com.hfg.bio.phylogeny

Class NewickTree

java.lang.Object

com.hfg.bio.phylogeny.NewickTree

public class NewickTree
extends java.lang.Object

Object representation of a Newick format phylogenetic tree. Does not work with negative distance values.

See Also:

The Newick tree format

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NewickTree.Flag

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BRANCH_TRAVERSAL_LIMIT_BASE_ID The ID used for the branch traversal limit ('branchLimit').

Constructor Summary

Constructors

Constructor and Description
NewickTree()
NewickTree(java.io.InputStream inStream)
NewickTree(java.lang.String inTree)

Method Summary

Modifier and Type	Method and Description
static java.lang.String	generateSvgJavascript()
java.util.List<PhyloNode>	getAllNodes()
java.util.List<PhyloNode>	getAllNodesOrderedByDistance()
java.awt.image.BufferedImage	getBufferedImage(TreeDisplaySettings inDisplaySettings)
java.awt.image.BufferedImage	getBufferedImageWithMaxWidth(TreeDisplaySettings inDisplaySettings, GfxSize inMaxWidth)
java.util.List<PhyloNode>	getLeafNodes()
java.util.List<Edge<PhyloNode>>	getMaxLeaf2LeafEdgeTrail()
java.lang.Float	getRootedTreeDistance()
PhyloNode	getRootNode()
java.util.List<java.util.List<PhyloNode>>	groupNodes(float inBranchLengthTraversalLimit, NewickTree.Flag... inFlags)
boolean	isRooted()
void	orderByNodeCount()
void	rootTreeByMidpointMethod()
NewickTree	setAsciiWidth(int inValue)
static void	setDefaultAsciiWidth(int inValue)
void	setMetaDataForDisplay(DataTable inMetaData)
void	setRootNode(PhyloNode inValue)
java.lang.String	toASCII() Constructs a phylogram in ASCII format.
DistanceMatrix	toDistanceMatrix() Note that this DistanceMatrix may not be equivalent to the DistanceMatrix originally used to construct the tree.
HTMLTag	toHTMLTag() Constructs a phylogram in HTML format.
void	toJPG(TreeDisplaySettings inDisplaySettings, java.io.OutputStream inStream)
java.lang.String	toString() Returns a Newick format representation of the tree.
XMLNode	toSVG()
XMLNode	toSVG(TreeDisplaySettings inDisplaySettings)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

BRANCH_TRAVERSAL_LIMIT_BASE_ID

public static final java.lang.String BRANCH_TRAVERSAL_LIMIT_BASE_ID

The ID used for the branch traversal limit ('branchLimit').

See Also:

Constant Field Values

Constructor Detail

NewickTree

public NewickTree()

NewickTree

public NewickTree(java.lang.String inTree)

NewickTree

public NewickTree(java.io.InputStream inStream)

Method Detail

setDefaultAsciiWidth

public static void setDefaultAsciiWidth(int inValue)

setAsciiWidth

public NewickTree setAsciiWidth(int inValue)

isRooted

public boolean isRooted()

getRootNode

public PhyloNode getRootNode()

setRootNode

public void setRootNode(PhyloNode inValue)

getLeafNodes

public java.util.List<PhyloNode> getLeafNodes()

getAllNodes

public java.util.List<PhyloNode> getAllNodes()

orderByNodeCount

public void orderByNodeCount()

getRootedTreeDistance

public java.lang.Float getRootedTreeDistance()

getMaxLeaf2LeafEdgeTrail

public java.util.List<Edge<PhyloNode>> getMaxLeaf2LeafEdgeTrail()

rootTreeByMidpointMethod

public void rootTreeByMidpointMethod()

groupNodes

public java.util.List<java.util.List<PhyloNode>> groupNodes(float inBranchLengthTraversalLimit,
                                                            NewickTree.Flag... inFlags)

toDistanceMatrix

public DistanceMatrix toDistanceMatrix()

Note that this DistanceMatrix may not be equivalent to the DistanceMatrix originally used to construct the tree.

Returns:

the DistanceMatrix for the tree

toString

public java.lang.String toString()

Returns a Newick format representation of the tree.

Overrides:

toString in class java.lang.Object

Returns:

Newick format string representation of the tree

toASCII

public java.lang.String toASCII()

Constructs a phylogram in ASCII format.

Returns:

an ASCII representation of the tree

toHTMLTag

public HTMLTag toHTMLTag()

Constructs a phylogram in HTML format.

Returns:

an HTML representation of the tree

setMetaDataForDisplay

public void setMetaDataForDisplay(DataTable inMetaData)

toSVG

public XMLNode toSVG()

toSVG

public XMLNode toSVG(TreeDisplaySettings inDisplaySettings)

generateSvgJavascript

public static java.lang.String generateSvgJavascript()
                                              throws java.io.IOException

Throws:

java.io.IOException

toJPG

public void toJPG(TreeDisplaySettings inDisplaySettings,
                  java.io.OutputStream inStream)
           throws java.io.IOException

Throws:

java.io.IOException

getBufferedImage

public java.awt.image.BufferedImage getBufferedImage(TreeDisplaySettings inDisplaySettings)

getBufferedImageWithMaxWidth

public java.awt.image.BufferedImage getBufferedImageWithMaxWidth(TreeDisplaySettings inDisplaySettings,
                                                                 GfxSize inMaxWidth)

getAllNodesOrderedByDistance

public java.util.List<PhyloNode> getAllNodesOrderedByDistance()