- NEW: Added a new command-line wrapper for running expected F1 gener…

…ation. Refs #9.

src/jhi/flapjack/io/cmd/GenerateExpectedF1s.java

@@ -0,0 +1,115 @@
+// Copyright 2009-2018 Information & Computational Sciences, JHI. All rights
+// reserved. Use is subject to the accompanying licence terms.
+
+package jhi.flapjack.io.cmd;
+
+import java.io.*;
+
+import jhi.flapjack.analysis.*;
+import jhi.flapjack.data.*;
+import jhi.flapjack.io.*;
+
+import org.apache.commons.cli.*;
+
+import scri.commons.gui.*;
+
+// Takes an input genotype file and the indices of two parents, then generates
+// an expected F1 line from them, writing the results to an output file
+public class GenerateExpectedF1s
+{
+	// The objects that will (hopefully) get created
+	private DataSet dataSet = new DataSet();
+
+	private CreateProjectSettings projectSettings;
+	private DataImportSettings importSettings;
+
+	private String filename;
+	private Integer parent1;
+	private Integer parent2;
+
+	public static void main(String[] args)
+	{
+		CmdOptions options = new CmdOptions()
+			.withAdvancedOptions()
+			.withGenotypeFile(true)
+			.withOutputPath(true)
+			.addRequiredOption("1", "parent-1", true, "INTEGER", "Index of parent-1 in file")
+			.addRequiredOption("2", "parent-2", true, "INTEGER", "Index of parent-2 in file");
+
+		try
+		{
+			CommandLine line = new DefaultParser().parse(options, args);
+
+			CreateProjectSettings projectSettings = options.getCreateProjectSettings(line);
+			DataImportSettings importSettings = options.getDataImportSettings(line);
+
+			// Uncommon required vars
+			String filename = options.getOutputPath(line);
+			Integer parent1 = Integer.parseInt(line.getOptionValue("parent-1"))-1;
+			Integer parent2 = Integer.parseInt(line.getOptionValue("parent-2"))-1;
+
+			GenerateExpectedF1s stats = new GenerateExpectedF1s(projectSettings,
+				importSettings, parent1, parent2, filename);
+			stats.doStatGeneration();
+
+			System.exit(0);
+		}
+		catch (Exception e)
+		{
+			options.printHelp("GenerateExpectdF1s");
+			System.exit(1);
+		}
+	}
+
+	private GenerateExpectedF1s(CreateProjectSettings projectSettings, DataImportSettings importSettings, Integer parent1,
+		Integer parent2, String filename)
+	{
+		this.projectSettings = projectSettings;
+		this.importSettings = importSettings;
+		this.parent1 = parent1;
+		this.parent2 = parent2;
+		this.filename = filename;
+	}
+
+	public void doStatGeneration()
+	{
+		RB.initialize("auto", "res.text.flapjack");
+		TaskDialog.setIsHeadless();
+
+		CreateProject createProject = new CreateProject(projectSettings, importSettings);
+
+		try
+		{
+			createProject.doProjectCreation();
+			dataSet = createProject.dataSet();
+
+			// Load the data into a view
+			GTViewSet viewSet = dataSet.getViewSets().get(0);
+
+			// Activate all chromosomes
+			boolean[] chromosomes = new boolean[viewSet.chromosomeCount()];
+			for (int i = 0; i < chromosomes.length; i++)
+				chromosomes[i] = true;
+
+			// Simulate the F1
+			SimulateF1 simulate = new SimulateF1(viewSet, parent1, parent2);
+			simulate.runJob(0);
+
+			// Remove all the lines *apart* from the generated F1
+			for (int i = simulate.getF1Index()-1; i >= 0; i--)
+				viewSet.getLines().remove(i);
+
+			// Write out the result
+			GenotypeDataExporter exporter = new GenotypeDataExporter(
+				new File(filename), viewSet, true, chromosomes, 0);
+			exporter.runJob(0);
+
+			System.out.println("Generated F1 was written to " + filename);
+		}
+		catch (Exception e)
+		{
+			e.printStackTrace();
+			System.exit(1);
+		}
+	}
+}