softparsmap
Class ComputeCompareGeneTrees

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

public class ComputeCompareGeneTrees
extends ComputeFamilyGroupPair

This program is used to compare the topology of gene trees from two family groups. If used without any arguments, the usage will be printed. Usage:

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


Constructor Summary
ComputeCompareGeneTrees()
           
 
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.
 void computeFamily(Family first, FamilyGroup familyGroup, boolean verbose)
          Compute a family.
 
Methods inherited from class softparsmap.ComputeFamilyGroupPair
computeTask, getFamilyGroup1, 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

ComputeCompareGeneTrees

public ComputeCompareGeneTrees()
Method Detail

beforeCompute

public void beforeCompute(FamilyGroup familyGroup)
Description copied from class: ComputeFamilyGroupPair
This method is called before any family from the family group is computed.

Overrides:
beforeCompute in class ComputeFamilyGroupPair
Parameters:
familyGroup - is the family group to be run.

computeFamily

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

Specified by:
computeFamily in class ComputeFamilyGroupPair
Parameters:
first - 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)
Description copied from class: ComputeFamilyGroupPair
This method is called after all families from the family group have been computed.

Overrides:
afterCompute in class ComputeFamilyGroupPair
Parameters:
familyGroup - is the family group which was run.