softparsmap
Class ComputeFamilyGroupPair

java.lang.Object
  extended byooc.LinkedTagInstance
      extended bysoftparsmap.Compute
          extended bysoftparsmap.ComputeFamilyGroupPair
All Implemented Interfaces:
Dependencies
Direct Known Subclasses:
ComputeCompareGeneTrees

public abstract class ComputeFamilyGroupPair
extends Compute

This program is used when computing a task on a pair of family groups. If used without any arguments, the usage will be printed. Usage:

 Compute [property file] [task did] [first family group did] [second family group did]
 


Constructor Summary
ComputeFamilyGroupPair()
           
 
Method Summary
 void afterCompute(FamilyGroup familyGroup)
          This method is called after all families from the family group have been computed.
 void beforeCompute(FamilyGroup familyGroup)
          This method is called before any family from the family group is computed.
abstract  void computeFamily(Family family, FamilyGroup familyGroup, boolean verbose)
          Compute a family.
 void computeTask()
          Is called by main method to run task.
 FamilyGroup getFamilyGroup1()
           
 FamilyGroup getFamilyGroup2()
           
 
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

ComputeFamilyGroupPair

public ComputeFamilyGroupPair()
Method Detail

getFamilyGroup1

public FamilyGroup getFamilyGroup1()

getFamilyGroup2

public FamilyGroup getFamilyGroup2()

computeTask

public void computeTask()
Description copied from class: Compute
Is called by main method to run task.

Specified by:
computeTask in class Compute

beforeCompute

public void beforeCompute(FamilyGroup familyGroup)
This method is called before any family from the family group is computed.

Parameters:
familyGroup - is the family group to be run.

computeFamily

public abstract void computeFamily(Family family,
                                   FamilyGroup familyGroup,
                                   boolean verbose)
                            throws java.lang.Throwable
Compute a family.

Parameters:
family - is the family that will be computed
familyGroup - is the family group from which family comes.
Throws:
java.lang.Throwable - because exceptions are logged for every family but the task will continue on the rest of the family group.

afterCompute

public void afterCompute(FamilyGroup familyGroup)
This method is called after all families from the family group have been computed.

Parameters:
familyGroup - is the family group which was run.