Serialized Form


Package org.metaqtl

Class org.metaqtl.EMCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

aic

double aic

aicc

double aicc

aic3

double aic3

bic

double bic

mir

double mir

icomp

double icomp

awe

double awe

Class org.metaqtl.Qtl.QTLCross extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name
The name of the cross design.


type

int type
The type of the cross.


gen

int gen
The number of generations.


size

int size
The number of individuals.

Class org.metaqtl.Qtl.QTLProj extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

mapOrigin

java.lang.String mapOrigin
The name of the map from which this QTL comes.


o_mrkIdxL

int o_mrkIdxL
The original indice of the left flanking marker.


o_mrkIdxR

int o_mrkIdxR
The original indice of the right flanking marker.


s_mrkIdxL

int s_mrkIdxL
The skeleton indice of the left flanking marker.


s_mrkIdxR

int s_mrkIdxR
The skeleton indice of the right flanking marker.


mapScale

double mapScale
The scale ratio between the original map and the map on which the QTL has been projected.


mapWeight

double mapWeight
The cumulated scale weights of the common marke sequences between the original map and the map on which the QTL has been projected.


intScale

double intScale
The scale ratio between the original flanking marker interval and the one on the map used for projection.


shareFlanking

boolean shareFlanking
True if the two maps share a common marker sequence around the QTL.


swap

boolean swap
True if the flanking marker order are inversed between the skeleton and the original map.

Class org.metaqtl.Qtl.QTLStats extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

rsquare

double rsquare
The r-square, i.e the proportion of variance explained by the QTL.


additive

double additive
The additive effect of the QTL.


dominance

double dominance
The dominance effect of the QTL.


lod

double lod
The lod score of the QTL.

Class org.metaqtl.Qtl.QTLSupport extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

ic1

double ic1
The recombination rate between the QTL position and the left border of the IC.


ic2

double ic2
The recombination rate between the QTL position and the right border of the IC.


from

double from
The position from the first marker to the left border of the IC.


to

double to
The position from the first marker to the right border of the IC.


lodDecrease

double lodDecrease
The value of the LOD decrease used to obtain the CI.

Class org.metaqtl.Qtl.QTLTrait extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name
The name of the trait.


unit

java.lang.String unit
The unit of the trait.


group

java.lang.String group
The name of the group to which the trait belongs.

Class org.metaqtl.TreeNode extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

idx

int idx
? The identifiant of the cluster.


label

java.lang.String label
The label of the cluster


card

int card
The number of sequences in the cluster


nidx

int[] nidx
The indices of the sub-nodes


leaf

boolean leaf
The status of the node.


dist

double dist
The distance between the node and its parent.


height

double height
The distance between the node and the root of the tree (if defined).


children

TreeNode[] children
Left and right children, or null


parent

TreeNode parent
The parent of the node


x

double x

y

double y

xc

double xc

Package org.metaqtl.bio.entity

Class org.metaqtl.bio.entity.BioEntityCollection extends java.util.ArrayList implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

parent

IBioEntity parent

properties

java.util.Properties properties

Package org.metaqtl.main

Class org.metaqtl.main.CmdLineParser.IllegalOptionValueException extends CmdLineParser.OptionException implements Serializable

Serialized Fields

option

CmdLineParser.Option option

value

java.lang.String value

Class org.metaqtl.main.CmdLineParser.NotFlagException extends CmdLineParser.UnknownOptionException implements Serializable

Serialized Fields

notflag

char notflag

Class org.metaqtl.main.CmdLineParser.OptionException extends java.lang.Exception implements Serializable

Class org.metaqtl.main.CmdLineParser.UnknownOptionException extends CmdLineParser.OptionException implements Serializable

Serialized Fields

optionName

java.lang.String optionName

Class org.metaqtl.main.CmdLineParser.UnknownSuboptionException extends CmdLineParser.UnknownOptionException implements Serializable

Serialized Fields

suboption

char suboption