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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 AddRefRangeAsAssemblyPlugin extends AbstractPlugin
This function is fairly obsolete. IT was used before the graph was able to take multiple methods as parameters. This class created to load a reference genome as an assembly. The method is hard-coded to "mummer4", which is the assembly method name at the time of this writing. All the variants are reference records. The addition of these haplotypes allows for pulling TODO: IT it is deemd this class is still useful, it should be updated to create a gvcf file as is done in LoadAllIntervalsToPHGdbPlugin, store the gvcf file data to the genomeFileData table, and save the gvcfFileId to the anchorDataPHG object.
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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 AddRefRangeAsAssemblyPlugin()
AddRefRangeAsAssemblyPlugin(Frame parentFrame)
AddRefRangeAsAssemblyPlugin(Frame parentFrame, boolean isInteractive)
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Method Summary
Modifier and Type Method Description DataSet
processData(DataSet input)
static void
main(Array<String> args)
ImageIcon
getIcon()
String
getButtonName()
String
getToolTipText()
String
refGenome()
Referemce Genome File for aligning against AddRefRangeAsAssemblyPlugin
refGenome(String value)
Set Reference Genome File. String
configFile()
Path to config file for db loading AddRefRangeAsAssemblyPlugin
configFile(String value)
Set config file for db access String
haplotypeMethod()
Name of method to be stored in db AddRefRangeAsAssemblyPlugin
haplotypeMethod(String value)
Set methodName String
pathName()
Name of method used for create PHG Path. AddRefRangeAsAssemblyPlugin
pathName(String value)
Set Path Method Name. String
lineName()
Name name to be stored in the genotypes table, e.g. AddRefRangeAsAssemblyPlugin
lineName(String value)
Set Line Name. -
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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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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refGenome
AddRefRangeAsAssemblyPlugin refGenome(String value)
Set Reference Genome File. Referemce Genome File for aligning against
- Parameters:
value
- Reference Genome File
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configFile
String configFile()
Path to config file for db loading
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configFile
AddRefRangeAsAssemblyPlugin configFile(String value)
Set config file for db access
- Parameters:
value
- config file
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haplotypeMethod
String haplotypeMethod()
Name of method to be stored in db
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haplotypeMethod
AddRefRangeAsAssemblyPlugin haplotypeMethod(String value)
Set methodName
- Parameters:
value
- methodName
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pathName
String pathName()
Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
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pathName
AddRefRangeAsAssemblyPlugin pathName(String value)
Set Path Method Name. Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
- Parameters:
value
- Path Method Name
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lineName
AddRefRangeAsAssemblyPlugin lineName(String value)
Set Line Name. Name name to be stored in the genotypes table, e.g. B73_Assembly
- Parameters:
value
- Line Name
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