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