net.maizegenetics.analysis.gbs.repgen

Class RepGenLoadSeqToDBPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class RepGenLoadSeqToDBPlugin
extends AbstractPlugin

Develops a discovery rGBS database based on a folder of sequencing files Keeps only good reads having no N's in the useful part of the sequence. Trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter. Originally the reference throughout was to "tag". This is being changed to "kmer" as the pipeline is a kmer alignment process.

Author:

Ed Buckler

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
RepGenLoadSeqToDBPlugin()
RepGenLoadSeqToDBPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
RepGenLoadSeqToDBPlugin	batchSize(Integer value) Set number of Fastq files processed simultaneously
static Map<Tag,Tuple<Integer,String>>	calculateTagAveQS(RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap tagCntQSMap, int qualityScoreBase)
String	getButtonName() Button name for this plugin to be used in buttons, etc.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
String	inputDirectory() Input directory containing FASTQ files in text or gzipped text.
RepGenLoadSeqToDBPlugin	inputDirectory(String value) Set Input Directory.
String	keyFile() Key file listing barcodes distinguishing the samples
RepGenLoadSeqToDBPlugin	keyFile(String value) Set Key File.
Integer	kmerLength() Maximum Tag Length
RepGenLoadSeqToDBPlugin	kmerLength(Integer value) Set Maximum Tag Length.
RepGenLoadSeqToDBPlugin	maximumKmerNumber(Integer value) Set maximum number of kmers
Integer	minimumKmerLength() Minimum Tag Length
RepGenLoadSeqToDBPlugin	minimumKmerLength(Integer value) Set Minimum Tag Length.
Integer	minimumQualityScore() Minimum quality score within the barcode and read length to be accepted
RepGenLoadSeqToDBPlugin	minimumQualityScore(Integer value) Set Minimum quality score.
Integer	minKmerCount() Minimum tag count
RepGenLoadSeqToDBPlugin	minKmerCount(Integer value) Set Min Tag Count.
Integer	minTaxa() Minimum taxa containing tag
RepGenLoadSeqToDBPlugin	minTaxa(Integer value) Set Min Taxa Count.
String	outputDatabaseFile() Output Database File
RepGenLoadSeqToDBPlugin	outputDatabaseFile(String value) Set Output Database File.
void	postProcessParameters()
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
void	setTagLenException()

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

RepGenLoadSeqToDBPlugin

public RepGenLoadSeqToDBPlugin()

RepGenLoadSeqToDBPlugin

public RepGenLoadSeqToDBPlugin(Frame parentFrame,
                               boolean isInteractive)

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

setTagLenException

public void setTagLenException()

calculateTagAveQS

public static Map<Tag,Tuple<Integer,String>> calculateTagAveQS(RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap tagCntQSMap,
                                                               int qualityScoreBase)

inputDirectory

public String inputDirectory()

Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Returns:

Input Directory

inputDirectory

public RepGenLoadSeqToDBPlugin inputDirectory(String value)

Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Parameters:

value - Input Directory

Returns:

this plugin

keyFile

public String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

Key File

keyFile

public RepGenLoadSeqToDBPlugin keyFile(String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

this plugin

kmerLength

public Integer kmerLength()

Maximum Tag Length

Returns:

Maximum Tag Length

kmerLength

public RepGenLoadSeqToDBPlugin kmerLength(Integer value)

Set Maximum Tag Length. Maximum Tag Length

Parameters:

value - Maximum Tag Length

Returns:

this plugin

minimumKmerLength

public Integer minimumKmerLength()

Minimum Tag Length

Returns:

Minimum Tag Length

minimumKmerLength

public RepGenLoadSeqToDBPlugin minimumKmerLength(Integer value)

Set Minimum Tag Length. Minimum Tag Length

Parameters:

value - Minimum Tag Length

Returns:

this plugin

minKmerCount

public Integer minKmerCount()

Minimum tag count

Returns:

Min Tag Count

minKmerCount

public RepGenLoadSeqToDBPlugin minKmerCount(Integer value)

Set Min Tag Count. Minimum tag count

Parameters:

value - Min Tag Count

Returns:

this plugin

minTaxa

public Integer minTaxa()

Minimum taxa containing tag

Returns:

Min Taxa Count

minTaxa

public RepGenLoadSeqToDBPlugin minTaxa(Integer value)

Set Min Taxa Count. Minimum Taxa count

Parameters:

value - Min Taxa containing a tag

Returns:

this plugin

outputDatabaseFile

public String outputDatabaseFile()

Output Database File

Returns:

Output Database File

outputDatabaseFile

public RepGenLoadSeqToDBPlugin outputDatabaseFile(String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

this plugin

minimumQualityScore

public Integer minimumQualityScore()

Minimum quality score within the barcode and read length to be accepted

Returns:

Minimum quality score

minimumQualityScore

public RepGenLoadSeqToDBPlugin minimumQualityScore(Integer value)

Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted

Parameters:

value - Minimum quality score

Returns:

this plugin

maximumKmerNumber

public RepGenLoadSeqToDBPlugin maximumKmerNumber(Integer value)

Set maximum number of kmers

Parameters:

value -

Returns:

batchSize

public RepGenLoadSeqToDBPlugin batchSize(Integer value)

Set number of Fastq files processed simultaneously

Parameters:

value -

Returns:

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String