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IBioAdaptable
- Interface in
org.thalia.bio
IBioAdapter
- Interface in
org.thalia.bio
IBioAllele
- Interface in
org.thalia.bio
Class Description Here
IBioConstants
- Interface in
org.thalia.bio.entity
Class Description Here
IBioCross
- Interface in
org.thalia.bio
Class Description Here
IBioCrossTypes
- Interface in
org.thalia.bio
Class Description Here
IBioEntity
- Interface in
org.thalia.bio
Class Description Here
IBioEntityTypes
- Interface in
org.thalia.bio
Class Description Here
IBioGenome
- Interface in
org.thalia.bio
IBioGenomeProperties
- Interface in
org.metaqtl
This interface defines both the keys and the default values of properties which can be handled by a org.thalia.bio.entity.IBioGenome.
IBioIndividual
- Interface in
org.thalia.bio
Class Description Here
IBioIndividualTree
- Interface in
org.thalia.bio
Class Description Here
IBioLGroup
- Interface in
org.thalia.bio
IBioLGroupProperties
- Interface in
org.metaqtl
This interface defines the key of properties which can be handled by a org.thalia.bio.entity.IBioLGroup.
IBioLocus
- Interface in
org.thalia.bio
IBioLocusProperties
- Interface in
org.metaqtl
This interface defines the key of the properties which can be handled by a org.thalia.bio.entity.IBioLocus.
IBioOntology
- Interface in
org.thalia.bio
This interface defines some rules to handle a ontology.
IBioOntologyTerm
- Interface in
org.thalia.bio
This class defines a term of an ontology.
IBioPopulation
- Interface in
org.thalia.bio
Class Description Here
ic1
- Variable in class org.metaqtl.
Qtl.QTLSupport
The recombination rate between the QTL position and the left border of the IC.
ic2
- Variable in class org.metaqtl.
Qtl.QTLSupport
The recombination rate between the QTL position and the right border of the IC.
ICOMP
- Static variable in class org.metaqtl.
EMCriteria
icomp
- Variable in class org.metaqtl.
EMCriteria
ICOMP_NAME
- Static variable in class org.metaqtl.
EMCriteria
id
- Variable in class org.metaqtl.
Qtl
The id of the Qtl
id
- Variable in class org.thalia.bio.entity.bean.
OntologyTermBean
The id of the term.
idx
- Variable in class org.metaqtl.
TreeNode
? The identifiant of the cluster.
idx1
- Variable in class org.metaqtl.
CMarkerSequence
The indices of the markers on the first chromosome for the common sequences.
idx2
- Variable in class org.metaqtl.
CMarkerSequence
The indices of the marker on the second chromosome for the common sequences.
IGeneticMapProperties
- Interface in
org.thalia.bio.entity
Class Description Here
ILGroupPosition
- Interface in
org.thalia.bio.util
Class Description Here
IMetaAlgorithm
- Interface in
org.metaqtl
This interface defines some methods which are common to data analysis algorithms.
IMetaQtlConstants
- Interface in
org.metaqtl
This interface defines some global constants which are used by several classes of the package.
IMIN(int, int)
- Static method in class org.metaqtl.numrec.
NumericalUtilities
Returns the min between
a
and
b
incms
- Variable in class org.metaqtl.
CMarkerSequence
indexx(int, double[], int[])
- Static method in class org.metaqtl.numrec.
NumericalUtilities
Sort the given array of double arrin[1..n] without destroying it and returns the sorted indices of the array elements into indx[1..n].
Individual
- Class in
org.thalia.bio.entity
Class Description Here
Individual()
- Constructor for class org.thalia.bio.entity.
Individual
Individual(String, IBioEntity)
- Constructor for class org.thalia.bio.entity.
Individual
INDIVIDUAL
- Static variable in interface org.thalia.bio.
IBioEntityTypes
The integer code for an individual entity
IndividualContainer
- Class in
org.thalia.bio.entity
Class Description Here
IndividualContainer()
- Constructor for class org.thalia.bio.entity.
IndividualContainer
IndividualContainer(String, IBioEntity)
- Constructor for class org.thalia.bio.entity.
IndividualContainer
individuals()
- Method in class org.thalia.bio.entity.
IndividualContainer
individuals()
- Method in interface org.thalia.bio.
IBioPopulation
InfoMap
- Class in
org.metaqtl.main
InfoMap()
- Constructor for class org.metaqtl.main.
InfoMap
init(Graphics2D, ChromGraph[])
- Method in class org.metaqtl.graph.
MetaGraph
initCmdLineParser()
- Method in class org.metaqtl.main.
MetaMain
initEM(double[], double[], EMResult, Random)
- Static method in class org.metaqtl.algo.
EMAlgorithm
Initializes the EM algorithm by randomly assigning observations to the clusters and do one M-Step to compute the first values of the parameters.
initNodeIdx()
- Method in class org.metaqtl.
Tree
initPalettes()
- Static method in class org.metaqtl.graph.
MetaGraphPar
initProbaPalette()
- Static method in class org.metaqtl.graph.
MetaGraphPar
initQTLPalette()
- Static method in class org.metaqtl.graph.
MetaGraphPar
initQTLPalette(int)
- Static method in class org.metaqtl.graph.
MetaGraphPar
initReverse()
- Method in class org.metaqtl.
Tree
intScale
- Variable in class org.metaqtl.
Qtl.QTLProj
The scale ratio between the original flanking marker interval and the one on the map used for projection.
IOntologyTermProperties
- Interface in
org.thalia.bio
IRISe
- Static variable in interface org.thalia.bio.
IBioCrossTypes
IRISi
- Static variable in interface org.thalia.bio.
IBioCrossTypes
isAssignableEntities(IResource, IBioEntity[])
- Static method in class org.thalia.bio.util.
ResourceBioEntityQuery
Returns true if all elements of entities are included in the resource.
isAssignableEntity(IResource, IBioEntity)
- Static method in class org.thalia.bio.util.
ResourceBioEntityQuery
Returns true if the resource contains the given entity.
isConnected(int)
- Method in class org.metaqtl.
ChromCluster.ClusterGraph
Test if the graph is connected
isConnected(int)
- Method in class org.metaqtl.
ChromCluster
Tests if the cluster of chromosome is connected using a graph approach.
isDubiousLocus(IBioLocus)
- Method in class org.metaqtl.
ChromCluster
If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.
isDubiousOrderLocus(IBioLocus)
- Static method in class org.metaqtl.util.
LocusProperties
Returns true if the given locus has a property order.dubious set to one, false otherwise
isIgnore()
- Method in class org.metaqtl.
Qtl
This methods returns true if the QTL must be ignored.
isLoggerEnable()
- Method in class org.metaqtl.algo.
MetaAlgorithm
ISWAP(int[], int, int)
- Static method in class org.metaqtl.numrec.
NumericalUtilities
Swaps elements i and j in a.
iterate(double[], double[], EMResult)
- Static method in class org.metaqtl.algo.
EMAlgorithm
This method performs one iteration of the EM-algorithm.
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