com.hfg.bio.phylogeny

Class PhylogeneticTree

java.lang.Object

com.hfg.bio.phylogeny.PhylogeneticTree

public class PhylogeneticTree
extends Object

Object representation of a 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	PhylogeneticTree.Flag

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
PhylogeneticTree()
PhylogeneticTree(InputStream inStream)
PhylogeneticTree(String inTree)

Method Summary

Modifier and Type	Method and Description
void	clearAttributes()
static String	generateSvgJavascript()
List<PhyloNode>	getAllNodes()
List<PhyloNode>	getAllNodesOrderedByDistance()
Object	getAttribute(String inName)
Collection<String>	getAttributeNames()
BufferedImage	getBufferedImage(TreeDisplaySettings inDisplaySettings)
BufferedImage	getBufferedImageWithMaxWidth(TreeDisplaySettings inDisplaySettings, GfxSize inMaxWidth)
PhyloNode	getClosestLeaf(PhyloNode inNode)
Edge	getClosestLeafPair()
List<PhyloNode>	getLeafNodes()
List<Edge<PhyloNode>>	getMaxLeaf2LeafEdgeTrail()
Float	getRootedTreeDistance()
PhyloNode	getRootNode()
String	getTitle()
List<List<PhyloNode>>	groupNodes(float inBranchLengthTraversalLimit, PhylogeneticTree.Flag... inFlags)
boolean	hasAttribute(String inName)
boolean	isRooted()
void	orderByNodeCount()
Object	removeAttribute(String inName)
void	removeNode(PhyloNode inNode)
void	rootTreeByMidpointMethod()
PhylogeneticTree	setAsciiWidth(int inValue)
void	setAttribute(String inName, Object inValue)
static void	setDefaultAsciiWidth(int inValue)
void	setMetaDataForDisplay(DataTable inMetaData)
void	setRootNode(PhyloNode inValue)
PhylogeneticTree	setTitle(String inValue)
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, OutputStream inStream)
String	toNewick() Returns a Newick format representation of the tree.
String	toString() Returns a Newick format representation of the tree.
SVG	toSVG()
SVG	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 String BRANCH_TRAVERSAL_LIMIT_BASE_ID

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

See Also:

Constant Field Values

Constructor Detail

PhylogeneticTree

public PhylogeneticTree()

PhylogeneticTree

public PhylogeneticTree(String inTree)

PhylogeneticTree

public PhylogeneticTree(InputStream inStream)

Method Detail

setTitle

public PhylogeneticTree setTitle(String inValue)

getTitle

public String getTitle()

setDefaultAsciiWidth

public static void setDefaultAsciiWidth(int inValue)

setAsciiWidth

public PhylogeneticTree setAsciiWidth(int inValue)

isRooted

public boolean isRooted()

getRootNode

public PhyloNode getRootNode()

setRootNode

public void setRootNode(PhyloNode inValue)

getLeafNodes

public List<PhyloNode> getLeafNodes()

getAllNodes

public List<PhyloNode> getAllNodes()

orderByNodeCount

public void orderByNodeCount()

getRootedTreeDistance

public Float getRootedTreeDistance()

removeNode

public void removeNode(PhyloNode inNode)

getClosestLeaf

public PhyloNode getClosestLeaf(PhyloNode inNode)

getClosestLeafPair

public Edge getClosestLeafPair()

getMaxLeaf2LeafEdgeTrail

public List<Edge<PhyloNode>> getMaxLeaf2LeafEdgeTrail()

rootTreeByMidpointMethod

public void rootTreeByMidpointMethod()

groupNodes

public List<List<PhyloNode>> groupNodes(float inBranchLengthTraversalLimit,
                                        PhylogeneticTree.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 String toString()

Returns a Newick format representation of the tree.

Overrides:

toString in class Object

Returns:

Newick format string representation of the tree

toNewick

public String toNewick()

Returns a Newick format representation of the tree.

Returns:

Newick format string representation of the tree

toASCII

public 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 SVG toSVG()

toSVG

public SVG toSVG(TreeDisplaySettings inDisplaySettings)

generateSvgJavascript

public static String generateSvgJavascript()
                                    throws IOException

Throws:

IOException

toJPG

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

Throws:

IOException

getBufferedImage

public BufferedImage getBufferedImage(TreeDisplaySettings inDisplaySettings)

getBufferedImageWithMaxWidth

public BufferedImage getBufferedImageWithMaxWidth(TreeDisplaySettings inDisplaySettings,
                                                  GfxSize inMaxWidth)

getAllNodesOrderedByDistance

public List<PhyloNode> getAllNodesOrderedByDistance()

setAttribute

public void setAttribute(String inName,
                         Object inValue)

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)