public class ImputeProgenyStatesPlugin
extends AbstractPlugin
public ImputeProgenyStatesPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.String pluginDescription()
public java.lang.Boolean rephase()
If true, rephase parents before imputing. If false, input haplotypes from file.
public ImputeProgenyStatesPlugin rephase(java.lang.Boolean value)
Set Rephase Parents First. If true, rephase parents before imputing. If false, input haplotypes from file.
value - Rephase Parents Firstpublic 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.
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.
value - Parentage Input Filepublic java.lang.String parentHaplotypeFilename()
The input file containing the parent haplotypes expressed as nucleotides.
public ImputeProgenyStatesPlugin parentHaplotypeFilename(java.lang.String value)
Set Parent Haplotypes Input File. The input file containing the parent haplotypes expressed as nucleotides.
value - Parent Haplotypes Input Filepublic java.lang.String progenyFile()
The input file containing the progeny states (parentcalls). Needed for rephasing using haplotype probabilities or for writing breakpoints.
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.
value - Progeny States Input Filepublic java.lang.String imputedFile()
The output file containing the imputed progeny genotypes in hapmap format.
public ImputeProgenyStatesPlugin imputedFile(java.lang.String value)
Set Imputed Genotypes Output File. The output file containing the imputed progeny genotypes in hapmap format.
value - Imputed Genotypes Output Filepublic java.lang.String statesFile()
The output file containing the new progeny states (parentcalls) in hapmap format
public ImputeProgenyStatesPlugin statesFile(java.lang.String value)
Set Progeny States Output File. The output file containing the new progeny states (parentcalls) in hapmap format
value - Progeny States Output Filepublic java.lang.String hapProbFile()
The output file containing the new parent haplotype probabilities, binary format. A .bin extension will be appended if not present.
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.
value - Updated Haplotype Probabilities Output Filepublic java.lang.Boolean writeBreakpoints()
Write breakpoint file from imputed genotypes and parentage.
public ImputeProgenyStatesPlugin writeBreakpoints(java.lang.Boolean value)
Set Write Breakpoints. Write breakpoint file from imputed genotypes and parentage.
value - Write Breakpointspublic java.lang.String breakpointOutFile()
The name of the output file for writing the breakpoints. If the file exists, it will be overwritten.
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.
value - Breakpoint Output File