net.maizegenetics.analysis.data

Class FileLoadPlugin

AbstractPlugin

net.maizegenetics.analysis.data.FileLoadPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FileLoadPlugin
extends AbstractPlugin

Field Detail

FILE_EXT_HAPMAP

public static java.lang.String FILE_EXT_HAPMAP

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Constant Field Values

FILE_EXT_HAPMAP_GZ

public static java.lang.String FILE_EXT_HAPMAP_GZ

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Constant Field Values

FILE_EXT_HAPMAP_GZ_LIX

public static java.lang.String FILE_EXT_HAPMAP_GZ_LIX

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Constant Field Values

FILE_EXT_PLINK_MAP

public static java.lang.String FILE_EXT_PLINK_MAP

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Constant Field Values

FILE_EXT_PLINK_PED

public static java.lang.String FILE_EXT_PLINK_PED

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Constant Field Values

FILE_EXT_SERIAL_GZ

public static java.lang.String FILE_EXT_SERIAL_GZ

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Constant Field Values

FILE_EXT_HDF5

public static java.lang.String FILE_EXT_HDF5

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Constant Field Values

FILE_EXT_VCF

public static java.lang.String FILE_EXT_VCF

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Constant Field Values

FILE_EXT_TOPM

public static java.lang.String FILE_EXT_TOPM

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Constant Field Values

FILE_EXT_TOPM_H5

public static java.lang.String FILE_EXT_TOPM_H5

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FILE_EXT_TOPM_BIN

public static java.lang.String FILE_EXT_TOPM_BIN

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Constant Field Values

FILE_EXT_TOPM_TEXT

public static java.lang.String FILE_EXT_TOPM_TEXT

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Constant Field Values

FILE_EXT_FASTA

public static java.lang.String FILE_EXT_FASTA

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Constant Field Values

FILE_EXT_PHYLIP

public static java.lang.String FILE_EXT_PHYLIP

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Constant Field Values

FILE_EXT_NEWICK

public static java.lang.String FILE_EXT_NEWICK

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Constant Field Values

Constructor Detail

FileLoadPlugin

public FileLoadPlugin(java.awt.Frame parentFrame,
                      boolean isInteractive,
                      boolean headless)

Creates a new instance of FileLoadPlugin. This only used by TASSEL GUI to bypass dialog and go straight to file browser. Bypassing the dialog causes it to bypass adding to Data Tree. This constructor tells FileLoadPlugin to add it to the Data Tree Manually.

FileLoadPlugin

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

Creates a new instance of FileLoadPlugin.

Method Detail

runPlugin

public static java.lang.Object runPlugin(java.lang.String filename)

runPluginDataSet

public static DataSet runPluginDataSet(java.lang.String filename)

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

getOpenFiles

public java.lang.String[] getOpenFiles()

setOpenFiles

public void setOpenFiles(java.io.File[] openFiles)

setOpenFiles

public void setOpenFiles(java.lang.String openFile)

setOpenFiles

public void setOpenFiles(java.lang.String[] openFiles)

fileType

public net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType fileType()

Export file format (Default format depends on data being exported)

Returns:

org.jetbrains.dokka.NodeRenderContent@d0ad705: Format

fileType

public FileLoadPlugin fileType(net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType value)

Set Format. Export file format (Default format depends on data being exported)

Parameters:

value - Format

Returns:

org.jetbrains.dokka.NodeRenderContent@15f3ab29: this plugin

getTheFileType

public net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType getTheFileType()

setTheFileType

public void setTheFileType(net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType theFileType)

sortPositions

public java.lang.Boolean sortPositions()

Whether to sort genotype positions if that's possible.

Returns:

org.jetbrains.dokka.NodeRenderContent@2889ce08: Sort Positions

sortPositions

public FileLoadPlugin sortPositions(java.lang.Boolean value)

Set Sort Positions. Whether to sort genotype positions if that's possible.

Parameters:

value - Sort Positions

Returns:

org.jetbrains.dokka.NodeRenderContent@444faf09: this plugin

keepDepth

public java.lang.Boolean keepDepth()

Whether to keep depth if that's possible.

Returns:

org.jetbrains.dokka.NodeRenderContent@1f26ea7a: Keep Depth

keepDepth

public FileLoadPlugin keepDepth(java.lang.Boolean value)

Set Keep Depth. Whether to keep depth if that's possible.

Parameters:

value - Keep Depth

Returns:

org.jetbrains.dokka.NodeRenderContent@1704b054: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

Icon for this plugin to be used in buttons, etc.

Returns:

org.jetbrains.dokka.NodeRenderContent@719bc532: ImageIcon

getButtonName

public java.lang.String getButtonName()

Button name for this plugin to be used in buttons, etc.

Returns:

org.jetbrains.dokka.NodeRenderContent@48951bef: String

getToolTipText

public java.lang.String getToolTipText()

Tool Tip Text for this plugin

Returns:

org.jetbrains.dokka.NodeRenderContent@60485dbd: String