softparsmap
Class AbstractInparalogous

java.lang.Object
  extended byooc.LinkedTagInstance
      extended bysoftparsmap.AbstractInparalogous
All Implemented Interfaces:
Dependencies, Inparalogous
Direct Known Subclasses:
InparalogousStandard

public abstract class AbstractInparalogous
extends LinkedTagInstance
implements Inparalogous

Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.


Constructor Summary
AbstractInparalogous()
           
 
Method Summary
 boolean allLeavesIsFromSameSpecies(GeneNode node)
          Returns true if all gene leaves are coming from the same species.
 java.util.Set getInparalogous(Family family, GeneNode node)
          Returns a set of nodes N where all nodes n in N only have in-paralogous sequences in its subtree.
 boolean removeBeforeSaving()
          Returns true iff inparalogous are removed before saving the final gene tree.
 GeneNode removeInparalogous(Family family, GeneNode node)
          Removes all inparalogous in the gene tree.
 boolean removeWhileMinimizingMutation()
          Returns true iff inparalogous are removed after each mid point re-root, before duplications and loss is counted, else false.
 void setInparalogousOrder(GeneNode root)
          When inparalogous are removed one of the gene leaves will be chosen as the final sequence to represent the species.
 
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, setupInstance
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface softparsmap.Inparalogous
getLeafComparator
 

Constructor Detail

AbstractInparalogous

public AbstractInparalogous()
Method Detail

allLeavesIsFromSameSpecies

public boolean allLeavesIsFromSameSpecies(GeneNode node)
Description copied from interface: Inparalogous
Returns true if all gene leaves are coming from the same species. That is if all genes are in-paralogous.

Specified by:
allLeavesIsFromSameSpecies in interface Inparalogous
Parameters:
node - is the root of the subtree
Returns:
true if all genes in this subtree are in-paralogous.
See Also:
GeneNode

getInparalogous

public java.util.Set getInparalogous(Family family,
                                     GeneNode node)
Description copied from interface: Inparalogous
Returns a set of nodes N where all nodes n in N only have in-paralogous sequences in its subtree.

Specified by:
getInparalogous in interface Inparalogous
Parameters:
family - is the family of the gene tree
node - is the root node of the gene tree
Returns:
a set of internal nodes where all are in-paralogous
See Also:
GeneNode, Family

removeWhileMinimizingMutation

public boolean removeWhileMinimizingMutation()
Description copied from interface: Inparalogous
Returns true iff inparalogous are removed after each mid point re-root, before duplications and loss is counted, else false.

Specified by:
removeWhileMinimizingMutation in interface Inparalogous
Returns:
true iff inparalogous are removed while minimizing mutation.

removeBeforeSaving

public boolean removeBeforeSaving()
Description copied from interface: Inparalogous
Returns true iff inparalogous are removed before saving the final gene tree.

Specified by:
removeBeforeSaving in interface Inparalogous
Returns:
true iff inparalogous are removed before saving the gene tree

setInparalogousOrder

public void setInparalogousOrder(GeneNode root)
Description copied from interface: Inparalogous
When inparalogous are removed one of the gene leaves will be chosen as the final sequence to represent the species. This order that is set here will then be used.

Specified by:
setInparalogousOrder in interface Inparalogous
Parameters:
root - is the root of the gene tree
See Also:
GeneNode

removeInparalogous

public GeneNode removeInparalogous(Family family,
                                   GeneNode node)
Description copied from interface: Inparalogous
Removes all inparalogous in the gene tree.

Specified by:
removeInparalogous in interface Inparalogous
Parameters:
family - is the family of the gene tree
node - is the root node of the gene tree
Returns:
the root node for the tree where all inparalogous are removed.
See Also:
Family, GeneNode