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org.metaqtl.* |
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org.metaqtl.EMCriteria | ||
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public static final int |
AIC |
0 |
public static final java.lang.String |
AIC_NAME |
"AIC" |
public static final int |
AIC3 |
1 |
public static final java.lang.String |
AIC3_NAME |
"AIC3" |
public static final int |
AICc |
5 |
public static final java.lang.String |
AICc_NAME |
"AICc" |
public static final int |
AWE |
4 |
public static final java.lang.String |
AWE_NAME |
"AWE" |
public static final int |
BIC |
3 |
public static final java.lang.String |
BIC_NAME |
"BIC" |
public static final int |
ICOMP |
2 |
public static final java.lang.String |
ICOMP_NAME |
"ICOMP" |
org.metaqtl.IBioGenomeProperties | ||
---|---|---|
public static final java.lang.String |
CROSS_SIZE |
"cross.size" |
public static final java.lang.String |
CROSS_TYPE |
"cross.type" |
public static final java.lang.String |
MAPPING_CROSS |
"mapping.cross" |
public static final java.lang.String |
MAPPING_EXPANSION |
"mapping.expansion" |
public static final java.lang.String |
MAPPING_FUNCTION |
"mapping.function" |
public static final java.lang.String |
MAPPING_FUNCTION_HALDANE |
"haldane" |
public static final java.lang.String |
MAPPING_FUNCTION_KOSAMBI |
"kosambi" |
public static final java.lang.String |
MAPPING_UNIT |
"mapping.unit" |
public static final java.lang.String |
MAPPING_UNIT_CM |
"cM" |
public static final java.lang.String |
MAPPING_UNIT_M |
"M" |
org.metaqtl.IBioLGroupProperties | ||
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public static final java.lang.String |
CHISQUARE |
"meta.chisquare" |
public static final java.lang.String |
DOF |
"meta.dof" |
public static final java.lang.String |
PVALUE |
"meta.pvalue" |
org.metaqtl.IBioLocusProperties | ||
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public static final java.lang.String |
DUBIOUS_ORDER |
"dubious.order" |
public static final java.lang.String |
OCCURENCE |
"meta.occurence" |
public static final java.lang.String |
QTL_CI_FROM |
"qtl.ci.from" |
public static final java.lang.String |
QTL_CI_LOD_DECREASE |
"qtl.ci.lod.decrease" |
public static final java.lang.String |
QTL_CI_TO |
"qtl.ci.to" |
public static final java.lang.String |
QTL_CROSS_NAME |
"qtl.cross.name" |
public static final java.lang.String |
QTL_CROSS_SIZE |
"qtl.cross.size" |
public static final java.lang.String |
QTL_CROSS_TYPE |
"qtl.cross.type" |
public static final java.lang.String |
QTL_PROJ_INTSCALE |
"qtl.proj.intScale" |
public static final java.lang.String |
QTL_PROJ_MAPSCALE |
"qtl.proj.mapScale" |
public static final java.lang.String |
QTL_PROJ_ORIGIN |
"qtl.proj.mapOrigin" |
public static final java.lang.String |
QTL_PROJ_SHAREFLANKING |
"qtl.proj.shareFlanking" |
public static final java.lang.String |
QTL_PROJ_SWAPFLANKING |
"qtl.proj.swapFlanking" |
public static final java.lang.String |
QTL_STATS_ADDITIVE |
"qtl.effect.additive" |
public static final java.lang.String |
QTL_STATS_DOMINANCE |
"qtl.effect.dominance" |
public static final java.lang.String |
QTL_STATS_RSQUARE |
"qtl.rsquare" |
public static final java.lang.String |
QTL_TRAIT_GROUP |
"qtl.trait.group" |
public static final java.lang.String |
QTL_TRAIT_NAME |
"qtl.trait.name" |
public static final java.lang.String |
QTL_TRAIT_UNIT |
"qtl.trait.unit" |
org.metaqtl.IMetaQtlConstants | ||
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public static final int |
CI_MISS_IGNORE |
2 |
public static final int |
CI_MISS_IMPUTATION |
1 |
public static final int |
CI_MODE_AVAILABLE |
1 |
public static final int |
CI_MODE_LOD |
2 |
public static final int |
CI_MODE_MAXIMAL |
4 |
public static final int |
CI_MODE_RSQUARE |
3 |
public static final int |
MAPPING_FUNCTION_HALDANE |
1 |
public static final int |
MAPPING_FUNCTION_KOSAMBI |
2 |
public static final int |
MAPPING_FUNCTION_UNKNOWN |
0 |
public static final int |
MAPPING_UNIT_CM |
2 |
public static final int |
MAPPING_UNIT_M |
1 |
public static final int |
MAPPING_UNIT_UNKNOWN |
0 |
public static final double |
TINY_MAPPING_DISTANCE |
1.0E-5 |
public static final double |
TINY_MAPPING_VARIANCE |
1.0E-32 |
public static final java.lang.String |
VERSION |
"1.0" |
org.metaqtl.QtlPartition | ||
---|---|---|
public static final int |
HORIZONTAL_MODE |
0 |
public static final int |
VERTICAL_MODE |
1 |
org.metaqtl.algo.EMAlgorithm | ||
---|---|---|
public static final int |
EM_CONTINUE |
1 |
public static final int |
EM_FAILURE |
2 |
public static final int |
EM_OK |
0 |
public static final double |
TINY_Z_PROBA |
4.9E-324 |
org.metaqtl.algo.HClustAlgorithm | ||
---|---|---|
public static final int |
CENTROID_METHOD |
1 |
public static final int |
WARD_METHOD |
2 |
org.metaqtl.bio.IBioCrossTypes | ||
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public static final int |
BC |
1 |
public static final int |
DH |
6 |
public static final int |
IRISe |
7 |
public static final int |
IRISi |
8 |
public static final int |
RF |
5 |
public static final int |
RILSe |
2 |
public static final int |
RILSi |
3 |
public static final int |
SF |
4 |
public static final int |
UNKNOWN |
0 |
org.metaqtl.bio.IBioEntityTypes | ||
---|---|---|
public static final int |
ALLELE |
8 |
public static final int |
COLLECTION |
9 |
public static final int |
GENOME |
3 |
public static final int |
INDIVIDUAL |
1 |
public static final int |
LGROUP |
4 |
public static final int |
LOCUS |
5 |
public static final int |
MARKERLOCUS |
6 |
public static final int |
ONTOLOGY |
11 |
public static final int |
ONTOLOGY_TERM |
10 |
public static final int |
POPULATION |
2 |
public static final int |
QTLLOCUS |
7 |
org.metaqtl.bio.IBioLocus | ||
---|---|---|
public static final int |
MARKER |
0 |
public static final int |
QTL |
1 |
org.metaqtl.bio.IOntologyTermProperties | ||
---|---|---|
public static final java.lang.String |
DEFINITION |
"term.definition" |
public static final java.lang.String |
SYNONYMS |
"term.synonyms" |
org.metaqtl.bio.entity.IGeneticMapProperties | ||
---|---|---|
public static final java.lang.String |
cartoFunctionHaldane |
"haldane" |
public static final java.lang.String |
cartoFunctionKey |
"carto.function" |
public static final java.lang.String |
cartoFunctionKosambi |
"kosambi" |
public static final java.lang.String |
distanceUnitCM |
"cM" |
public static final java.lang.String |
distanceUnitKey |
"distance.unit" |
org.metaqtl.bio.util.ILGroupPosition | ||
---|---|---|
public static final int |
ESTIMATED |
2 |
public static final int |
STATIC |
1 |
org.metaqtl.factory.MetaQtlModelFactory | ||
---|---|---|
public static final java.lang.String |
SEPARATOR |
"\t" |
org.metaqtl.graph.ChromLayer | ||
---|---|---|
public static final int |
ALIGN_FIRST_COMMON |
0 |
public static final int |
ALIGN_FIRST_MARKER |
1 |
public static final int |
LEFT_LABEL |
1 |
public static final int |
NEG_COMMON |
1 |
public static final int |
POS_COMMON |
0 |
public static final int |
RIGHT_LABEL |
0 |
public static final int |
SINGLE_COMMON |
2 |
org.metaqtl.graph.ChromShape | ||
---|---|---|
public static final int |
LEFT_LABEL |
1 |
public static final int |
RIGHT_LABEL |
0 |
org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion | ||
---|---|---|
public static final double |
C_coeff |
1.0 |
public static final double |
D_coeff |
1.0 |
public static final double |
E_coeff |
2.0 |
public static final double |
F_coeff |
0.5 |
public static final double |
G_coeff |
0.5 |
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