net.maizegenetics.analysis.imputation

Class ImputeProgenyStatesPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ImputeProgenyStatesPlugin
extends AbstractPlugin

Constructor Detail

ImputeProgenyStatesPlugin

public ImputeProgenyStatesPlugin(java.awt.Frame parentFrame,
                                 boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

pluginDescription

public java.lang.String pluginDescription()

rephase

public java.lang.Boolean rephase()

If true, rephase parents before imputing. If false, input haplotypes from file.

Returns:

org.jetbrains.dokka.NodeRenderContent@264b8382: Rephase Parents First

rephase

public ImputeProgenyStatesPlugin rephase(java.lang.Boolean value)

Set Rephase Parents First. If true, rephase parents before imputing. If false, input haplotypes from file.

Parameters:

value - Rephase Parents First

Returns:

org.jetbrains.dokka.NodeRenderContent@28771907: this plugin

parentageFile

public java.lang.String parentageFile()

The input file containing the parentage which lists the parents of each progeny and whether they were derived by self or outcross.

Returns:

org.jetbrains.dokka.NodeRenderContent@5c805aff: Parentage Input File

parentageFile

public ImputeProgenyStatesPlugin parentageFile(java.lang.String value)

Set Parentage Input File. The input file containing the parentage which lists the parents of each progeny and whether they were derived by self or outcross.

Parameters:

value - Parentage Input File

Returns:

org.jetbrains.dokka.NodeRenderContent@35cfd2a9: this plugin

parentHaplotypeFilename

public java.lang.String parentHaplotypeFilename()

The input file containing the parent haplotypes expressed as nucleotides.

Returns:

org.jetbrains.dokka.NodeRenderContent@4fe21001: Parent Haplotypes Input File

parentHaplotypeFilename

public ImputeProgenyStatesPlugin parentHaplotypeFilename(java.lang.String value)

Set Parent Haplotypes Input File. The input file containing the parent haplotypes expressed as nucleotides.

Parameters:

value - Parent Haplotypes Input File

Returns:

org.jetbrains.dokka.NodeRenderContent@5fcd87db: this plugin

progenyFile

public java.lang.String progenyFile()

The input file containing the progeny states (parentcalls). Needed for rephasing using haplotype probabilities or for writing breakpoints.

Returns:

org.jetbrains.dokka.NodeRenderContent@1c4697f: Progeny States Input File

progenyFile

public ImputeProgenyStatesPlugin progenyFile(java.lang.String value)

Set Progeny States Input File. The input file containing the progeny states (parentcalls). Needed for rephasing using haplotype probabilities or for writing breakpoints.

Parameters:

value - Progeny States Input File

Returns:

org.jetbrains.dokka.NodeRenderContent@4ad5b974: this plugin

imputedFile

public java.lang.String imputedFile()

The output file containing the imputed progeny genotypes in hapmap format.

Returns:

org.jetbrains.dokka.NodeRenderContent@15e8da37: Imputed Genotypes Output File

imputedFile

public ImputeProgenyStatesPlugin imputedFile(java.lang.String value)

Set Imputed Genotypes Output File. The output file containing the imputed progeny genotypes in hapmap format.

Parameters:

value - Imputed Genotypes Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@26a8640e: this plugin

statesFile

public java.lang.String statesFile()

The output file containing the new progeny states (parentcalls) in hapmap format

Returns:

org.jetbrains.dokka.NodeRenderContent@4857e35: Progeny States Output File

statesFile

public ImputeProgenyStatesPlugin statesFile(java.lang.String value)

Set Progeny States Output File. The output file containing the new progeny states (parentcalls) in hapmap format

Parameters:

value - Progeny States Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@63fc69c8: this plugin

hapProbFile

public java.lang.String hapProbFile()

The output file containing the new parent haplotype probabilities, binary format. A .bin extension will be appended if not present.

Returns:

org.jetbrains.dokka.NodeRenderContent@30162ee2: Updated Haplotype Probabilities Output File

hapProbFile

public ImputeProgenyStatesPlugin hapProbFile(java.lang.String value)

Set Updated Haplotype Probabilities Output File. The output file containing the new parent haplotype probabilities, binary format. A .bin extension will be appended if not present.

Parameters:

value - Updated Haplotype Probabilities Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@55fbb4fa: this plugin

writeBreakpoints

public java.lang.Boolean writeBreakpoints()

Write breakpoint file from imputed genotypes and parentage.

Returns:

org.jetbrains.dokka.NodeRenderContent@7a201ca6: Write Breakpoints

writeBreakpoints

public ImputeProgenyStatesPlugin writeBreakpoints(java.lang.Boolean value)

Set Write Breakpoints. Write breakpoint file from imputed genotypes and parentage.

Parameters:

value - Write Breakpoints

Returns:

org.jetbrains.dokka.NodeRenderContent@7a929803: this plugin

breakpointOutFile

public java.lang.String breakpointOutFile()

The name of the output file for writing the breakpoints. If the file exists, it will be overwritten.

Returns:

org.jetbrains.dokka.NodeRenderContent@7b72d88d: Breakpoint Output File

breakpointOutFile

public ImputeProgenyStatesPlugin breakpointOutFile(java.lang.String value)

Set Breakpoint Output File. The name of the output file for writing the breakpoints. If the file exists, it will be overwritten.

Parameters:

value - Breakpoint Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@73a6ef7d: this plugin