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This interface is responsible of handling inparalogous.
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. |
java.util.Comparator |
getLeafComparator(Family family)
Returns a comparator that compare gene leaves. |
boolean |
removeBeforeSaving()
Returns true iff inparalogous are removed before saving the final gene tree. |
GeneNode |
removeInparalogous(Family family,
GeneNode root)
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. |
Method Detail |
public java.util.Set getInparalogous(Family family, GeneNode node)
family
- is the family of the gene treenode
- is the root node of the gene tree
GeneNode
,
Family
public boolean allLeavesIsFromSameSpecies(GeneNode node)
node
- is the root of the subtree
GeneNode
public GeneNode removeInparalogous(Family family, GeneNode root)
family
- is the family of the gene treeroot
- is the root node of the gene tree
Family
,
GeneNode
public boolean removeWhileMinimizingMutation()
public boolean removeBeforeSaving()
public void setInparalogousOrder(GeneNode root)
root
- is the root of the gene treeGeneNode
public java.util.Comparator getLeafComparator(Family family)
family
- is the family that this comparator will be used on
Family
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