/*******************************************************************************
 * Caleydo - Visualization for Molecular Biology - http://caleydo.org
 * Copyright (c) The Caleydo Team. All rights reserved.
 * Licensed under the new BSD license, available at http://caleydo.org/license
 ******************************************************************************/
package org.caleydo.data.importer.tcga.regular;

import org.caleydo.core.manager.GeneralManager;
import org.caleydo.data.importer.tcga.Settings;
import org.kohsuke.args4j.Option;


public class TCGASettings extends Settings {
	@Option(name = "-s", aliases = { "--server" }, usage = "TCGA Server URL that hosts TCGA Caleydo project files default: \"http://compbio.med.harvard.edu/tcga/stratomex/data/\"")
	private String tcgaServerURL = "http://data.icg.tugraz.at/caleydo/download/" + GeneralManager.VERSION + "/tcga/";

	@Option(name = "-g", aliases = { "--sampledGenes" }, usage = "whether to use the sampled genes or not default: \"true\"")
	private String sampleGenes = "true";

	public String getTcgaServerURL() {
		return tcgaServerURL;
	}

	public boolean isSampleGenes() {
		return Boolean.parseBoolean(sampleGenes);
	}
}

@@ -1042,16 +1042,121 @@
 true%22;%0A%0A
+%09@Option(name = %22--fullGenes%22, usage = %22inverse of --sampledGenes%22)%0A%09private boolean fullGenes = false;%0A%0A
 %09public 
@@ -1253,16 +1253,30 @@
 %09%09return
+ !fullGenes %7C%7C
  Boolean

add "--fullGenes" <=> "--sampledGenes false"