package org.caleydo.data.importer.tcga.regular;

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://compbio.med.harvard.edu/tcga/stratomex/data/";

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

	public String getTcgaServerURL() {
		return tcgaServerURL;
	}

	public boolean isSampleGenes() {
		return sampleGenes;
	}
}

@@ -486,24 +486,25 @@
  %7B %22--sample
+d
 Genes%22 %7D, us
@@ -580,23 +580,22 @@
 private 
-boolean
+String
  sampleG
@@ -601,20 +601,22 @@
 Genes = 
+%22
 true
+%22
 ;%0D%0A%0D%0A%09pu
@@ -724,16 +724,37 @@
 %09return 
+Boolean.parseBoolean(
 sampleGe
@@ -756,16 +756,17 @@
 pleGenes
+)
 ;%0D%0A%09%7D%0D%0A%7D

convert -g to a string option to allow setting to false (boolean flags are just for enabling, not disabling things)