All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class Mummer4DoonerBZStats
extends AbstractPlugin
                    
```
This method takes a coords file, the genome fastas, ranges to be covered Prints out tab-delimited file of metrics related to the region. THe output is tab-delimited, rows are anchors. columns are anchor-coordinates, covered coordinates (list, semicolon separated) percent covered.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

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
`Mummer4DoonerBZStats()`
`Mummer4DoonerBZStats(Frame parentFrame)`
`Mummer4DoonerBZStats(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static void`	`main(Array<String> args)`
`DataSet`	`processData(DataSet input)`
`Map<Integer, ReferenceRange>`	`getAnchorFromIntervalsFile(String intervalsFile, String chrom)`
`static Map<Integer, ReferenceRange>`	`refRangesForChrom(Connection dbConn, String chrom)`
`static Map<Integer, Range<Integer>>`	`getRangesForChrom(Map<Integer, ReferenceRange> refRangeMap, Chromosome chrom, DBLoadingUtils.AnchorType anchorType)`
`static void`	`addToCoordsMap(RangeMap<Integer, String> coordsFileRefToDataMap, String line)`
`RangeMap<Integer, String>`	`getCoordsEntriesForAnchor(Range<Integer> anchorRange, RangeMap<Integer, String> coordsFileRefToDataMap)`
`RangeSet<Integer>`	`getAnchorRangeSet(RangeMap<Integer, String> anchorOverlapEntries)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`coordsFile()`	Output of Mummer coords file
`Mummer4DoonerBZStats`	`coordsFile(String value)`	Set Mummer Coords File.
`String`	`intervalsFile()`	Anchor Intervals file to be used when intervals are different than DB, e.g.
`Mummer4DoonerBZStats`	`intervalsFile(String value)`	Set Anchor Intervals File.
`String`	`mummerParams()`	Mummer parameters used
`Mummer4DoonerBZStats`	`mummerParams(String value)`	Set Mummer Parameters.
`String`	`prefix()`	Name to prefix to output results file
`Mummer4DoonerBZStats`	`prefix(String value)`	Set Output File refix.
`String`	`outputDir()`	Output directory including trailing / for writing files
`Mummer4DoonerBZStats`	`outputDir(String value)`	Set Output Directory.
`String`	`configFile()`	File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
`Mummer4DoonerBZStats`	`configFile(String value)`	Set DB Config File.
`String`	`refChrom()`	Name of reference chromsome as stored in the database.
`Mummer4DoonerBZStats`	`refChrom(String value)`	Set Reference Chromosome 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
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
  - Mummer4DoonerBZStats
```
Mummer4DoonerBZStats()
```
  - Mummer4DoonerBZStats
```
Mummer4DoonerBZStats(Frame parentFrame)
```
  - Mummer4DoonerBZStats
```
Mummer4DoonerBZStats(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - main
```
 static void main(Array<String> args)
```
  - processData
```
 DataSet processData(DataSet input)
```
  - getAnchorFromIntervalsFile
```
 Map<Integer, ReferenceRange> getAnchorFromIntervalsFile(String intervalsFile, String chrom)
```
  - refRangesForChrom
```
 static Map<Integer, ReferenceRange> refRangesForChrom(Connection dbConn, String chrom)
```
  - getRangesForChrom
```
 static Map<Integer, Range<Integer>> getRangesForChrom(Map<Integer, ReferenceRange> refRangeMap, Chromosome chrom, DBLoadingUtils.AnchorType anchorType)
```
  - addToCoordsMap
```
 static void addToCoordsMap(RangeMap<Integer, String> coordsFileRefToDataMap, String line)
```
  - getCoordsEntriesForAnchor
```
 RangeMap<Integer, String> getCoordsEntriesForAnchor(Range<Integer> anchorRange, RangeMap<Integer, String> coordsFileRefToDataMap)
```
  - getAnchorRangeSet
```
 RangeSet<Integer> getAnchorRangeSet(RangeMap<Integer, String> anchorOverlapEntries)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - coordsFile
```
 String coordsFile()
```
    Output of Mummer coords file
  - coordsFile
```
 Mummer4DoonerBZStats coordsFile(String value)
```
    Set Mummer Coords File. Output of Mummer coords file
    
    Parameters:
    
    value - Mummer Coords File
  - intervalsFile
```
 String intervalsFile()
```
    Anchor Intervals file to be used when intervals are different than DB, e.g. when using just a small region
  - intervalsFile
```
 Mummer4DoonerBZStats intervalsFile(String value)
```
    Set Anchor Intervals File. Anchor Intervals file to be used when intervals are different than DB, e.g. when using just a small region
    
    Parameters:
    
    value - Anchor Intervals File
  - mummerParams
```
 String mummerParams()
```
    Mummer parameters used
  - mummerParams
```
 Mummer4DoonerBZStats mummerParams(String value)
```
    Set Mummer Parameters. Mummer parameters used
    
    Parameters:
    
    value - Mummer Parameters
  - prefix
```
 String prefix()
```
    Name to prefix to output results file
  - prefix
```
 Mummer4DoonerBZStats prefix(String value)
```
    Set Output File refix. Name to prefix to output results file
    
    Parameters:
    
    value - Output File refix
  - outputDir
```
 String outputDir()
```
    Output directory including trailing / for writing files
  - outputDir
```
 Mummer4DoonerBZStats outputDir(String value)
```
    Set Output Directory. Output directory including trailing / for writing files
    
    Parameters:
    
    value - Output Directory
  - configFile
```
 String configFile()
```
    File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
  - configFile
```
 Mummer4DoonerBZStats configFile(String value)
```
    Set DB Config File. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
    
    Parameters:
    
    value - DB Config File
  - refChrom
```
 String refChrom()
```
    Name of reference chromsome as stored in the database. This is the chromosome whose anchors will be pulled.
  - refChrom
```
 Mummer4DoonerBZStats refChrom(String value)
```
    Set Reference Chromosome Name. Name of reference chromsome as stored in the database. This is the chromosome whose anchors will be pulled.
    
    Parameters:
    
    value - Reference Chromosome Name

Class Mummer4DoonerBZStats

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class net.maizegenetics.plugindef.Plugin

Methods inherited from class java.lang.Object

Constructor Detail

Mummer4DoonerBZStats

Mummer4DoonerBZStats

Mummer4DoonerBZStats

Method Detail

main

processData

getAnchorFromIntervalsFile

refRangesForChrom

getRangesForChrom

addToCoordsMap

getCoordsEntriesForAnchor

getAnchorRangeSet

getIcon

getButtonName

getToolTipText

coordsFile

coordsFile

intervalsFile

intervalsFile

mummerParams

mummerParams

prefix

prefix

outputDir

outputDir

configFile

configFile

refChrom

refChrom