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java.lang.Objectorg.metaqtl.algo.MetaAlgorithm
org.metaqtl.algo.ClustAlgorithm
public abstract class ClustAlgorithm
Field Summary | |
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protected java.lang.String |
chrName
The name of the chromosome to study. |
protected Chromosome[] |
chromosomes
The chromosome on which the clustering is performed. |
protected int |
missing_sd_mode
This global variable defines the mode of imputation for the QTL for which the standard deviation of the position is not available. |
protected IBioOntology |
ontology
The optional trait ontology to use to group Qtl. |
protected MetaQtlAnalysis |
result
The result of the clustering. |
protected int |
sd_mode
This global variable defines the mode of compuation of the standard deviation of the QTL positions. |
Fields inherited from class org.metaqtl.algo.MetaAlgorithm |
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logger, loggerUp, workAmount, workProgress |
Constructor Summary | |
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ClustAlgorithm(IBioGenome map,
IBioOntology ontology)
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ClustAlgorithm(IBioGenome map,
java.lang.String name,
IBioOntology ontology)
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Method Summary | |
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MetaQtlAnalysis |
getResult()
When the algorithm is finished use this method to get the result. |
void |
setCIMiss(int missing_sd_mode)
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void |
setCIMode(int sd_mode)
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Methods inherited from class org.metaqtl.algo.MetaAlgorithm |
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disableLogger, getLogger, getWorkAmount, getWorkProgress, isLoggerEnable, setLogger, setLogger |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.metaqtl.IMetaAlgorithm |
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run |
Field Detail |
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protected MetaQtlAnalysis result
protected Chromosome[] chromosomes
protected IBioOntology ontology
protected java.lang.String chrName
protected int sd_mode
protected int missing_sd_mode
Constructor Detail |
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public ClustAlgorithm(IBioGenome map, IBioOntology ontology)
map
- ontology
- public ClustAlgorithm(IBioGenome map, java.lang.String name, IBioOntology ontology)
Method Detail |
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public void setCIMode(int sd_mode)
sd_mode
- public void setCIMiss(int missing_sd_mode)
missing_sd_mode
- public MetaQtlAnalysis getResult()
MetaQtlAnalysis
instance
which store in each chromosome the different clustering models
which have been tested.
MetaQtlAnalysis
.MetaQtlAnalysis
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