softparsmap
Class StandardEdgeType

java.lang.Object
  extended byooc.LinkedTagInstance
      extended bysoftparsmap.AbstractEdgeType
          extended bysoftparsmap.StandardEdgeType
All Implemented Interfaces:
Dependencies, EdgeType

public class StandardEdgeType
extends AbstractEdgeType

This is a edge type that can me configured within limits. See the def.xml file for more information.


Constructor Summary
StandardEdgeType()
           
 
Method Summary
 java.lang.String getName()
          Returns the name of the edge type.
 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 n1, GeneNode n2)
          Returns the edge value retained when joining the edges of the two gene nodes.
 void setLimit(double newLimit)
          Sets the limit that defines if an edge value is weak or not.
 double splitEdge(GeneNode n)
          Returns the new edge value after splitting the edge value for the gene node.
 java.lang.String toStringAll()
          Returns the name, limit, and divide value.
 
Methods inherited from class softparsmap.AbstractEdgeType
getDefaultLeafEdge, getDefaultNodeEdge, getPropertyFile, setupInstance
 
Methods inherited from class ooc.LinkedTagInstance
containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

StandardEdgeType

public StandardEdgeType()
Method Detail

setLimit

public void setLimit(double newLimit)
Sets the limit that defines if an edge value is weak or not.

Parameters:
newLimit - is the new limit

isEdgeWeak

public boolean isEdgeWeak(GeneNode node)
Description copied from interface: EdgeType
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 n)
Description copied from interface: EdgeType
Returns the new edge value after splitting the edge value for the gene node. Used when re-rooting gene trees among other things.

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

joinEdges

public double joinEdges(GeneNode n1,
                        GeneNode n2)
Description copied from interface: EdgeType
Returns the edge value retained when joining the edges of the two gene nodes.

Parameters:
n1 - the first gene node
n2 - 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()
Description copied from interface: EdgeType
Returns the name of the edge type.

Returns:
the name of this edge type

getShortName

public java.lang.String getShortName()
Description copied from interface: EdgeType
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

toStringAll

public java.lang.String toStringAll()
Returns the name, limit, and divide value.

Returns:
the name, limit, and divide value