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- All Implemented Interfaces:
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java.lang.Runnable
,net.maizegenetics.plugindef.Plugin
,net.maizegenetics.plugindef.PluginListener
,net.maizegenetics.util.ProgressListener
public class CreateGeneIntervalsFromConservedGFFPlugin extends AbstractPlugin
Creates bed file with chromosome and coordinates to be used to create PHG reference ranges. Gene names are included with each reference range. The gene name column is ignored when loading the bed file - it is there for when we want to associate reference ranges with the genes on which they were based.
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Field Summary
Fields Modifier and Type Field Description public final static String
DEFAULT_CITATION
public final static String
POSITION_LIST_NONE
public final static String
TAXA_LIST_NONE
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Constructor Summary
Constructors Constructor Description CreateGeneIntervalsFromConservedGFFPlugin()
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame)
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame, boolean isInteractive)
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Method Summary
Modifier and Type Method Description static void
main(Array<String> args)
DataSet
processData(DataSet input)
ImageIcon
getIcon()
String
getButtonName()
String
getToolTipText()
String
gffFile()
Tab delimited . CreateGeneIntervalsFromConservedGFFPlugin
gffFile(String value)
Set Gene File. String
outputFile()
Name of output file to be written CreateGeneIntervalsFromConservedGFFPlugin
outputFile(String value)
Set Output File. String
conservedGeneFile()
File containing list of conserved genes to include as anchor regions CreateGeneIntervalsFromConservedGFFPlugin
conservedGeneFile(String value)
Set Conserved Gene File. -
Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
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Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Constructor Detail
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CreateGeneIntervalsFromConservedGFFPlugin
CreateGeneIntervalsFromConservedGFFPlugin()
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CreateGeneIntervalsFromConservedGFFPlugin
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame)
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CreateGeneIntervalsFromConservedGFFPlugin
CreateGeneIntervalsFromConservedGFFPlugin(Frame parentFrame, boolean isInteractive)
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Method Detail
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processData
DataSet processData(DataSet input)
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getButtonName
String getButtonName()
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getToolTipText
String getToolTipText()
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gffFile
String gffFile()
Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
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gffFile
CreateGeneIntervalsFromConservedGFFPlugin gffFile(String value)
Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
- Parameters:
value
- Gene File
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outputFile
String outputFile()
Name of output file to be written
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outputFile
CreateGeneIntervalsFromConservedGFFPlugin outputFile(String value)
Set Output File. Name of file to be written
- Parameters:
value
- Output Directory
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conservedGeneFile
String conservedGeneFile()
File containing list of conserved genes to include as anchor regions
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conservedGeneFile
CreateGeneIntervalsFromConservedGFFPlugin conservedGeneFile(String value)
Set Conserved Gene File. File containing list of conserved genes to include as anchor regions
- Parameters:
value
- Conserved Gene File
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