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java.lang.Objectorg.metaqtl.Chromosome
public class Chromosome
On a Chromosome there are two types of locus :
Field Summary | |
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int |
cg
The number of generations of the offspring population. |
int |
cs
The size of the offspring population. |
int |
ct
The type of the offspring population. |
java.lang.String |
mapName
The name of the map in which this chromosome is defined. |
MetaQtlResult[] |
metaQtlAnalysis
The results of a meta-analysis of QTL. |
int |
mfc
The mapping function for this chromosome |
Qtl[] |
mqtls
The meta Qtls on this chromosome. |
double[] |
mr
The adjacent recombination rate between ordered markers |
java.lang.String[] |
mrkNames
The ordered marker names |
int |
mut
The mapping unit for this chromosome |
java.lang.String |
name
The name of the chromosome. |
int |
nm
The number of markers. |
double[][] |
proba
Probabilities defined along the chromosome. |
Qtl[] |
qtls
The QTLs located on this chromosome. |
boolean |
skeleton
The skeleton status for this member |
double |
totd
The total distance of the chromosome. |
Constructor Summary | |
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Chromosome()
|
Method Summary | |
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boolean |
areMarkersAroundQTL(int mrkIdxL,
int mrkIdxR,
int qtlIdx)
Returns true if the QTL position is inside the marker interval which markers indices are mrkIdxL
and mrkIdxR . |
void |
attachQTL(IBioLocus[] qtls)
Add |
void |
attachQtl(Qtl[] qtls)
|
void |
computeQtlSD(int mode)
According to the given standard deviation computation mode this method computes for each QTL the value of the standard deviation of the QTL position. |
double |
getDistance(int i)
This methods returns the distance between the first marker and the marker with the given indice using the default mapping context. |
double |
getDistance(int mrkIdx,
int mapping_function,
int mapping_unit)
This methods returns the distance between the first marker and the marker with the given indice using the given mapping context. |
double |
getDistanceBetween(int mrkIdxL,
int mrkIdxR)
|
double |
getDistanceBetween(int mrkIdxL,
int mrkIdxR,
int mapping_function,
int mapping_unit)
This methods returns the distance between the markers with the given indices assuming that mrkIdxL < mrkIdxR . |
static double[] |
getDistHeterogeneity(int ncm,
int[][] mrkIdx,
Chromosome chrom,
Chromosome ref)
|
static int |
getFirstCommonMrkIdx(Chromosome chrom,
Chromosome chrom2)
|
java.lang.String |
getMapName()
|
int |
getMarkerIdxWithName(java.lang.String string)
This method looks if it exists a marker on the chromosome with the given name and returns its indice. |
java.lang.String |
getMarkerName(int i)
Returns the names of the marker at the i^th position on the chromosome. |
Qtl[] |
getMetaQtls()
|
java.lang.String |
getName()
Returns the name of the chromosome. |
double[][] |
getProba()
|
double |
getQTLInMrkIntProb(int mrkIdxL,
int mrkIdxR,
int qtlIdx)
This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL indice. |
double |
getQTLInMrkIntProb(int mrkIdxL,
int mrkIdxR,
Qtl qtl)
This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL. |
int |
getQtlNumber()
|
Qtl[] |
getQtls()
This method returns a copy of the QTL located on thic chromosome. |
static double[] |
getRecHeterogeneity(int ncm,
int[][] mrkIdx,
Chromosome chrom,
Chromosome ref)
|
Chromosome |
getSubChromosome(java.lang.String[] markerNames)
|
boolean |
hasQTL()
This method tests if the chromosome have a set of QTL defined. |
void |
r2R()
|
void |
R2r()
|
void |
r2R(int type,
int gen)
Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r. |
void |
R2r(int type,
int gen)
Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r. |
void |
setMetaQtls(Qtl[] metaQtl)
|
void |
setProba(double[][] proba)
|
java.lang.String |
toString()
|
void |
updateMappingContext(int mapping_function,
int mapping_unit)
Updates the mapping context of the chromosome. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public int nm
public int cs
public int ct
public int cg
public int mfc
public int mut
public boolean skeleton
public double totd
public double[] mr
public java.lang.String[] mrkNames
public java.lang.String name
public java.lang.String mapName
public Qtl[] qtls
public Qtl[] mqtls
public MetaQtlResult[] metaQtlAnalysis
public double[][] proba
Constructor Detail |
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public Chromosome()
Method Detail |
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public double getQTLInMrkIntProb(int mrkIdxL, int mrkIdxR, int qtlIdx)
mrkIdxL < mrkIdxR
mrkIdxL
- the left marker indice.mrkIdxR
- the right marker indice.qtlIdx
- the QTL indice.
public double getQTLInMrkIntProb(int mrkIdxL, int mrkIdxR, Qtl qtl)
mrkIdxL < mrkIdxR
mrkIdxL
- the left marker indice.mrkIdxR
- the right marker indice.qtl
- the QTL.
public boolean areMarkersAroundQTL(int mrkIdxL, int mrkIdxR, int qtlIdx)
mrkIdxL
and mrkIdxR
.
This assumes that mrkIdxL < mrkIdxR
mrkIdxL
- the left marker indice.mrkIdxR
- the right marker indice.qtlIdx
- the qtl indice.
public boolean hasQTL()
public java.lang.String toString()
toString
in class java.lang.Object
public int getMarkerIdxWithName(java.lang.String string)
string
- the name of the marker.
public double getDistanceBetween(int mrkIdxL, int mrkIdxR, int mapping_function, int mapping_unit)
mrkIdxL < mrkIdxR
.
The distance is computed using the given mapping context.
mrkIdxL
- the left marker indice.mrkIdxR
- the right marker indice.mapping_function
- the mapping function.mapping_unit
- the mapping unit.
public double getDistanceBetween(int mrkIdxL, int mrkIdxR)
mrkIdxL
- mrkIdxR
-
public double getDistance(int mrkIdx, int mapping_function, int mapping_unit)
mrkIdx
- the marker indice.mapping_function
- the mapping function.mapping_unit
- the mapping unit.
public void updateMappingContext(int mapping_function, int mapping_unit)
mapping_function
- the new mapping function.mapping_unit
- the new mapping unit.public double getDistance(int i)
i
- the indice of the marker.
public void r2R()
public void r2R(int type, int gen)
public void R2r()
public void R2r(int type, int gen)
public void computeQtlSD(int mode)
mode
- the standard deviation computation mode.IMetaQtlConstants
public Qtl[] getMetaQtls()
public void setMetaQtls(Qtl[] metaQtl)
metaQtl
- public Qtl[] getQtls()
public int getQtlNumber()
public void attachQtl(Qtl[] qtls)
mqtls2
- public void attachQTL(IBioLocus[] qtls)
loci
- public java.lang.String getMarkerName(int i)
i
- the position of the marker.
public java.lang.String getName()
public static double[] getRecHeterogeneity(int ncm, int[][] mrkIdx, Chromosome chrom, Chromosome ref)
ncm
- mrkIdx
- chrom
- ref
-
public static double[] getDistHeterogeneity(int ncm, int[][] mrkIdx, Chromosome chrom, Chromosome ref)
public double[][] getProba()
public void setProba(double[][] proba)
proba
- public static int getFirstCommonMrkIdx(Chromosome chrom, Chromosome chrom2)
chromosome
- chromosome2
-
public Chromosome getSubChromosome(java.lang.String[] markerNames)
strings
-
public java.lang.String getMapName()
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