softparsmap
Class InparalogousStandard

java.lang.Object
  extended byooc.LinkedTagInstance
      extended bysoftparsmap.AbstractInparalogous
          extended bysoftparsmap.InparalogousStandard
All Implemented Interfaces:
Dependencies, Inparalogous

public class InparalogousStandard
extends AbstractInparalogous

The comparator created below will decide which sequence that will be chosen. For details see method description.


Constructor Summary
InparalogousStandard()
           
 
Method Summary
 java.util.Comparator getLeafComparator(Family family)
          Returns a comparator that compare gene leaves.
 
Methods inherited from class softparsmap.AbstractInparalogous
allLeavesIsFromSameSpecies, getInparalogous, removeBeforeSaving, removeInparalogous, removeWhileMinimizingMutation, setInparalogousOrder
 
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

InparalogousStandard

public InparalogousStandard()
Method Detail

getLeafComparator

public java.util.Comparator getLeafComparator(Family family)
Returns a comparator that compare gene leaves. If used when sorting the most preferred comes first. Given two sequences A, B, the preferred will be chosen as follows.
  1. if A is complete and B is not, A is preferred
  2. if above could not decide then if B is complete and A is not, B is preferred
  3. if above could not decide then if A is longer then B then A is preferred
  4. if above could not decide then if B is longer then A then B is preferred
  5. if above could not decide then if A's GI number is higher then B's GI number, then A is preferred
  6. if above could not decide then if B's GI number is higher then A's GI number, then B is preferred
  7. if above could not decide then A is preferred

Parameters:
family - is the family that this comparator will be used on
Returns:
a comparator that will be used to choose the right sequence
See Also:
Family