net.maizegenetics.pangenome.processAssemblyGenomes

Class Mummer4DoonerBZStats

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class Mummer4DoonerBZStats
extends net.maizegenetics.plugindef.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.

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

Method Summary

Modifier and Type	Method and Description
static void	addToCoordsMap(com.google.common.collect.RangeMap<Integer,String> coordsFileRefToDataMap, String line)
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	coordsFile() Output of Mummer coords file
Mummer4DoonerBZStats	coordsFile(String value) Set Mummer Coords File.
Map<Integer,ReferenceRange>	getAnchorFromIntervalsFile(String intervalsFile, String chrom)
com.google.common.collect.RangeSet<Integer>	getAnchorRangeSet(com.google.common.collect.RangeMap<Integer,String> anchorOverlapEntries)
String	getButtonName()
com.google.common.collect.RangeMap<Integer,String>	getCoordsEntriesForAnchor(com.google.common.collect.Range<Integer> anchorRange, com.google.common.collect.RangeMap<Integer,String> coordsFileRefToDataMap)
ImageIcon	getIcon()
static Map<Integer,com.google.common.collect.Range<Integer>>	getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap, net.maizegenetics.dna.map.Chromosome chrom, DBLoadingUtils.AnchorType anchorType)
String	getToolTipText()
String	intervalsFile() Anchor Intervals file to be used when intervals are different than DB, e.g.
Mummer4DoonerBZStats	intervalsFile(String value) Set Anchor Intervals File.
static void	main(String[] args)
String	mummerParams() Mummer parameters used
Mummer4DoonerBZStats	mummerParams(String value) Set Mummer Parameters.
String	outputDir() Output directory including trailing / for writing files
Mummer4DoonerBZStats	outputDir(String value) Set Output Directory.
String	prefix() Name to prefix to output results file
Mummer4DoonerBZStats	prefix(String value) Set Output File refix.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refChrom() Name of reference chromsome as stored in the database.
Mummer4DoonerBZStats	refChrom(String value) Set Reference Chromosome Name.
static Map<Integer,ReferenceRange>	refRangesForChrom(Connection dbConn, String chrom)

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

Mummer4DoonerBZStats

public Mummer4DoonerBZStats()

Mummer4DoonerBZStats

public Mummer4DoonerBZStats(Frame parentFrame)

Mummer4DoonerBZStats

public Mummer4DoonerBZStats(Frame parentFrame,
                            boolean isInteractive)

Method Detail

main

public static void main(String[] args)

Parameters:

args -

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

getAnchorFromIntervalsFile

public Map<Integer,ReferenceRange> getAnchorFromIntervalsFile(String intervalsFile,
                                                              String chrom)

refRangesForChrom

public static Map<Integer,ReferenceRange> refRangesForChrom(Connection dbConn,
                                                            String chrom)

getRangesForChrom

public static Map<Integer,com.google.common.collect.Range<Integer>> getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap,
                                                                                      net.maizegenetics.dna.map.Chromosome chrom,
                                                                                      DBLoadingUtils.AnchorType anchorType)

addToCoordsMap

public static void addToCoordsMap(com.google.common.collect.RangeMap<Integer,String> coordsFileRefToDataMap,
                                  String line)

getCoordsEntriesForAnchor

public com.google.common.collect.RangeMap<Integer,String> getCoordsEntriesForAnchor(com.google.common.collect.Range<Integer> anchorRange,
                                                                                    com.google.common.collect.RangeMap<Integer,String> coordsFileRefToDataMap)

getAnchorRangeSet

public com.google.common.collect.RangeSet<Integer> getAnchorRangeSet(com.google.common.collect.RangeMap<Integer,String> anchorOverlapEntries)

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 Mummer4DoonerBZStats coordsFile(String value)

Set Mummer Coords File. Output of Mummer coords file

Parameters:

value - Mummer Coords File

Returns:

this plugin

intervalsFile

public String intervalsFile()

Anchor Intervals file to be used when intervals are different than DB, e.g. when using just a small region

Returns:

Anchor Intervals File

intervalsFile

public 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

Returns:

this plugin

mummerParams

public String mummerParams()

Mummer parameters used

Returns:

Mummer Parameters

mummerParams

public Mummer4DoonerBZStats mummerParams(String value)

Set Mummer Parameters. Mummer parameters used

Parameters:

value - Mummer Parameters

Returns:

this plugin

prefix

public String prefix()

Name to prefix to output results file

Returns:

Output File refix

prefix

public Mummer4DoonerBZStats 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 Mummer4DoonerBZStats 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 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

Returns:

this plugin

refChrom

public String refChrom()

Name of reference chromsome as stored in the database. This is the chromosome whose anchors will be pulled.

Returns:

Reference Chromosome Name

refChrom

public 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

Returns:

this plugin