net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin Maven / Gradle / Ivy

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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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package net.maizegenetics.analysis.imputation;

import java.awt.Frame;
import java.util.List;
import javax.swing.ImageIcon;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.PluginEvent;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

public class ViterbiAlgorithmPlugin extends AbstractPlugin {

	private static final Logger myLogger = LogManager.getLogger(ViterbiAlgorithmPlugin.class);
	private boolean fillGapsInAlignment = true;
	private double probHeterozygous = 0.07;
	private boolean useVariableTransition = false;
	private String variableRecombFilename = "";
	
	public ViterbiAlgorithmPlugin(Frame parentFrame) {
		super(parentFrame, false);
	}
	
	@Override
	public DataSet performFunction(DataSet input) {
		List theData = input.getDataOfType(PopulationData.class);
		for (Datum data:theData) {
			PopulationData family = (PopulationData) data.getData();
			GenotypeTable tba = family.imputed;
			//if (family.imputed instanceof TBitAlignment) {
			//	tba = (TBitAlignment) family.imputed;
			//} else {
			//	tba = TBitAlignment.getInstance(family.imputed);
			//}
			
			double phet;
			if (family.inbredCoef >= 0 && family.inbredCoef <= 1) {
				phet = (1 - family.inbredCoef) / 2;
			} else {
				phet = probHeterozygous;
			}
			
			family.imputed = NucleotideImputationUtils.imputeUsingViterbiFiveState(tba, phet, family.name, useVariableTransition);
			
			if (fillGapsInAlignment) NucleotideImputationUtils.fillGapsInAlignment(family);
			
		}
		
		DataSet resultDS = new DataSet(theData, this);
		fireDataSetReturned(new PluginEvent(resultDS, ViterbiAlgorithmPlugin.class));
		return resultDS;
	}

	@Override
	public void setParameters(String[] args) {
		if (args == null || args.length == 0) {
			return;
		}
		
		int narg = args.length;
		for (int i = 0; i < narg; i++) {
			if (args[i].equals("-g") || args[i].equalsIgnoreCase("-fillgaps")) {
				String val = args[++i];
				if (val.toUpperCase().startsWith("T")) fillGapsInAlignment = true;
				else fillGapsInAlignment = false;
			} else if (args[i].equals("-h") || args[i].equalsIgnoreCase("-phet")) {
				probHeterozygous = Double.parseDouble(args[++i]);
			} else if (args[i].equals("-v") || args[i].equalsIgnoreCase("-varRecomb")) {
				String vr = args[++i];
				if (vr.toLowerCase().startsWith("t")) useVariableTransition = true;
			} else if (args[i].equals("-f") || args[i].equalsIgnoreCase("-varRecombFile")) {
				variableRecombFilename = args[++i];
			} else if (args[i].equals("?")) myLogger.info(getUsage());
		}
	}

	@Override
	public ImageIcon getIcon() {
		return null;
	}

	@Override
	public String getButtonName() {
		return "Viterbi";
	}

	@Override
	public String getToolTipText() {
		return null;
	}

	public void setFillGapsInAlignment(boolean fillGapsInAlignment) {
		this.fillGapsInAlignment = fillGapsInAlignment;
	}

	public void setProbHeterozygous(double probHeterozygous) {
		this.probHeterozygous = probHeterozygous;
	}

	public String getUsage() {
		StringBuilder usage = new StringBuilder("The ViterbiAlgorithmPlugin can take the following optional parameters:\n");
		usage.append("-g or -fillgaps : true if missing values between SNPs from the same parent should be imputed to that parent, false otherwise (default = true)\n");
		usage.append("-h or -phet : expected frequency of heterozygous loci (default = 0.07). If the inbreeding coefficient is specified in the pedigree file that will used to calculate this value.\n");
		usage.append("-v or -varRecomb : If true use recombination rates that vary along the chromosome\n");
		usage.append("-f or -varRecombFile : The name of the file containing recombination rate as a function of position\n");
		usage.append("? : print the parameter list.\n");

		return usage.toString();
	}

	public void setUseVariableTransition(boolean useVariableTransition) {
		this.useVariableTransition = useVariableTransition;
	}

	public void setVariableRecombFilename(String variableRecombFilename) {
		this.variableRecombFilename = variableRecombFilename;
	}

}