net.maizegenetics.analysis.monetdb

Class ColumnsToBinaryFullGenomeTablePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class ColumnsToBinaryFullGenomeTablePlugin
extends AbstractPlugin

This plugin is copied from the ColumnsToBinarySNPOnlyTablePlugin (which was copied Kelly's ColumnsToBinaryPlugin, which re-worked various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGEnomeDB of the Rare Alleles monetdb instance. THe difference between this plugin and the ColumnsToBinarySNPOnlyTablePlugin is the latter creates entries only for identified hmp321 SNPs This method (ColumnsToBinaryFullGenomePlugin) creates entries for all positions listed in in the reference genome. To be consistent with the existing columns in monetdb maize tables, the reference file must be a link to a copy of the Zea_mays.AGPv3.20.dna.genome.fa file stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files. This plugin may also be used to create binaries for the maizeChrom10DB. In this case, we still use the full reference genome, but only chrom 10 is processed. The inputFile paramaeter shoudl be just 1 file containing chromosome 10 data.

Author:

kelly, 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
ColumnsToBinaryFullGenomeTablePlugin()
ColumnsToBinaryFullGenomeTablePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
ColumnsToBinaryFullGenomeTablePlugin	colByte(String value) Set Columns keep as Byte.
String	colsAllele() Comma separated list of column names to generate byte binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsAllele(String value) Set Columns translate allele values to 0-5.
String	colsByte() Comma separated list of column names to generate byte binaries for
String	colsChar() Comma separated list of column names to generate char binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsChar(String value) Set Columns keep as Char.
String	colsFloat() Comma separated list of column names to generate real binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsFloat(String value) Set Columns keep as Real (Float).
String	colsInt() Comma separated list of column names to generate int binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsInt(String value) Set Columns keep as Int.
String	colsLog10() Comma separated list of column names to first transform using -log10 then generate binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsLog10(String value) Set Columns to Keep and transform -log10.
String	colsLong() Comma separated list of column names to generate long binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsLong(String value) Set Columns keep as Long.
String	colsShort() Comma separated list of column names to generate short binaries for
ColumnsToBinaryFullGenomeTablePlugin	colsShort(String value) Set Columns keep as Short.
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	inputFile() File or a Directory containing Tab-delimited files with data to add to the database.
ColumnsToBinaryFullGenomeTablePlugin	inputFile(String value) Set Input Directory.
static void	main(String[] args)
Boolean	missToZero() Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
ColumnsToBinaryFullGenomeTablePlugin	missToZero(Boolean value) Set Missing float values to zero?.
Boolean	negToZero() Will set negative float denoted column values to zero (otherwise they are set to Float.MIN
ColumnsToBinaryFullGenomeTablePlugin	negToZero(Boolean value) Set Negative floats to zero?.
Boolean	oneBased() Will assume positions and ranges are 1-based unless otherwise set.
ColumnsToBinaryFullGenomeTablePlugin	oneBased(Boolean value) Set positions to 1-based unless this variable is "false".
String	outBase() Output directory and base filename to hold the binary files.
ColumnsToBinaryFullGenomeTablePlugin	outBase(String value) Set outBase.
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
Boolean	range() Columns for range data.
ColumnsToBinaryFullGenomeTablePlugin	range(Boolean value) Set Range information?.
String	refFile() Link to maize reference file.
ColumnsToBinaryFullGenomeTablePlugin	refFile(String value) Set refFile.

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

ColumnsToBinaryFullGenomeTablePlugin

public ColumnsToBinaryFullGenomeTablePlugin(Frame parentFrame,
                                            boolean isInteractive)

ColumnsToBinaryFullGenomeTablePlugin

public ColumnsToBinaryFullGenomeTablePlugin()

Method Detail

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.

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

main

public static void main(String[] args)

inputFile

public String inputFile()

File or a Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!

Returns:

Input File

inputFile

public ColumnsToBinaryFullGenomeTablePlugin inputFile(String value)

Set Input Directory. Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!

Parameters:

value - Input Directory or File

Returns:

this plugin

refFile

public String refFile()

Link to maize reference file.

Returns:

refFile

refFile

public ColumnsToBinaryFullGenomeTablePlugin refFile(String value)

Set refFile.

Parameters:

value - refFile

Returns:

this plugin

outBase

public String outBase()

Output directory and base filename to hold the binary files. Will make directory if neccesary

Returns:

outBase

outBase

public ColumnsToBinaryFullGenomeTablePlugin outBase(String value)

Set outBase. Output directory and base filename to hold the binary files. Will make directory if neccesary

Parameters:

value - outBase

Returns:

this plugin

colsFloat

public String colsFloat()

Comma separated list of column names to generate real binaries for

Returns:

Columns keep as Real (Float)

colsFloat

public ColumnsToBinaryFullGenomeTablePlugin colsFloat(String value)

Set Columns keep as Real (Float). Comma separated list of column names to generate real binaries for

Parameters:

value - Columns keep as Real (Float)

Returns:

this plugin

colsInt

public String colsInt()

Comma separated list of column names to generate int binaries for

Returns:

Columns keep as Int

colsInt

public ColumnsToBinaryFullGenomeTablePlugin colsInt(String value)

Set Columns keep as Int. Comma separated list of column names to generate int binaries for

Parameters:

value - Columns keep as Int

Returns:

this plugin

colsShort

public String colsShort()

Comma separated list of column names to generate short binaries for

Returns:

Columns keep as Short

colsShort

public ColumnsToBinaryFullGenomeTablePlugin colsShort(String value)

Set Columns keep as Short. Comma separated list of column names to generate short binaries for

Parameters:

value - Columns keep as Short

Returns:

this plugin

colsLong

public String colsLong()

Comma separated list of column names to generate long binaries for

Returns:

Columns keep as Long

colsLong

public ColumnsToBinaryFullGenomeTablePlugin colsLong(String value)

Set Columns keep as Long. Comma separated list of column names to generate long binaries for

Parameters:

value - Columns keep as Long

Returns:

this plugin

colsByte

public String colsByte()

Comma separated list of column names to generate byte binaries for

Returns:

Columns keep as Byte

colByte

public ColumnsToBinaryFullGenomeTablePlugin colByte(String value)

Set Columns keep as Byte. Comma separated list of column names to generate byte binaries for

Parameters:

value - Columns keep as bhte

Returns:

this plugin

colsAllele

public String colsAllele()

Comma separated list of column names to generate byte binaries for

Returns:

Columns keep as Byte

colsAllele

public ColumnsToBinaryFullGenomeTablePlugin colsAllele(String value)

Set Columns translate allele values to 0-5. Comma separated list of column names of single character alleles to be translated from A/C/G/T/+/- to 0-5.

Parameters:

value - Columns keep for translated alleles stored as bytes

Returns:

this plugin

colsChar

public String colsChar()

Comma separated list of column names to generate char binaries for

Returns:

Columns keep as Char

colsChar

public ColumnsToBinaryFullGenomeTablePlugin colsChar(String value)

Set Columns keep as Char. Comma separated list of column names to generate char binaries for

Parameters:

value - Columns keep as Char

Returns:

this plugin

colsLog10

public String colsLog10()

Comma separated list of column names to first transform using -log10 then generate binaries for

Returns:

Columns to Keep and transform -log10

colsLog10

public ColumnsToBinaryFullGenomeTablePlugin colsLog10(String value)

Set Columns to Keep and transform -log10. Comma separated list of column names to first transform using -log10 then generate binaries for

Parameters:

value - Columns to Keep and transform -log10

Returns:

this plugin

range

public Boolean range()

Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'

Returns:

Range information?

range

public ColumnsToBinaryFullGenomeTablePlugin range(Boolean value)

Set Range information?. Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'

Parameters:

value - Range information?

Returns:

this plugin

negToZero

public Boolean negToZero()

Will set negative float denoted column values to zero (otherwise they are set to Float.MIN

Returns:

Negative floats to zero?

negToZero

public ColumnsToBinaryFullGenomeTablePlugin negToZero(Boolean value)

Set Negative floats to zero?. Will set negative float denoted column values to zero (otherwise they are set to Float.MIN

Parameters:

value - Negative floats to zero?

Returns:

this plugin

missToZero

public Boolean missToZero()

Will set missing float denoted column values to zero (otherwise they are set to Float.MIN

Returns:

Missing float values to zero?

missToZero

public ColumnsToBinaryFullGenomeTablePlugin missToZero(Boolean value)

Set Missing float values to zero?. Will set missing float denoted column values to zero (otherwise they are set to Float.MIN

Parameters:

value - Missing float values to zero?

Returns:

this plugin

oneBased

public Boolean oneBased()

Will assume positions and ranges are 1-based unless otherwise set.

Returns:

positions are 1-based?

oneBased

public ColumnsToBinaryFullGenomeTablePlugin oneBased(Boolean value)

Set positions to 1-based unless this variable is "false".

Parameters:

value - 1-based positions?

Returns:

this plugin