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- All Implemented Interfaces:
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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.
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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
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Constructor Summary
Constructors Constructor Description MummerAnalysisMetricsPlugin()
MummerAnalysisMetricsPlugin(Frame parentFrame)
MummerAnalysisMetricsPlugin(Frame parentFrame, boolean isInteractive)
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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
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Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Method Detail
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processData
DataSet processData(DataSet input)
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getNumAlignedBases
int getNumAlignedBases(RangeSet<Integer> asmCoordSet)
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getRegionCoverage
Tuple<Integer, Double> getRegionCoverage(RangeSet<Integer> rangeSet, Range<Integer> targetRange)
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refRangesForChrom
Map<Integer, ReferenceRange> refRangesForChrom(Connection dbConn, String chrom)
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getRangesForChrom
static RangeSet<Integer> getRangesForChrom(Map<Integer, ReferenceRange> refRangeMap, Chromosome chrom, DBLoadingUtils.AnchorType anchorType)
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getButtonName
String getButtonName()
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getToolTipText
String getToolTipText()
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coordsFile
String coordsFile()
Output of Mummer coords file
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coordsFile
MummerAnalysisMetricsPlugin coordsFile(String value)
Set Mummer Coords File. Output of Mummer coords file
- Parameters:
value
- Mummer Coords File
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refFasta
MummerAnalysisMetricsPlugin refFasta(String value)
Set Reference Fasta File. Input reference fasta file
- Parameters:
value
- Reference Fasta File
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assemblyFasta
String assemblyFasta()
Assembly fasta file used when aligning
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assemblyFasta
MummerAnalysisMetricsPlugin assemblyFasta(String value)
Set Assembly Genome File. Assembly fasta file used when aligning
- Parameters:
value
- Assembly Genome File
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query
MummerAnalysisMetricsPlugin query(String value)
Set Query name . Name of assembly in mummer query, this is usually the assembly
- Parameters:
value
- Query name
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target
MummerAnalysisMetricsPlugin target(String value)
Set Target name. Name of target in mummer query, this is usually the reference
- Parameters:
value
- Target name
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mummerParams
String mummerParams()
Parameters used when running mummer
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mummerParams
MummerAnalysisMetricsPlugin mummerParams(String value)
Set Mummer Parameters. Value of parameters used when running mummer
- Parameters:
value
- Mummer parameters
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prefix
MummerAnalysisMetricsPlugin prefix(String value)
Set Output File refix. Name to prefix to output results file
- Parameters:
value
- Output File refix
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outputDir
MummerAnalysisMetricsPlugin outputDir(String value)
Set Output Directory. Output directory including trailing / for writing files
- Parameters:
value
- Output Directory
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configFile
String configFile()
File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
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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
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asmBZStart
Integer asmBZStart()
Start position for bz region on the assembly
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asmBZStart
MummerAnalysisMetricsPlugin asmBZStart(Integer value)
Set BZ Assembly Start. Start position for bz region on the assembly
- Parameters:
value
- BZ Assembly Start
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asmBZEnd
MummerAnalysisMetricsPlugin asmBZEnd(Integer value)
Set BZ Assembly End. End position for bz region on the assembly
- Parameters:
value
- BZ Assembly End
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