net.maizegenetics.pangenome.pipelineTests

Class CountConsensusTaxaAtRefRange

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange

All Implemented Interfaces:

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

public class CountConsensusTaxaAtRefRange
extends net.maizegenetics.plugindef.AbstractPlugin

This class counts the number of taxa represented at each genome_interval region based on the method supplied. NOTE: Some intervals are not represented when the consensus data was created. This is due to gvcf files returning no data, or another bug in the consensus creation code. To find the total number of reference_ranges (focus only), run the following on your DB: select count(*) from reference_ranges inner join ref_range_ref_range_group where ref_range_ref_range_group.ref_range_id=reference_ranges.ref_range_id and ref_range_ref_range_group.ref_range_group_id=1; To find total number of reference_ranges (non-focus only), run the following on your DB: select count(*) from reference_ranges inner join ref_range_ref_range_group where ref_range_ref_range_group.ref_range_id=reference_ranges.ref_range_id and ref_range_ref_range_group.ref_range_group_id=2; Current count (sept 25, 2017) should be 37804 (anchors) or 75448 (anchors + inter-anchors)

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
CountConsensusTaxaAtRefRange()
CountConsensusTaxaAtRefRange(Frame parentFrame)
CountConsensusTaxaAtRefRange(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	databaseName() Database name
CountConsensusTaxaAtRefRange	databaseName(String value) Set Database Name.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	hostname() Hostname where database resides
CountConsensusTaxaAtRefRange	hostname(String value) Set Hostname.
String	method() Consensus Method
CountConsensusTaxaAtRefRange	method(String value) Set Consensus Method.
Boolean	onlyAnchors() Whether to include only anchors (i.e.
CountConsensusTaxaAtRefRange	onlyAnchors(Boolean value) Set Only Anchors.
String	outputFile() Output File
CountConsensusTaxaAtRefRange	outputFile(String value) Set Output File.
String	password() Password for database
CountConsensusTaxaAtRefRange	password(String value) Set Password.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	userid() Userid for database
CountConsensusTaxaAtRefRange	userid(String value) Set Userid.

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

CountConsensusTaxaAtRefRange

public CountConsensusTaxaAtRefRange()

CountConsensusTaxaAtRefRange

public CountConsensusTaxaAtRefRange(Frame parentFrame)

CountConsensusTaxaAtRefRange

public CountConsensusTaxaAtRefRange(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()

hostname

public String hostname()

Hostname where database resides

Returns:

Hostname

hostname

public CountConsensusTaxaAtRefRange hostname(String value)

Set Hostname. Hostname where database resides

Parameters:

value - Hostname

Returns:

this plugin

userid

public String userid()

Userid for database

Returns:

Userid

userid

public CountConsensusTaxaAtRefRange userid(String value)

Set Userid. Userid for database

Parameters:

value - Userid

Returns:

this plugin

password

public String password()

Password for database

Returns:

Password

password

public CountConsensusTaxaAtRefRange password(String value)

Set Password. Password for database

Parameters:

value - Password

Returns:

this plugin

databaseName

public String databaseName()

Database name

Returns:

Database Name

databaseName

public CountConsensusTaxaAtRefRange databaseName(String value)

Set Database Name. Database name

Parameters:

value - Database Name

Returns:

this plugin

method

public String method()

Consensus Method

Returns:

Consensus Method

method

public CountConsensusTaxaAtRefRange method(String value)

Set Consensus Method. Consensus Method

Parameters:

value - Consensus Method

Returns:

this plugin

onlyAnchors

public Boolean onlyAnchors()

Whether to include only anchors (i.e. no regions between anchors)

Returns:

Only Anchors

onlyAnchors

public CountConsensusTaxaAtRefRange onlyAnchors(Boolean value)

Set Only Anchors. Whether to include only anchors (i.e. no regions between anchors)

Parameters:

value - Only Anchors

Returns:

this plugin

outputFile

public String outputFile()

Output File

Returns:

Output File

outputFile

public CountConsensusTaxaAtRefRange outputFile(String value)

Set Output File. Output File

Parameters:

value - Output File

Returns:

this plugin