Change blast properties reader

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/BiggMain.java

@@ -24,12 +24,12 @@ public class BiggMain {
 		
 		List<String> listArgs = readParamsFile(paramsPath);
 		
-		String eValue = listArgs.get(2);
-		String bitScore = listArgs.get(3);
-		String queryCoverage = listArgs.get(4);
 		
-		Properties properties = new Properties(bitScore, queryCoverage, eValue);
-
+		
+		Properties properties = new Properties();
+		properties = validateProperties(properties, listArgs);
+		
+		
 		String filePath = workFolderID.concat("workerSubmissions/queryGenome.faa");
 		
 		int option = Integer.parseInt(listArgs.get(0));
@@ -113,5 +113,31 @@ public class BiggMain {
 		
 		return models;
 	}
+	
+	private static Properties validateProperties(Properties properties, List<String> listArgs) {
+		
+		try {
+			String eValue = listArgs.get(2);
+			String bitScore = listArgs.get(3);
+			String queryCoverage = listArgs.get(4);
+			
+			if(bitScore != null && bitScore != "")
+				properties.setBitScore(Double.valueOf(bitScore));
+			
+			if(queryCoverage != null && queryCoverage != "")
+				properties.setQueryCoverage(Double.valueOf(queryCoverage));
+			
+			if(eValue != null && eValue != "")
+				properties.setBlastEValue(Double.valueOf(eValue));
+			
+		}catch(Exception ex) {
+			System.out.println("Please check your properties values.");
+			System.out.println(ex.getMessage());
+		}
+		
+		
+		
+		return properties;
+	}
 
 }

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/Properties.java

@@ -51,13 +51,13 @@ public class Properties {
 		}
 	}
 	
-	public Properties(String bitScore, String queryCoverage, String evalue) {
-		this.bitScore = Double.valueOf(bitScore);
-		
-		this.queryCoverage = Double.valueOf(queryCoverage);
-		
-		this.blastEvalue = Double.valueOf(evalue);
-	}
+//	public Properties(String bitScore, String queryCoverage, String evalue) {
+//		this.bitScore = Double.valueOf(bitScore);
+//		
+//		this.queryCoverage = Double.valueOf(queryCoverage);
+//		
+//		this.blastEvalue = Double.valueOf(evalue);
+//	}
 	
 	
 	/**
@@ -135,6 +135,20 @@ public class Properties {
 	public void seteValueThreshold(double eValueThreshold) {
 		this.eValueThreshold = eValueThreshold;
 	}
+	
+	/**
+	 * @param queryCoverage the queryCoverage to set
+	 */
+	public void setBlastEValue(double blastEvalue) {
+		this.blastEvalue = blastEvalue;
+	}
+	
+	/**
+	 * @param queryCoverage the queryCoverage to set
+	 */
+	public void setBitScore(double bitScore) {
+		this.bitScore = bitScore;
+	}
 
 	
 	/**

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/ProvideBiggReactionsToGenes.java

@@ -28,6 +28,7 @@ public class ProvideBiggReactionsToGenes {
 
 	private static Map<String, List<String>> seqIdReactionRelation = new HashMap<>();
 	private String queryPath;
+	private Map<String, List<String>> gprsMap = new HashMap<String,List<String>>();
 	
 	public ProvideBiggReactionsToGenes(String workFolderID, String queryPathParameters, Properties properties, int option, String items) {
 		this.queryPath = queryPathParameters;
@@ -68,6 +69,7 @@ public class ProvideBiggReactionsToGenes {
 		
 		findGPRs(workFolderID);
 		
+		
 	}
 
 	
@@ -107,18 +109,20 @@ public class ProvideBiggReactionsToGenes {
 			File fout = new File(filePath);
 			FileOutputStream fos = new FileOutputStream(fout);
 			BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos)); 
-
+			
+			
+			
 			for(Entry<String, List<String>> entry : gprs.entrySet()) {
+				List<String> genesList = new ArrayList<String>();
 				String genes="";
 				for(String gene: entry.getValue()) {
 					genes = genes + gene + "; ";
+					genesList.add(gene);
 				}
 				writer.write(entry.getKey() + "- {"+genes+"}");
 				writer.newLine();
+				gprsMap.put(entry.getKey(), genesList);
 				
-					
-					
-					
 			}
 			writer.close();