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package net.maizegenetics.analysis.numericaltransform;
import java.awt.Frame;
import java.util.List;
import javax.swing.ImageIcon;
import net.maizegenetics.phenotype.Phenotype;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.GeneratePluginCode;
import net.maizegenetics.plugindef.PluginParameter;
public class BoxCoxTransformationPlugin extends AbstractPlugin{
private PluginParameter startLambda =
new PluginParameter.Builder<>("startLambda",-5.0,Double.class)
.description("Parameter to set the starting point for the Lambda search in Box Cox. "
+ "The algorithm will start at this value and iterate by Lambda Step until it reaches End Lambda.")
.build();
private PluginParameter endLambda =
new PluginParameter.Builder<>("endLambda",5.0,Double.class)
.description("Parameter to set the ending point for the Lambda search in Box Cox. "
+ "The algorithm will start at Start Lambda and iterate by Lambda Step until it reaches this value.")
.build();
private PluginParameter stepLambda =
new PluginParameter.Builder<>("LambdaStep",0.2,Double.class)
.description("Parameter to set the iteration step for the Lambda search in Box Cox. "
+ "The algorithm will start at Start Lambda and iterate by this value until it reaches the End Lambda.")
.build();
private PluginParameter addSmallValue =
new PluginParameter.Builder<>("addSmallValue", true, Boolean.class)
.description("Boolean to allow for a small random value to be added to each observed value. The value is calculated by the following:\n"
+ "rand(0:1) * .5 * minObservedValue")
.build();
private PluginParameter randomSeed =
new PluginParameter.Builder<>("randomSeed",12345l,Long.class)
.description("Random Seed to be used in the Random Small Number Generation")
.dependentOnParameter(addSmallValue)
.build();
public BoxCoxTransformationPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
public DataSet processData(DataSet input) {
//do whatever your plugin does
List datumList = input.getDataOfType(Phenotype.class);
//check size of datumList, throw error if not equal to one
if (datumList.size() != 1){
throw new IllegalArgumentException("BoxCoxTransformationPluging: select exactly one phenotype dataset to average.");
}
if(startLambda.value()>endLambda.value()) {
throw new IllegalArgumentException("Start Lambda must be smaller than End Lambda");
}
BoxCoxTransformation boxCoxPheno = new BoxCoxTransformation();
try {
Phenotype myPhenotype = boxCoxPheno.applyBoxCox((Phenotype) datumList.get(0).getData(),addSmallValue.value(),randomSeed.value(),
startLambda.value(),endLambda.value(),stepLambda.value());
if (myPhenotype != null) {
String name = myPhenotype.name();
Datum td = new Datum(name, myPhenotype, null);
//todo need to add logic of directories.
DataSet tds = new DataSet(td, this);
return tds;
}
}
catch(Exception e) {
throw new IllegalArgumentException(e.getMessage());
}
return null; // Note: this can return null
}
@Override
public ImageIcon getIcon() {
return null;
}
@Override
public String getButtonName() {
return "Box Cox Transformation";
}
@Override
public String getToolTipText() {
return "Box Cox Transformation.";
}
@Override
public String getCitation() {
return "Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. "
+ "(2007) TASSEL: Software for association mapping of complex traits in diverse "
+ "samples. Bioinformatics 23:26332635.";
}
@Override
public String pluginUserManualURL() {
//TODO add in the documentation link once it is written up
return "https://bitbucket.org/tasseladmin/tassel5source/wiki/UserManual/Kinship/Kinship";
}
// The following getters and setters were auto-generated.
// Please use this method to re-generate.
//
// public static void main(String[] args) {
// GeneratePluginCode.generate(BoxCoxTransformationPlugin.class);
// }
/**
* Convenience method to run plugin with one return object.
*/
// TODO: Replace with specific type.
public Phenotype runPlugin(DataSet input) {
return (Phenotype) performFunction(input).getData(0).getData();
}
/**
* Add Small Value
*
* @return Add Small Value
*/
public Boolean addSmallValue() {
return addSmallValue.value();
}
/**
* Set Add Small Value. Add Small Value
*
* @param value Add Small Value
*
* @return this plugin
*/
public BoxCoxTransformationPlugin addSmallValue(Boolean value) {
addSmallValue = new PluginParameter<>(addSmallValue, value);
return this;
}
/**
* Random Seed
*
* @return Random Seed
*/
public Long randomSeed() {
return randomSeed.value();
}
/**
* Set Random Seed. Random Seed
*
* @param value Random Seed
*
* @return this plugin
*/
public BoxCoxTransformationPlugin randomSeed(Long value) {
randomSeed = new PluginParameter<>(randomSeed, value);
return this;
}
/**
* Start Lambda
*
* @return Start Lambda
*/
public Double startLambda() {
return startLambda.value();
}
/**
* Set Start Lambda. Start Lambda
*
* @param value Start Lambda
*
* @return this plugin
*/
public BoxCoxTransformationPlugin startLambda(Double value) {
startLambda = new PluginParameter<>(startLambda, value);
return this;
}
/**
* End Lambda
*
* @return End Lambda
*/
public Double endLambda() {
return endLambda.value();
}
/**
* Set End Lambda. End Lambda
*
* @param value End Lambda
*
* @return this plugin
*/
public BoxCoxTransformationPlugin endLambda(Double value) {
endLambda = new PluginParameter<>(endLambda, value);
return this;
}
/**
* Step Lambda
*
* @return Step Lambda
*/
public Double stepLambda() {
return stepLambda.value();
}
/**
* Set Step Lambda. Step Lambda
*
* @param value Step Lambda
*
* @return this plugin
*/
public BoxCoxTransformationPlugin stepLambda(Double value) {
stepLambda = new PluginParameter<>(stepLambda, value);
return this;
}
}
