blast changes

src/main/java/blast/Blast.java

@@ -92,7 +92,7 @@ public class Blast implements Observer{
 
 		logger.info("Blast process initialized!");
 
-		RunSimilaritySearch run_similaritySearch = new RunSimilaritySearch(tcdbGenes, 0.1,
+		RunSimilaritySearch run_similaritySearch = new RunSimilaritySearch(tcdbGenes, 0.3,
 				Method.SmithWaterman, sequences, new AtomicBoolean(false), new AtomicInteger(0), new AtomicInteger(0), AlignmentScoreType.ALIGNMENT);
 
 		run_similaritySearch.setTcdbFastaFilePath(tcdbFastaFile);

src/main/java/tcdb/reactionsGenerator/GenerateTransportReactions.java

@@ -1677,13 +1677,13 @@ public class GenerateTransportReactions {
 
 		for(int i = 0; i < reactants.size(); i++) {
 
-			String auxReact = reactants.get(i).replaceAll("\\(in\\)", "").replaceAll("\\(out\\)", "").replace("\\+", "");
+			String auxReact = reactants.get(i).replaceAll("\\(in\\)", "").replaceAll("\\(out\\)", "").replace("\\+", "");		//this replace("\\+", "") might not be correct
 
 			String[] auxReactMetab = auxReact.split("\\s+");
 
 			for(int j = 0; j < products.size(); j++) {
 
-				String auxProd = products.get(j).replaceAll("\\(in\\)", "").replaceAll("\\(out\\)", "").replace("\\+", "");
+				String auxProd = products.get(j).replaceAll("\\(in\\)", "").replaceAll("\\(out\\)", "").replace("\\+", "");		//this replace("\\+", "") might not be correct
 
 				String[] auxProdMetab = auxProd.split("\\s+");
 

target/classes/META-INF/maven/tcdb/triage/pom.properties

 #Generated by Maven Integration for Eclipse
-#Fri Jul 06 12:51:19 BST 2018
+#Tue Jul 10 13:55:49 BST 2018
 m2e.projectLocation=C\:\\Users\\Davide\\Biosynth2\\triage
 m2e.projectName=triage
 groupId=tcdb