValue)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail
- PhyloNode
```
public PhyloNode()
```

Method Detail

setId
```
public PhyloNode setId(int inValue)
```

setId

public PhyloNode setId(String inValue)

getId
```
public String getId()
```

setLabel

public PhyloNode setLabel(String inValue)

getLabel
```
public String getLabel()
```

setTooltip

public PhyloNode setTooltip(String inValue)

getTooltip
```
public String getTooltip()
```

setColor

public PhyloNode setColor(Color inValue)

getColor
```
public Color getColor()
```

getEdges

public List<Edge<PhyloNode>> getEdges()

addEdge

public void addEdge(PhyloNode in2ndNode,
                    Float inDistance)

setAngle

public PhyloNode setAngle(Double inAngleInRadians)

getAngle
```
public Double getAngle()
```

addEdge

protected void addEdge(Edge<PhyloNode> inEdge)

removeEdge

protected boolean removeEdge(Edge<PhyloNode> inEdge)

removeEdgeFrom

protected boolean removeEdgeFrom(PhyloNode inNode)

isLeaf
```
public boolean isLeaf()
```

makeRoot
```
public void makeRoot()
```

setRootDirection

protected void setRootDirection(Edge<PhyloNode> inEdge)

getParentNode
```
public PhyloNode getParentNode()
```

getChildNodes

public List<PhyloNode> getChildNodes()

getParentEdge
```
public Edge<PhyloNode> getParentEdge()
```
Returns the root-facing edge.

Returns:

the root-facing Edge for the node

getLeafFacingEdges
```
public List<Edge<PhyloNode>> getLeafFacingEdges()
```
Returns the leaf-facing edges.

Returns:

the leaf-facing Edge for the node

orderEdgesByLeafCount
```
public void orderEdgesByLeafCount()
```

getDistanceFromRoot
```
public Float getDistanceFromRoot()
```

getMaxDistanceToLeaf
```
public Float getMaxDistanceToLeaf()
```

getSubnodeCount
```
public int getSubnodeCount()
```

distanceTo
```
public Float distanceTo(PhyloNode inNode2)
```
Calculates the distance between two nodes in the tree.

Parameters:

inNode2 - the node to calculate the distance to

Returns:

the distance between this node and the specified node

toString
```
public String toString()
```
Overrides:

toString in class Object

setAttribute

public void setAttribute(String inName,
                         Object inValue)

hasAttributes
```
public boolean hasAttributes()
```

hasAttribute

public boolean hasAttribute(String inName)

getAttribute

public Object getAttribute(String inName)

getAttributeNames

public Collection<String> getAttributeNames()

clearAttributes
```
public void clearAttributes()
```

removeAttribute

public Object removeAttribute(String inName)

setLineIndex

protected void setLineIndex(int inValue)

getLineIndex
```
protected Integer getLineIndex()
```

setVerticalLineStartIndex

protected void setVerticalLineStartIndex(int inValue)

getVericalLineStartIndex

protected Integer getVericalLineStartIndex()

setVerticalLineEndIndex

protected void setVerticalLineEndIndex(int inValue)

getVericalLineEndIndex

protected Integer getVericalLineEndIndex()

Class PhyloNode

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PhyloNode

Method Detail

setId

setId

getId

setLabel

getLabel

setTooltip

getTooltip

setColor

getColor

getEdges

addEdge

setAngle

getAngle

addEdge

removeEdge

removeEdgeFrom

isLeaf

makeRoot

setRootDirection

getParentNode

getChildNodes

getParentEdge

getLeafFacingEdges

orderEdgesByLeafCount

getDistanceFromRoot

getMaxDistanceToLeaf

getSubnodeCount

distanceTo

toString

setAttribute

hasAttributes

hasAttribute

getAttribute

getAttributeNames

clearAttributes

removeAttribute

setLineIndex

getLineIndex

setVerticalLineStartIndex

getVericalLineStartIndex

setVerticalLineEndIndex

getVericalLineEndIndex