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java.lang.Objectooc.LinkedTagInstance
softparsmap.AbstractInparalogous
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()
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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 java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface softparsmap.Inparalogous |
getLeafComparator |
Constructor Detail |
public AbstractInparalogous()
Method Detail |
public boolean allLeavesIsFromSameSpecies(GeneNode node)
Inparalogous
allLeavesIsFromSameSpecies
in interface Inparalogous
node
- is the root of the subtree
GeneNode
public java.util.Set getInparalogous(Family family, GeneNode node)
Inparalogous
getInparalogous
in interface Inparalogous
family
- is the family of the gene treenode
- is the root node of the gene tree
GeneNode
,
Family
public boolean removeWhileMinimizingMutation()
Inparalogous
removeWhileMinimizingMutation
in interface Inparalogous
public boolean removeBeforeSaving()
Inparalogous
removeBeforeSaving
in interface Inparalogous
public void setInparalogousOrder(GeneNode root)
Inparalogous
setInparalogousOrder
in interface Inparalogous
root
- is the root of the gene treeGeneNode
public GeneNode removeInparalogous(Family family, GeneNode node)
Inparalogous
removeInparalogous
in interface Inparalogous
family
- is the family of the gene treenode
- is the root node of the gene tree
Family
,
GeneNode
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