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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 AddRefRangeGroupPlugin extends AbstractPlugin
This class creates a user defined ref range group, adds it to the specified db, associates requested reference ranges with the new group. Input: 1. anchor bed file: Should be a subset of reference ranges currently existing in the DB. Format is tab-delimited file with columns: chr startpos endpos No header, positions are BED file formatted, ie 0-based, inclusive/exclusive 2. Name for the new method, which is the ref range group. 3. Method details: user description for method 4. Config file with db connection info Output: 1. Database tables "methods" and "ref_range_ref_range_method" are updated. Algorithm: 1. Read bed file into an object 2. Read all reference ranges from db 3. Verify all entries from the bed file exist in the reference_ranges table (throw exception if false) 4. Verify method name does not exist in methods table (throw exception if false) 5. Add method name to db. 6. Add specified reference ranges to the ref_range_ref_range_methods table with method_id = new method id.
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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 AddRefRangeGroupPlugin()
AddRefRangeGroupPlugin(Frame parentFrame)
AddRefRangeGroupPlugin(Frame parentFrame, boolean isInteractive)
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Method Summary
Modifier and Type Method Description DataSet
processData(DataSet input)
static List<Integer>
verifyRanges(String rangeFile, PHGDataWriter phg)
ImageIcon
getIcon()
String
getButtonName()
String
getToolTipText()
String
methodName()
Method name for this reference range group. AddRefRangeGroupPlugin
methodName(String value)
Set Method Name. String
methodDetails()
Desscription for this group of reference ranges. AddRefRangeGroupPlugin
methodDetails(String value)
Set Method Details. String
ranges()
Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. AddRefRangeGroupPlugin
ranges(String value)
Set Ranges File. String
configFile()
Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres. AddRefRangeGroupPlugin
configFile(String value)
Set DataBase Configuration 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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Method Detail
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processData
DataSet processData(DataSet input)
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verifyRanges
static List<Integer> verifyRanges(String rangeFile, PHGDataWriter phg)
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getButtonName
String getButtonName()
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getToolTipText
String getToolTipText()
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methodName
String methodName()
Method name for this reference range group.
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methodName
AddRefRangeGroupPlugin methodName(String value)
Set Method Name. Method name for this reference range group.
- Parameters:
value
- Method Name
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methodDetails
String methodDetails()
Desscription for this group of reference ranges.
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methodDetails
AddRefRangeGroupPlugin methodDetails(String value)
Set Method Details. Desscription for this group of reference ranges.
- Parameters:
value
- Method Details
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ranges
String ranges()
Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
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ranges
AddRefRangeGroupPlugin ranges(String value)
Set Ranges File. Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
- Parameters:
value
- Ranges File
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configFile
String configFile()
Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
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configFile
AddRefRangeGroupPlugin configFile(String value)
Set DataBase Configuration File. Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
- Parameters:
value
- DataBase Configuration File
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