gt: 		Object obj = props.get(namedProperty);
context: /** 
   * Author:  anthony.fodor@gmail.com    
   * This code is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version,
  * provided that any use properly credits the author.
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  * GNU General Public License for more details at http://www.gnu.org * * */
  
  
  package utils;
  
  import java.io.InputStream;
  
  import java.util.Properties;
  
  public class ConfigReader
  {
  	public static final String PROPERTIES_FILE = "MetagenomicsTools.properties";
  
  	private static ConfigReader configReader = null;
  	private static Properties props = new Properties();
  	
  	public static final String JOBIN_GA_STOOL_RDP_DIR = "JOBIN_GA_STOOL_RDP_DIR";
  	public static final String JOBIN_GA_STOOL_DIR = "JOBIN_GA_STOOL_DIR";
  	
  	public static final String TOPE_ADENOMA_RDP_DIR = "TOPE_ADENOMA_RDP_DIR";
  
  	public static final String TRUE = "TRUE";
  	public static final String YES = "YES";
  
  	public static final String BLAST_DIRECTORY = "BLAST_DIRECTORY";
  	public static final String VERBOSE_CONSOLE = "VERBOSE_CONSOLE";
  	
  	public static final String PANCREATITIS_DIR = "PANCREATITIS_DIR";
  	
  	public static final String MACHINE_LEARNING_DIR = "MACHINE_LEARNING_DIR";
  	
  	public static final String BURKHOLDERIA_DIR = "BURKHOLDERIA_DIR";
  	public static final String BIG_BLAST_DIR = "BIG_BLAST_DIR";
  	
  	public static final String GENBANK_CACHE_DIR = "GENBANK_CACHE_DIR";
  	public static final String REDUCE_OTU_DIR = "REDUCE_OTU_DIR";
  	
  	public static final String SACCHARINE_RAT_DIR = "SACCHARINE_RAT_DIR";
  	
  	public static final String IAN_ANOREXIA_DIR = "IAN_ANOREXIA_DIR";
  	
  	public static final String MOTHUR_DIR = "MOTHUR_DIR";
  	public static final String CROSSOVER_EXERCISE_DIR = "CROSSOVER_EXERCISE_DIR";
  	
  	public static final String ERIN_DATA_DIR = "ERIN_DATA_DIR";
  	
  	public static final String BLAST_DIR = "BLAST_DIR";
  	public static final String E_TREE_TEST_DIR = "E_TREE_TEST_DIR";
  	
  	public static final String RDP_JAR_PATH= "RDP_JAR_PATH";
  	public static final String MOCK_SEQ_DIR="MOCK_SEQ_DIR";
  	
  	public static final String D3_DIR = "D3_DIR";
  	
  	public static final String R_DIRECTORY = "R_DIRECTORY";
  	public static final String NINA_WITH_DUPLICATES_DIR = "NINA_WITH_DUPLICATES_DIR";
  	
  	public static final String SANDRA_RIVER_JUNE_2012_Dir = "SANDRA_RIVER_JUNE_2012_Dir";
  	
  	public static final String METABOLITES_CASE_CONTROL = "METABOLITES_CASE_CONTROL";
  	public static final String SVM_DIR = "SVM_DIR";
  	public static final String JANELLE_RNA_SEQ_DIR = "JANELLE_RNA_SEQ_DIR";
  	public static final String KLEB_DIR="KLEB_DIR";
  	public static final String BIG_DATA_SCALING_FACTORS = "BIG_DATA_SCALING_FACTORS";
  	
  	public static final String TOPE_CHECK_DIR = "TOPE_CHECK_DIR";
  	public static final String SCOTT_PILOT_DIR = "SCOTT_PILOT_DIR";
  	public static final String CHINA_DIR = "CHINA_DIR";
  	public static final String HMP_DIR = "HMP_DIR";
  	
  	public static String getJobinGAStoolRDPDir() throws Exception {
  		return getConfigReader().getAProperty(JOBIN_GA_STOOL_RDP_DIR);
  	}
  	
  	public static String getJobinGAStoolDir() throws Exception {
  		return getConfigReader().getAProperty(JOBIN_GA_STOOL_DIR);
  	}
  	
  	public static String getTopeAdenomaRDPDir() throws Exception {
  		return getConfigReader().getAProperty(TOPE_ADENOMA_RDP_DIR);
  	}
  	
  	public static boolean isVerboseConsole() throws Exception
  	{
  		return getConfigReader().isSetToTrue(VERBOSE_CONSOLE);
  	}
  	
  	public static String getNinaWithDuplicatesDir() throws Exception
  	{
  		return getConfigReader().getAProperty(NINA_WITH_DUPLICATES_DIR);
  	}
  	
  	public static String getSvmDir() throws Exception
  	{
  		return getConfigReader().getAProperty(SVM_DIR);
  	}
  	
  	public static String getTopeCheckDir() throws Exception
  	{
  		return getConfigReader().getAProperty(TOPE_CHECK_DIR);
  	}
  	
  	public static String getMetabolitesCaseControl() throws Exception
  	{
  		return getConfigReader().getAProperty(METABOLITES_CASE_CONTROL);
  	}
  	
  	public static String getHMPDir() throws Exception
  	{
  		return getConfigReader().getAProperty(HMP_DIR);
  	}
  	
  	public static String getChinaDir() throws Exception
  	{
  		return getConfigReader().getAProperty(CHINA_DIR);
  	}
  	
  	public static String getKlebDir() throws Exception
  	{
  		return getConfigReader().getAProperty(KLEB_DIR);
  	}
  	
  	public static String getScottPilotDataDir() throws Exception
  	{
  		return getConfigReader().getAProperty(SCOTT_PILOT_DIR);
  	}
  
  	public static String getMachineLearningDir() throws Exception
  	{
  		return getConfigReader().getAProperty(MACHINE_LEARNING_DIR);
  	}
  	
  	public static String getSaccharineRatDir() throws Exception
  	{
  		return getConfigReader().getAProperty(SACCHARINE_RAT_DIR);
  	}
  	
  	public static String getD3Dir() throws Exception
  	{
  		return getConfigReader().getAProperty(D3_DIR);
  	}
  	
  	public static String getBigDataScalingFactorsDir() throws Exception
  	{
  		return getConfigReader().getAProperty(BIG_DATA_SCALING_FACTORS);
  	}
  	
  	public static String getSandraRiverJune2012Dir() throws Exception
  	{
  		return getConfigReader().getAProperty(SANDRA_RIVER_JUNE_2012_Dir);
  	}
  	
  	public static String getETreeTestDir() throws Exception
  	{
  		return getConfigReader().getAProperty(E_TREE_TEST_DIR);
  	}
  	
  	public static String getMockSeqDir() throws Exception
  	{
  		return getConfigReader().getAProperty(MOCK_SEQ_DIR);
  	}
  	
  	public static String getRDirectory() throws Exception
  	{
  		return getConfigReader().getAProperty(R_DIRECTORY);
  	}
  	
  	public static String getRDPJarPath() throws Exception
  	{
  		return getConfigReader().getAProperty(RDP_JAR_PATH);
  	}
  	
  	public static String getIanAnorexiaDir() throws Exception
  	{
  		return getConfigReader().getAProperty(IAN_ANOREXIA_DIR);
  	}
  	
  	public static String getJanelleRNASeqDir() throws Exception
  	{
  		return getConfigReader().getAProperty(JANELLE_RNA_SEQ_DIR);
  	}
  	
  	private boolean isSetToTrue(String namedProperty)
  	{
  		Object obj = props.get(namedProperty);
  
  		if (obj == null)
  			return false;
  
  		if (obj.toString().equalsIgnoreCase(TRUE)
  				|| obj.toString().equalsIgnoreCase(YES))
  			return true;
  
  		return false;
  	}
  	
  	public static String getReducedOTUDir() throws Exception
  	{
  		return getConfigReader().getAProperty(REDUCE_OTU_DIR);
  	}
  
  	private static String getAProperty(String namedProperty) throws Exception
  	{
  