net.maizegenetics.analysis.filter

Class FilterSiteBuilderPlugin

AbstractPlugin

net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FilterSiteBuilderPlugin
extends AbstractPlugin

Constructor Detail

FilterSiteBuilderPlugin

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

FilterSiteBuilderPlugin

public FilterSiteBuilderPlugin()

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

postProcessParameters

protected void postProcessParameters()

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

pluginUserManualURL

public java.lang.String pluginUserManualURL()

build

public FilterSite build()

useFilterValues

public FilterSiteBuilderPlugin useFilterValues(FilterSite filter)

runPlugin

public FilterSite runPlugin()

Convenience method to run plugin with one return object.

runPlugin

public GenotypeTable runPlugin(DataSet input)

runPlugin

public GenotypeTable runPlugin(GenotypeTable input)

filterName

public java.lang.String filterName()

Filter Name

Returns:

org.jetbrains.dokka.NodeRenderContent@48f0623f: Filter Name

filterName

public FilterSiteBuilderPlugin filterName(java.lang.String value)

Set Filter Name. Filter Name

Parameters:

value - Filter Name

Returns:

org.jetbrains.dokka.NodeRenderContent@4b9c2de3: this plugin

siteMinCount

public java.lang.Integer siteMinCount()

Site Minimum Count of Alleles not Unknown

Returns:

org.jetbrains.dokka.NodeRenderContent@28363914: Site Min Count

siteMinCount

public FilterSiteBuilderPlugin siteMinCount(java.lang.Integer value)

Set Site Min Count. Site Minimum Count of Alleles not Unknown

Parameters:

value - Site Min Count

Returns:

org.jetbrains.dokka.NodeRenderContent@5b6e2c93: this plugin

siteMinAlleleFreq

public java.lang.Double siteMinAlleleFreq()

Site Minimum Minor Allele Frequency

Returns:

org.jetbrains.dokka.NodeRenderContent@10c45c5b: Site Min Allele Freq

siteMinAlleleFreq

public FilterSiteBuilderPlugin siteMinAlleleFreq(java.lang.Double value)

Set Site Min Allele Freq. Site Minimum Minor Allele Frequency

Parameters:

value - Site Min Allele Freq

Returns:

org.jetbrains.dokka.NodeRenderContent@3a1d9895: this plugin

siteMaxAlleleFreq

public java.lang.Double siteMaxAlleleFreq()

Site Maximum Minor Allele Frequency

Returns:

org.jetbrains.dokka.NodeRenderContent@23faf85b: Site Max Allele Freq

siteMaxAlleleFreq

public FilterSiteBuilderPlugin siteMaxAlleleFreq(java.lang.Double value)

Set Site Max Allele Freq. Site Maximum Minor Allele Frequency

Parameters:

value - Site Max Allele Freq

Returns:

org.jetbrains.dokka.NodeRenderContent@9da4203: this plugin

minHeterozygous

public java.lang.Double minHeterozygous()

Min Heterozygous Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@3bcee1e7: Min Heterozygous Proportion

minHeterozygous

public FilterSiteBuilderPlugin minHeterozygous(java.lang.Double value)

Set Min Heterozygous Proportion. Min Heterozygous Proportion

Parameters:

value - Min Heterozygous Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@6dc10f3b: this plugin

maxHeterozygous

public java.lang.Double maxHeterozygous()

Max Heterozygous Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@190d0af8: Max Heterozygous Proportion

maxHeterozygous

public FilterSiteBuilderPlugin maxHeterozygous(java.lang.Double value)

Set Max Heterozygous Proportion. Max Heterozygous Proportion

Parameters:

value - Max Heterozygous Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@421c9980: this plugin

removeMinorSNPStates

public java.lang.Boolean removeMinorSNPStates()

Remove Minor SNP States

Returns:

org.jetbrains.dokka.NodeRenderContent@e9199fd: Remove Minor SNP States

removeMinorSNPStates

public FilterSiteBuilderPlugin removeMinorSNPStates(java.lang.Boolean value)

Set Remove Minor SNP States. Remove Minor S N P States

Parameters:

value - Remove Minor S N P States

Returns:

org.jetbrains.dokka.NodeRenderContent@6bcce7c3: this plugin

removeSitesWithIndels

public java.lang.Boolean removeSitesWithIndels()

Removes sites containing an indel (+ or -)

Returns:

org.jetbrains.dokka.NodeRenderContent@1ae77a88: Remove Sites With Indels

removeSitesWithIndels

public FilterSiteBuilderPlugin removeSitesWithIndels(java.lang.Boolean value)

Set Remove Sites With Indels. Removes sites containing an indel (+ or -)

Parameters:

value - Remove Sites With Indels

Returns:

org.jetbrains.dokka.NodeRenderContent@3c1130cd: this plugin

siteFilter

public net.maizegenetics.dna.snp.FilterSite.SITE_RANGE_FILTER_TYPES siteFilter()

True if filtering by site numbers. False if filtering by chromosome and position

Returns:

org.jetbrains.dokka.NodeRenderContent@3e4d18c3: Site Filter

siteFilter

public FilterSiteBuilderPlugin siteFilter(net.maizegenetics.dna.snp.FilterSite.SITE_RANGE_FILTER_TYPES value)

Set Site Filter. True if filtering by site numbers. False if filtering by chromosome and position

Parameters:

value - Site Filter

Returns:

org.jetbrains.dokka.NodeRenderContent@32b31236: this plugin

startSite

public java.lang.Integer startSite()

Start Site

Returns:

org.jetbrains.dokka.NodeRenderContent@13a11dd2: Start Site

startSite

public FilterSiteBuilderPlugin startSite(java.lang.Integer value)

Set Start Site. Start Site

Parameters:

value - Start Site

Returns:

org.jetbrains.dokka.NodeRenderContent@2683d033: this plugin

endSite

public java.lang.Integer endSite()

End Site

Returns:

org.jetbrains.dokka.NodeRenderContent@705e4f20: End Site

endSite

public FilterSiteBuilderPlugin endSite(java.lang.Integer value)

Set End Site. End Site

Parameters:

value - End Site

Returns:

org.jetbrains.dokka.NodeRenderContent@5ad6d1bf: this plugin

startChr

public Chromosome startChr()

Start Chr

Returns:

org.jetbrains.dokka.NodeRenderContent@418218ba: Start Chr

startChr

public FilterSiteBuilderPlugin startChr(Chromosome value)

Set Start Chr. Start Chr

Parameters:

value - Start Chr

Returns:

org.jetbrains.dokka.NodeRenderContent@79385af1: this plugin

startPos

public java.lang.Integer startPos()

Start Pos

Returns:

org.jetbrains.dokka.NodeRenderContent@7b1d2db9: Start Pos

startPos

public FilterSiteBuilderPlugin startPos(java.lang.Integer value)

Set Start Pos. Start Pos

Parameters:

value - Start Pos

Returns:

org.jetbrains.dokka.NodeRenderContent@17aa404c: this plugin

endChr

public Chromosome endChr()

End Chr

Returns:

org.jetbrains.dokka.NodeRenderContent@46bccdcb: End Chr

endChr

public FilterSiteBuilderPlugin endChr(Chromosome value)

Set End Chr. End Chr

Parameters:

value - End Chr

Returns:

org.jetbrains.dokka.NodeRenderContent@7d68f83f: this plugin

endPos

public java.lang.Integer endPos()

End Pos

Returns:

org.jetbrains.dokka.NodeRenderContent@6f0a62ce: End Pos

endPos

public FilterSiteBuilderPlugin endPos(java.lang.Integer value)

Set End Pos. End Pos

Parameters:

value - End Pos

Returns:

org.jetbrains.dokka.NodeRenderContent@2ae7e743: this plugin

includeSites

public java.lang.Boolean includeSites()

Include Sites

Returns:

org.jetbrains.dokka.NodeRenderContent@a95a541: Include Sites

includeSites

public FilterSiteBuilderPlugin includeSites(java.lang.Boolean value)

Set Include Sites.

Parameters:

value - Include Sites

Returns:

org.jetbrains.dokka.NodeRenderContent@30061d2c: this plugin

positionList

public PositionList positionList()

Position List

Returns:

org.jetbrains.dokka.NodeRenderContent@c2605f0: Position List

positionList

public FilterSiteBuilderPlugin positionList(PositionList value)

Set Position List.

Parameters:

value - Position List

Returns:

org.jetbrains.dokka.NodeRenderContent@19ee36c8: this plugin

siteNamesList

public java.util.List<java.lang.String> siteNamesList()

Site Names List

Returns:

org.jetbrains.dokka.NodeRenderContent@3e763719: Site Names List

siteNamesList

public FilterSiteBuilderPlugin siteNamesList(java.util.List<java.lang.String> value)

Set Site Names List. Site Names List

Parameters:

value - Site Names List

Returns:

org.jetbrains.dokka.NodeRenderContent@3e19b286: this plugin

bedFile

public java.lang.String bedFile()

Filter based on BED file.

Returns:

org.jetbrains.dokka.NodeRenderContent@2ac3930: Bed File

bedFile

public FilterSiteBuilderPlugin bedFile(java.lang.String value)

Set Bed File. Filter based on BED file.

Parameters:

value - Bed File

Returns:

org.jetbrains.dokka.NodeRenderContent@6a1c07db: this plugin

chrPosFile

public java.lang.String chrPosFile()

Filter based on list of chromsome / position in file.

Returns:

org.jetbrains.dokka.NodeRenderContent@65dd3b7e: Chr Pos File

chrPosFile

public FilterSiteBuilderPlugin chrPosFile(java.lang.String value)

Set Chr Pos File. Filter based on list of chromsome / position in file.

Parameters:

value - Chr Pos File

Returns:

org.jetbrains.dokka.NodeRenderContent@16a338c1: this plugin