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I

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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