org.metaqtl.algo
Class MetaMapAlgorithm
java.lang.Object
org.metaqtl.algo.MetaAlgorithm
org.metaqtl.algo.MetaMapAlgorithm
- All Implemented Interfaces:
- IMetaAlgorithm
public class MetaMapAlgorithm
- extends MetaAlgorithm
This class is dedicated to the construction of a consensus
genetic map from a set of genetic maps based on a Weigthed
Least Square approach.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MetaMapAlgorithm
public MetaMapAlgorithm(IBioGenome[] maps,
IBioGenome skeleton,
IBioLocus[] dubious,
MetaDico mrkDico)
- Parameters:
maps
- skeleton
- dubious
- mrkDico
-
getResult
public MetaMap getResult()
- Returns:
run
public void run()
- This method builds a consensus genetic map from the given
array of
maps
. The consensus map is returned
as a MetaMap
. If skeleton
is not null
then the positions of the markers on this map are assumed to
be known and are used as anchor points in the construction
of the consensus map. If dubious is no null or not
empty then the loci of this array won't be included in the consensus
map.
- Parameters:
maps
- the array of genetic maps.skeleton
- a genetic map used as skeleton.dubious
- an array of dubious loci to not include in the construction.
buildMetaChrom
protected MetaChrom buildMetaChrom(ChromCluster cluster)
- For a cluster of chromosomes
cluster
this method
builds the consensus chromosome using a Weighted Least Square
strategy and returns the result as a MetaChrom
object.
- Parameters:
cluster
- the cluster of chromosomes.
- Returns:
- the consensus chromosome.
setMarkerDico
public void setMarkerDico(MetaDico mrkDico)
- Parameters:
mrkDico
-
setMrkThreshold
public void setMrkThreshold(int mrkThresh)
- Parameters:
mrkThresh
-