softparsmap
Class ComputeRoot

java.lang.Object
  extended byooc.LinkedTagInstance
      extended bysoftparsmap.Compute
          extended bysoftparsmap.ComputeFamilyGroup
              extended bysoftparsmap.ComputeRoot
All Implemented Interfaces:
Dependencies

public class ComputeRoot
extends ComputeFamilyGroup

This task will root unrooted gene trees by minimizing duplications and loss. In-paralogous may also be removed. The result will be written to one file per family.


Constructor Summary
ComputeRoot()
           
 
Method Summary
 void computeFamily(Family family, boolean verbose)
          Compute a family.
 
Methods inherited from class softparsmap.ComputeFamilyGroup
afterCompute, beforeCompute, computeTask
 
Methods inherited from class softparsmap.Compute
getArg, getArgs, getInparalogous, getPrintFamilyInfo, getPropertyFile, getTargetFile, getTreeParser, initiateDataSource, main, numberArgs, setArgs, useProgressIndicator
 
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
 

Constructor Detail

ComputeRoot

public ComputeRoot()
Method Detail

computeFamily

public void computeFamily(Family family,
                          boolean verbose)
                   throws java.lang.Throwable
Description copied from class: ComputeFamilyGroup
Compute a family.

Specified by:
computeFamily in class ComputeFamilyGroup
Parameters:
family - is the family that will be computed
verbose - is true if extra information is printed
Throws:
java.lang.Throwable - because exceptions are logged for every family but the task will continue on the rest of the family group.