MummerAnalysisMetricsPlugin (net.maizegenetics:phg 0.0.1 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener
```
public class MummerAnalysisMetricsPlugin
extends net.maizegenetics.plugindef.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

Author:

lcj34

Field Summary
- Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin
  DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors
Constructor and Description
`MummerAnalysisMetricsPlugin()`
`MummerAnalysisMetricsPlugin(Frame parentFrame)`
`MummerAnalysisMetricsPlugin(Frame parentFrame, boolean isInteractive)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Integer`	`asmBZEnd()` End position for bz region on the assembly
`MummerAnalysisMetricsPlugin`	`asmBZEnd(Integer value)` Set BZ Assembly End.
`Integer`	`asmBZStart()` Start position for bz region on the assembly
`MummerAnalysisMetricsPlugin`	`asmBZStart(Integer value)` Set BZ Assembly Start.
`String`	`assemblyFasta()` Assembly fasta file used when aligning
`MummerAnalysisMetricsPlugin`	`assemblyFasta(String value)` Set Assembly Genome File.
`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.
`String`	`coordsFile()` Output of Mummer coords file
`MummerAnalysisMetricsPlugin`	`coordsFile(String value)` Set Mummer Coords File.
`String`	`getButtonName()`
`ImageIcon`	`getIcon()`
`int`	`getNumAlignedBases(com.google.common.collect.RangeSet<Integer> asmCoordSet)`
`static com.google.common.collect.RangeSet<Integer>`	`getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap, net.maizegenetics.dna.map.Chromosome chrom, DBLoadingUtils.AnchorType anchorType)`
`net.maizegenetics.util.Tuple<Integer,Double>`	`getRegionCoverage(com.google.common.collect.RangeSet<Integer> rangeSet, com.google.common.collect.Range<Integer> targetRange)`
`String`	`getToolTipText()`
`static void`	`main(String[] args)`
`String`	`mummerParams()` Parameters used when running mummer
`MummerAnalysisMetricsPlugin`	`mummerParams(String value)` Set Mummer Parameters.
`String`	`outputDir()` Output directory including trailing / for writing files
`MummerAnalysisMetricsPlugin`	`outputDir(String value)` Set Output Directory.
`String`	`prefix()` Name to prefix to output results file
`MummerAnalysisMetricsPlugin`	`prefix(String value)` Set Output File refix.
`net.maizegenetics.plugindef.DataSet`	`processData(net.maizegenetics.plugindef.DataSet input)`
`String`	`query()` Name of assembly in mummer query, this is usually the assembly
`MummerAnalysisMetricsPlugin`	`query(String value)` Set Query name .
`String`	`refFasta()` Input reference fasta file
`MummerAnalysisMetricsPlugin`	`refFasta(String value)` Set Reference Fasta File.
`Map<Integer,ReferenceRange>`	`refRangesForChrom(Connection dbConn, String chrom)`
`String`	`target()` Name of target in mummer query, this is usually the reference
`MummerAnalysisMetricsPlugin`	`target(String value)` Set Target name.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin
getPluginInstance, getPluginInstance, isPlugin

- Constructor Detail
  - MummerAnalysisMetricsPlugin
```
public MummerAnalysisMetricsPlugin()
```
  - MummerAnalysisMetricsPlugin
```
public MummerAnalysisMetricsPlugin(Frame parentFrame)
```
  - MummerAnalysisMetricsPlugin
```
public MummerAnalysisMetricsPlugin(Frame parentFrame,
                                   boolean isInteractive)
```
- Method Detail
  - processData
```
public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)
```
    Specified by:
    
    processData in interface net.maizegenetics.plugindef.Plugin
    
    Overrides:
    
    processData in class net.maizegenetics.plugindef.AbstractPlugin
  - getNumAlignedBases
```
public int getNumAlignedBases(com.google.common.collect.RangeSet<Integer> asmCoordSet)
```
  - getRegionCoverage
```
public net.maizegenetics.util.Tuple<Integer,Double> getRegionCoverage(com.google.common.collect.RangeSet<Integer> rangeSet,
                                                                      com.google.common.collect.Range<Integer> targetRange)
```
  - refRangesForChrom
```
public Map<Integer,ReferenceRange> refRangesForChrom(Connection dbConn,
                                                     String chrom)
```
  - getRangesForChrom
```
public static com.google.common.collect.RangeSet<Integer> getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap,
                                                                            net.maizegenetics.dna.map.Chromosome chrom,
                                                                            DBLoadingUtils.AnchorType anchorType)
```
  - main
```
public static void main(String[] args)
```
    Parameters:
    
    args -
  - getIcon
```
public ImageIcon getIcon()
```
  - getButtonName
```
public String getButtonName()
```
  - getToolTipText
```
public String getToolTipText()
```
  - coordsFile
```
public String coordsFile()
```
    Output of Mummer coords file
    
    Returns:
    
    Mummer Coords File
  - coordsFile
```
public MummerAnalysisMetricsPlugin coordsFile(String value)
```
    Set Mummer Coords File. Output of Mummer coords file
    
    Parameters:
    
    value - Mummer Coords File
    
    Returns:
    
    this plugin
  - refFasta
```
public String refFasta()
```
    Input reference fasta file
    
    Returns:
    
    Reference Fasta File
  - refFasta
```
public MummerAnalysisMetricsPlugin refFasta(String value)
```
    Set Reference Fasta File. Input reference fasta file
    
    Parameters:
    
    value - Reference Fasta File
    
    Returns:
    
    this plugin
  - assemblyFasta
```
public String assemblyFasta()
```
    Assembly fasta file used when aligning
    
    Returns:
    
    Assembly Fasta File
  - assemblyFasta
```
public MummerAnalysisMetricsPlugin assemblyFasta(String value)
```
    Set Assembly Genome File. Assembly fasta file used when aligning
    
    Parameters:
    
    value - Assembly Genome File
    
    Returns:
    
    this plugin
  - query
```
public String query()
```
    Name of assembly in mummer query, this is usually the assembly
    
    Returns:
    
    Query name
  - query
```
public MummerAnalysisMetricsPlugin query(String value)
```
    Set Query name . Name of assembly in mummer query, this is usually the assembly
    
    Parameters:
    
    value - Query name
    
    Returns:
    
    this plugin
  - target
```
public String target()
```
    Name of target in mummer query, this is usually the reference
    
    Returns:
    
    Target name
  - target
```
public MummerAnalysisMetricsPlugin target(String value)
```
    Set Target name. Name of target in mummer query, this is usually the reference
    
    Parameters:
    
    value - Target name
    
    Returns:
    
    this plugin
  - mummerParams
```
public String mummerParams()
```
    Parameters used when running mummer
    
    Returns:
    
    Value of Mummer parameters
  - mummerParams
```
public MummerAnalysisMetricsPlugin mummerParams(String value)
```
    Set Mummer Parameters. Value of parameters used when running mummer
    
    Parameters:
    
    value - Mummer parameters
    
    Returns:
    
    this plugin
  - prefix
```
public String prefix()
```
    Name to prefix to output results file
    
    Returns:
    
    Output File refix
  - prefix
```
public MummerAnalysisMetricsPlugin prefix(String value)
```
    Set Output File refix. Name to prefix to output results file
    
    Parameters:
    
    value - Output File refix
    
    Returns:
    
    this plugin
  - outputDir
```
public String outputDir()
```
    Output directory including trailing / for writing files
    
    Returns:
    
    Output Directory
  - outputDir
```
public MummerAnalysisMetricsPlugin outputDir(String value)
```
    Set Output Directory. Output directory including trailing / for writing files
    
    Parameters:
    
    value - Output Directory
    
    Returns:
    
    this plugin
  - configFile
```
public String configFile()
```
    File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
    
    Returns:
    
    DB Config File
  - configFile
```
public 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
    
    Returns:
    
    this plugin
  - asmBZStart
```
public Integer asmBZStart()
```
    Start position for bz region on the assembly
    
    Returns:
    
    BZ Assembly Start
  - asmBZStart
```
public MummerAnalysisMetricsPlugin asmBZStart(Integer value)
```
    Set BZ Assembly Start. Start position for bz region on the assembly
    
    Parameters:
    
    value - BZ Assembly Start
    
    Returns:
    
    this plugin
  - asmBZEnd
```
public Integer asmBZEnd()
```
    End position for bz region on the assembly
    
    Returns:
    
    BZ Assembly End
  - asmBZEnd
```
public MummerAnalysisMetricsPlugin asmBZEnd(Integer value)
```
    Set BZ Assembly End. End position for bz region on the assembly
    
    Parameters:
    
    value - BZ Assembly End
    
    Returns:
    
    this plugin

Class MummerAnalysisMetricsPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

Constructor Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.plugindef.Plugin

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