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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 HaplotypeGraphBuilderPlugin extends AbstractPlugin
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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 HaplotypeGraphBuilderPlugin(Frame parentFrame, boolean isInteractive)
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Method Summary
Modifier and Type Method Description DataSet
processData(DataSet input)
HaplotypeGraph
build()
static List<Tuple<String, String>>
convertMethods(String methodPairs)
String
configFile()
Database configuration file HaplotypeGraphBuilderPlugin
configFile(String value)
Set Database Config File. String
methods()
Pairs of methods (haplotype method name and range group method name). HaplotypeGraphBuilderPlugin
methods(String value)
Set Methods. Boolean
includeSequences()
Whether to include sequences in haplotype nodes. HaplotypeGraphBuilderPlugin
includeSequences(Boolean value)
Set Include Sequences. Boolean
includeVariantContexts()
Whether to include variant contexts in haplotype nodes. HaplotypeGraphBuilderPlugin
includeVariantContexts(Boolean value)
Set Include Variant Contexts. SortedSet<Integer>
hapids()
List of haplotype ids to include in the graph. HaplotypeGraphBuilderPlugin
hapids(SortedSet<Integer> value)
Set Haplotype Ids. List<String>
chromosomes()
Chromosomes HaplotypeGraphBuilderPlugin
chromosomes(List<String> value)
Set Chromosomes. TaxaList
taxaList()
Optional list of taxa to include. HaplotypeGraphBuilderPlugin
taxaList(TaxaList value)
Set Taxa. HaplotypeGraphBuilderPlugin
taxaList(String value)
String
localGVCFFolder()
Local folder to which gvcf file will be downloaded. HaplotypeGraphBuilderPlugin
localGVCFFolder(String value)
Set local gvcf folder path ImageIcon
getIcon()
String
getButtonName()
String
getToolTipText()
static void
main(Array<String> args)
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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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HaplotypeGraphBuilderPlugin
HaplotypeGraphBuilderPlugin(Frame parentFrame, boolean isInteractive)
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Method Detail
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processData
DataSet processData(DataSet input)
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build
HaplotypeGraph build()
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convertMethods
static List<Tuple<String, String>> convertMethods(String methodPairs)
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configFile
String configFile()
Database configuration file
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configFile
HaplotypeGraphBuilderPlugin configFile(String value)
Set Database Config File. Database configuration file
- Parameters:
value
- Database Config File
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methods
String methods()
Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
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methods
HaplotypeGraphBuilderPlugin methods(String value)
Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,
- Parameters:
value
- Methods
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includeSequences
Boolean includeSequences()
Whether to include sequences in haplotype nodes.
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includeSequences
HaplotypeGraphBuilderPlugin includeSequences(Boolean value)
Set Include Sequences. Whether to include sequences in haplotype nodes.
- Parameters:
value
- Include Sequences
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includeVariantContexts
Boolean includeVariantContexts()
Whether to include variant contexts in haplotype nodes.
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includeVariantContexts
HaplotypeGraphBuilderPlugin includeVariantContexts(Boolean value)
Set Include Variant Contexts. Whether to include variant contexts in haplotype nodes.
- Parameters:
value
- Include Variant Contexts
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hapids
SortedSet<Integer> hapids()
List of haplotype ids to include in the graph. If not specified, all ids are included.
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hapids
HaplotypeGraphBuilderPlugin hapids(SortedSet<Integer> value)
Set Haplotype Ids. List of haplotype ids to include in the graph. If not specified, all ids are included.
- Parameters:
value
- Haplotype Ids
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chromosomes
List<String> chromosomes()
Chromosomes
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chromosomes
HaplotypeGraphBuilderPlugin chromosomes(List<String> value)
Set Chromosomes. Chromosomes
- Parameters:
value
- Chromosomes
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taxaList
TaxaList taxaList()
Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
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taxaList
HaplotypeGraphBuilderPlugin taxaList(TaxaList value)
Set Taxa. Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
- Parameters:
value
- Taxa
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taxaList
HaplotypeGraphBuilderPlugin taxaList(String value)
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localGVCFFolder
String localGVCFFolder()
Local folder to which gvcf file will be downloaded.
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localGVCFFolder
HaplotypeGraphBuilderPlugin localGVCFFolder(String value)
Set local gvcf folder path
- Parameters:
value
- Local GVCF Folder path
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getButtonName
String getButtonName()
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getToolTipText
String getToolTipText()
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