All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class MummerAnalysisMetricsPlugin
extends AbstractPlugin
                    
```
This method provides summary statistics on mummer output. The ref and assembly fastas are to provide length values. Assumptions: 1. file has been sorted and filtered to contain just 1 chromosome 2. User indicates which chrom name in "query (usually assembly)" and "target (usually ref)" parameters 3. This file is NOT run on bz region fastas. WIll be a problem with db for ref name vs refchrom name in the fasta file - they won't match Dec 20, 2019: I'm deprecating this plugin as it was written to analyze Mummer output when we were deciding which aligner to use. It would still work, though, so I don't want to remove it. - But don't want it listed as a plugin for the PHG paper.

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

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`int`	`getNumAlignedBases(RangeSet<Integer> asmCoordSet)`
`Tuple<Integer, Double>`	`getRegionCoverage(RangeSet<Integer> rangeSet, Range<Integer> targetRange)`
`Map<Integer, ReferenceRange>`	`refRangesForChrom(Connection dbConn, String chrom)`
`static RangeSet<Integer>`	`getRangesForChrom(Map<Integer, ReferenceRange> refRangeMap, Chromosome chrom, DBLoadingUtils.AnchorType anchorType)`
`static void`	`main(Array<String> args)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`coordsFile()`	Output of Mummer coords file
`MummerAnalysisMetricsPlugin`	`coordsFile(String value)`	Set Mummer Coords File.
`String`	`refFasta()`	Input reference fasta file
`MummerAnalysisMetricsPlugin`	`refFasta(String value)`	Set Reference Fasta File.
`String`	`assemblyFasta()`	Assembly fasta file used when aligning
`MummerAnalysisMetricsPlugin`	`assemblyFasta(String value)`	Set Assembly Genome File.
`String`	`query()`	Name of assembly in mummer query, this is usually the assembly
`MummerAnalysisMetricsPlugin`	`query(String value)`	Set Query name .
`String`	`target()`	Name of target in mummer query, this is usually the reference
`MummerAnalysisMetricsPlugin`	`target(String value)`	Set Target name.
`String`	`mummerParams()`	Parameters used when running mummer
`MummerAnalysisMetricsPlugin`	`mummerParams(String value)`	Set Mummer Parameters.
`String`	`prefix()`	Name to prefix to output results file
`MummerAnalysisMetricsPlugin`	`prefix(String value)`	Set Output File refix.
`String`	`outputDir()`	Output directory including trailing / for writing files
`MummerAnalysisMetricsPlugin`	`outputDir(String value)`	Set Output Directory.
`String`	`configFile()`	File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
`MummerAnalysisMetricsPlugin`	`configFile(String value)`	Set DB Config File.
`Integer`	`asmBZStart()`	Start position for bz region on the assembly
`MummerAnalysisMetricsPlugin`	`asmBZStart(Integer value)`	Set BZ Assembly Start.
`Integer`	`asmBZEnd()`	End position for bz region on the assembly
`MummerAnalysisMetricsPlugin`	`asmBZEnd(Integer value)`	Set BZ Assembly End.

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
  - MummerAnalysisMetricsPlugin
```
MummerAnalysisMetricsPlugin()
```
  - MummerAnalysisMetricsPlugin
```
MummerAnalysisMetricsPlugin(Frame parentFrame)
```
  - MummerAnalysisMetricsPlugin
```
MummerAnalysisMetricsPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getNumAlignedBases
```
 int getNumAlignedBases(RangeSet<Integer> asmCoordSet)
```
  - getRegionCoverage
```
 Tuple<Integer, Double> getRegionCoverage(RangeSet<Integer> rangeSet, Range<Integer> targetRange)
```
  - refRangesForChrom
```
 Map<Integer, ReferenceRange> refRangesForChrom(Connection dbConn, String chrom)
```
  - getRangesForChrom
```
 static RangeSet<Integer> getRangesForChrom(Map<Integer, ReferenceRange> refRangeMap, Chromosome chrom, DBLoadingUtils.AnchorType anchorType)
```
  - main
```
 static void main(Array<String> args)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - coordsFile
```
 String coordsFile()
```
    Output of Mummer coords file
  - coordsFile
```
 MummerAnalysisMetricsPlugin coordsFile(String value)
```
    Set Mummer Coords File. Output of Mummer coords file
    
    Parameters:
    
    value - Mummer Coords File
  - refFasta
```
 String refFasta()
```
    Input reference fasta file
  - refFasta
```
 MummerAnalysisMetricsPlugin refFasta(String value)
```
    Set Reference Fasta File. Input reference fasta file
    
    Parameters:
    
    value - Reference Fasta File
  - assemblyFasta
```
 String assemblyFasta()
```
    Assembly fasta file used when aligning
  - assemblyFasta
```
 MummerAnalysisMetricsPlugin assemblyFasta(String value)
```
    Set Assembly Genome File. Assembly fasta file used when aligning
    
    Parameters:
    
    value - Assembly Genome File
  - query
```
 String query()
```
    Name of assembly in mummer query, this is usually the assembly
  - query
```
 MummerAnalysisMetricsPlugin query(String value)
```
    Set Query name . Name of assembly in mummer query, this is usually the assembly
    
    Parameters:
    
    value - Query name
  - target
```
 String target()
```
    Name of target in mummer query, this is usually the reference
  - target
```
 MummerAnalysisMetricsPlugin target(String value)
```
    Set Target name. Name of target in mummer query, this is usually the reference
    
    Parameters:
    
    value - Target name
  - mummerParams
```
 String mummerParams()
```
    Parameters used when running mummer
  - mummerParams
```
 MummerAnalysisMetricsPlugin mummerParams(String value)
```
    Set Mummer Parameters. Value of parameters used when running mummer
    
    Parameters:
    
    value - Mummer parameters
  - prefix
```
 String prefix()
```
    Name to prefix to output results file
  - prefix
```
 MummerAnalysisMetricsPlugin 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
```
 MummerAnalysisMetricsPlugin 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
```
 MummerAnalysisMetricsPlugin 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
  - asmBZStart
```
 Integer asmBZStart()
```
    Start position for bz region on the assembly
  - asmBZStart
```
 MummerAnalysisMetricsPlugin asmBZStart(Integer value)
```
    Set BZ Assembly Start. Start position for bz region on the assembly
    
    Parameters:
    
    value - BZ Assembly Start
  - asmBZEnd
```
 Integer asmBZEnd()
```
    End position for bz region on the assembly
  - asmBZEnd
```
 MummerAnalysisMetricsPlugin asmBZEnd(Integer value)
```
    Set BZ Assembly End. End position for bz region on the assembly
    
    Parameters:
    
    value - BZ Assembly End

Class MummerAnalysisMetricsPlugin

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

MummerAnalysisMetricsPlugin

MummerAnalysisMetricsPlugin

MummerAnalysisMetricsPlugin

Method Detail

processData

getNumAlignedBases

getRegionCoverage

refRangesForChrom

getRangesForChrom

main

getIcon

getButtonName

getToolTipText

coordsFile

coordsFile

refFasta

refFasta

assemblyFasta

assemblyFasta

query

query

target

target

mummerParams

mummerParams

prefix

prefix

outputDir

outputDir

configFile

configFile

asmBZStart

asmBZStart

asmBZEnd

asmBZEnd