softparsmap
Class ComputeMapInfo

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

public class ComputeMapInfo
extends ComputeFamilyGroup

This task will map species from the species tree to the the nodes of the gene tree for all families in a given family group. The result will be written to one file per family.


Constructor Summary
ComputeMapInfo()
           
 
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

ComputeMapInfo

public ComputeMapInfo()
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.