net.maizegenetics.pangenome.db_loading

Class LoadHaplotypeCountsTablePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin

All Implemented Interfaces:

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

public class LoadHaplotypeCountsTablePlugin
extends net.maizegenetics.plugindef.AbstractPlugin

This method reads haplotype counts from an incoming DataSet object, and stores results to a specified database. This method will be called from FastqToHapCount plugin, which will pass a DataSet containing the hits counts (perfect and exclusion) as well as the taxon. Assumptions: The haplotype counts files are specific to a single taxon. That taxon name may be determined from the file name. The db genotypes table is queried for a line_name that matches the taxon. IF none exists, a new entry is added. The new genotypes entries will only link to the haplotype_counts table. 1. method: unique name for method used to create counts. 2. methodDetails: anything user wants to say about the method. 3. configFile: name of file containing parameters for connecting to DB, including host, user, password, type (sqlite or postgres) 4. fastqFile: name of file used to process the data. Outputs: Data is stored to the haplotype_counts table.

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
LoadHaplotypeCountsTablePlugin()
LoadHaplotypeCountsTablePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	configFile() Name of config file to use for db connection
LoadHaplotypeCountsTablePlugin	configFile(String value) Set DB Config File.
String	fastqFile() Name of fastQ file used in FastqToHapCountPlugin
LoadHaplotypeCountsTablePlugin	fastqFile(String value) Set Fastq File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	method() Name of method used for determining inclusion/exclusion counts
LoadHaplotypeCountsTablePlugin	method(String value) Set Hapcount Method.
String	methodDetails() Text describing method used to create inclusion/exclusion counts.
LoadHaplotypeCountsTablePlugin	methodDetails(String value) Set Method Details.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)

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

LoadHaplotypeCountsTablePlugin

public LoadHaplotypeCountsTablePlugin()

LoadHaplotypeCountsTablePlugin

public LoadHaplotypeCountsTablePlugin(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

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

method

public String method()

Name of method used for determining inclusion/exclusion counts

Returns:

Hapcount Method

method

public LoadHaplotypeCountsTablePlugin method(String value)

Set Hapcount Method. Name of method used for determining inclusion/exclusion counts

Parameters:

value - Hapcount Method

Returns:

this plugin

methodDetails

public String methodDetails()

Text describing method used to create inclusion/exclusion counts.

Returns:

Method Details

methodDetails

public LoadHaplotypeCountsTablePlugin methodDetails(String value)

Set Method Details. Text describing method used to create inclusion/exclusion counts.

Parameters:

value - Method Details

Returns:

this plugin

configFile

public String configFile()

Name of config file to use for db connection

Returns:

DB Config File

configFile

public LoadHaplotypeCountsTablePlugin configFile(String value)

Set DB Config File. Name of config file to use for db connection

Parameters:

value - DB Config File

Returns:

this plugin

fastqFile

public String fastqFile()

Name of fastQ file used in FastqToHapCountPlugin

Returns:

Fastq File

fastqFile

public LoadHaplotypeCountsTablePlugin fastqFile(String value)

Set Fastq File. Name of fastq file used in FastqToHapCountPlugin

Parameters:

value - Fastq File

Returns:

this plugin