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Commit 65220629 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

blast changes

parent c2fb1c3c
......@@ -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);
......
......@@ -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+");
......
#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
......
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