softparsmap
Class ComputeCompareGeneTrees
java.lang.Object
ooc.LinkedTagInstance
softparsmap.Compute
softparsmap.ComputeFamilyGroupPair
softparsmap.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]
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 |
ComputeCompareGeneTrees
public ComputeCompareGeneTrees()
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 computedfamilyGroup
- 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.