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Commit ff0e238f authored by Davide Lagoa's avatar Davide Lagoa
Browse files

tests

parent 4d8a6613
......@@ -142,9 +142,16 @@ public class GenerateTransportReactions {
// }
}
if(newTcContainer.getAllReactionsIds().size() == 0) //reactions with generic reactions such as
if(newTcContainer.getAllReactionsIds().size() == 0) { //reactions with generic reactions such as
noMetabolitesNoReactionsCounter++; //solute1 + solute2 <-> solute1 + solute2 are also included here because no metabolites where found for them
if(tcNumberContainer.getFamily() != null)
newTcContainer.setFamily(tcNumberContainer.getFamily());
if(tcNumberContainer.getSuperFamily() != null)
newTcContainer.setSuperFamily(tcNumberContainer.getSuperFamily());
}
newTcContainer = filterUnwantedReactions(tcNumber, newTcContainer);
newContainers.put(tcNumber, newTcContainer);
......@@ -207,11 +214,11 @@ public class GenerateTransportReactions {
//
//
if(tc.equals("3.A.1.7.5 O51235")) {
System.out.println(positions);
System.out.println(metabolites);
}
// if(tc.equals("3.A.1.7.5 O51235")) {
//
// System.out.println(positions);
// System.out.println(metabolites);
// }
for(int key : positions.keySet()) {
......@@ -242,10 +249,10 @@ public class GenerateTransportReactions {
if(tc.equals("3.A.1.7.5 O51235")) {
System.out.println(newReactContainer.getReaction());
}
// if(tc.equals("3.A.1.7.5 O51235")) {
//
// System.out.println(newReactContainer.getReaction());
// }
// else {
......
......@@ -21,19 +21,18 @@ public class Retriever {
public static void main(String[] args) {
//
// Set<String> tcNumbers = TcdbExplorer.getTcNumbers();
// Set<String> tcNumbers = TcdbExplorer.getTcNumbers(false);
//
// System.out.println(tcNumbers.size());
try {
///////// - SEARCHER
Properties properties = new Properties();
TcdbRetriever.getSubstrates(properties.getQueriesBackupDirectory());
// @SuppressWarnings("resource")
// Scanner reader = new Scanner(System.in);
System.out.println("Retrieving TCDB FASTA file...");
Set<String> tcNumbers = TcdbExplorer.getTcNumbers(true);
......@@ -49,9 +48,13 @@ public class Retriever {
FilesUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\proteinFamilyDescriptions.txt", proteinFamilyDescription);
//////////
// Map<String, String> proteinFamilyDescription = FilesUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\proteinFamilyDescriptions.txt");
System.out.println("SEARCH COMPLETE...");
//
// int n = 1;
......@@ -76,7 +79,7 @@ public class Retriever {
System.out.println("IGNORE PREVIOUS ERRORS");
List<String[]> excel = ReadExcelFile.getData("C:\\Users\\Davide\\OneDrive - Universidade do Minho\\UMinho\\Tese\\Internal database\\results.xlsx");
List<String[]> excel = ReadExcelFile.getData("C:\\Users\\Davide\\OneDrive - Universidade do Minho\\UMinho\\Tese\\Internal database\\results2.xlsx");
Map<String, TcdbMetabolitesContainer> tcdbMetabolites = ProcessTcdbMetabolitesExcel.processData(excel);
......@@ -84,6 +87,11 @@ public class Retriever {
JSONFilesUtils.writeJSONtcReactions(transportReactions);
// for(String key : transportReactions.keySet())
// System.out.println(key + "\t" + transportReactions.get(key).keySet());
// System.out.println(transportReactions.get("Q9UYH7").get("2.A.102.4.1").getFamily());
///////////////DESCOMENTAR
// n = 99;
......
#Generated by Maven Integration for Eclipse
#Thu Jul 26 15:55:37 BST 2018
#Tue Aug 07 14:33:35 BST 2018
m2e.projectLocation=C\:\\Users\\Davide\\Biosynth2\\triage
m2e.projectName=triage
groupId=tcdb
......
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