softparsmap
Interface EdgeType

All Known Implementing Classes:
AbstractEdgeType

public interface EdgeType

This interface is used to define different properties of an edge in a gene tree. In order to define your own properties, extend the class AbstractEdgeType and make the necessary changes in your property file.


Method Summary
 double getDefaultLeafEdge()
           
 double getDefaultNodeEdge()
           
 java.lang.String getName()
          Returns the name of the edge type.
 PropertyFile getPropertyFile()
          Returns the property file.
 java.lang.String getShortName()
          Returns a short name of this edge type.
 boolean isEdgeWeak(GeneNode node)
          Returns true if the edge value for the gene node is weak, else false.
 double joinEdges(GeneNode node1, GeneNode node2)
          Returns the edge value retained when joining the edges of the two gene nodes.
 double splitEdge(GeneNode node)
          Returns the new edge value after splitting the edge value for the gene node.
 

Method Detail

getPropertyFile

public PropertyFile getPropertyFile()
Returns the property file. Used in the gene node to access the property file.

Returns:
the property file
See Also:
PropertyFile

isEdgeWeak

public boolean isEdgeWeak(GeneNode node)
Returns true if the edge value for the gene node is weak, else false.

Parameters:
node - the gene node
Returns:
true if the edge value for the gene node is weak, else false.
See Also:
GeneNode

splitEdge

public double splitEdge(GeneNode node)
Returns the new edge value after splitting the edge value for the gene node. Used when re-rooting gene trees among other things.

Parameters:
node - the gene node
Returns:
the new edge value
See Also:
GeneNode

joinEdges

public double joinEdges(GeneNode node1,
                        GeneNode node2)
Returns the edge value retained when joining the edges of the two gene nodes.

Parameters:
node1 - the first gene node
node2 - the second gene node
Returns:
the edge value as the result of joining the two gene nodes edge values
See Also:
GeneNode

getName

public java.lang.String getName()
Returns the name of the edge type.

Returns:
the name of this edge type

getShortName

public java.lang.String getShortName()
Returns a short name of this edge type. Should not be longer then 2-3 letters long. This method is used in concentrated outputs.

Returns:
a short name of the edge type

getDefaultNodeEdge

public double getDefaultNodeEdge()

getDefaultLeafEdge

public double getDefaultLeafEdge()