-
- All Implemented Interfaces:
-
java.lang.Runnable
,net.maizegenetics.plugindef.Plugin
,net.maizegenetics.plugindef.PluginListener
,net.maizegenetics.util.ProgressListener
public class FilterFastqUsingBAMPlugin extends AbstractPlugin
Created by zrm22 on 9/13/17.
-
-
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
-
Constructor Summary
Constructors Constructor Description FilterFastqUsingBAMPlugin(Frame parentFrame, boolean isInteractive)
-
Method Summary
Modifier and Type Method Description DataSet
processData(DataSet input)
String
pluginUserManualURL()
ImageIcon
getIcon()
String
getButtonName()
String
getToolTipText()
String
reference()
File Name of the reference fasta FilterFastqUsingBAMPlugin
reference(String value)
Set Ref File. String
reads()
File Name of the read fastq FilterFastqUsingBAMPlugin
reads(String value)
Set Read File. String
bamFile()
File Name of the bam file FilterFastqUsingBAMPlugin
bamFile(String value)
Set Bam File. String
output()
File Name of the filtered read output FilterFastqUsingBAMPlugin
output(String value)
Set Output 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, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
-
Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
-
Constructor Detail
-
FilterFastqUsingBAMPlugin
FilterFastqUsingBAMPlugin(Frame parentFrame, boolean isInteractive)
-
-
Method Detail
-
processData
DataSet processData(DataSet input)
-
pluginUserManualURL
String pluginUserManualURL()
-
getButtonName
String getButtonName()
-
getToolTipText
String getToolTipText()
-
reference
FilterFastqUsingBAMPlugin reference(String value)
Set Ref File. File Name of the reference fasta
- Parameters:
value
- Ref File
-
reads
FilterFastqUsingBAMPlugin reads(String value)
Set Read File. File Name of the read fastq
- Parameters:
value
- Read File
-
bamFile
FilterFastqUsingBAMPlugin bamFile(String value)
Set Bam File. File Name of the bam file
- Parameters:
value
- Bam File
-
output
FilterFastqUsingBAMPlugin output(String value)
Set Output File. File Name of the filtered read output
- Parameters:
value
- Output File
-
-
-
-