blast operation created

.classpath

@@ -12,11 +12,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

src/main/java/betaBarrels/Navigate.java

 package betaBarrels;
 
-import java.util.concurrent.TimeUnit;
-
 import org.openqa.selenium.By;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;

src/main/java/betaBarrels/main.java

 package betaBarrels;
 
-import java.util.HashMap;
-import java.util.Map;
-
 public class main {
 
 	public static void main(String[] args) {

src/main/java/blast/Blast.java

+package blast;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Observable;
+import java.util.Observer;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.sequence.template.AbstractSequence;
+
+import pt.uminho.ceb.biosystems.merlin.bioapis.externalAPI.ncbi.CreateGenomeFile;
+import pt.uminho.ceb.biosystems.merlin.local.alignments.core.RunSimilaritySearch;
+import pt.uminho.ceb.biosystems.merlin.utilities.Enumerators.AlignmentScoreType;
+import pt.uminho.ceb.biosystems.merlin.utilities.Enumerators.Method;
+import pt.uminho.ceb.biosystems.merlin.utilities.containers.capsules.AlignmentCapsule;
+import tcdb.tcdbTransportTypesRetriever.TcdbExplorer;
+
+public class Blast implements Observer{
+
+	public Blast() {
+		
+		try {
+			performBlast();
+		} 
+		catch (Exception e) {
+			e.printStackTrace();
+		}
+		
+		
+	}
+	
+	private void performBlast() throws Exception {
+		
+		//BLAST
+		
+		System.out.println("INIT BLAST!!");
+		
+		String filePath = "C:/Users/Davide/Documents/reactionsBuilderTriage/temp/";
+		String tcdbFastaFile = filePath.concat("tcdbSEQs.txt");
+
+		Map<String, AbstractSequence<?>> tcdbGenes = getTcdbInMapFormat();
+		
+		 System.out.println("BIOJAVA TCDB!!");
+
+		CreateGenomeFile.buildFastaFile(tcdbFastaFile, tcdbGenes);
+		
+		System.out.println("BIOJAVA RENATO!!");
+		
+		ConcurrentHashMap<String, AbstractSequence<?>> sequences= new ConcurrentHashMap<String, AbstractSequence<?>>();
+       sequences.putAll(FastaReaderHelper.readFastaProteinSequence(new File("C:/Users/Davide/Downloads/nvulgaris_29421_protein.faa")));
+		
+       System.out.println("BLAST!!");
+       
+       RunSimilaritySearch run_similaritySearch = new RunSimilaritySearch(tcdbGenes, 0.1,
+               Method.SmithWaterman, sequences, new AtomicBoolean(false), new AtomicInteger(0), new AtomicInteger(0), AlignmentScoreType.ALIGNMENT);
+       
+       run_similaritySearch.setTcdbFastaFilePath(tcdbFastaFile);
+       run_similaritySearch.addObserver(this);
+       run_similaritySearch.setCurrentTempFolderDirectory(filePath);
+       //////set temp directory here!!!
+
+       ConcurrentLinkedQueue<AlignmentCapsule> results = null;
+       
+       if(sequences.keySet().size()>0)
+           results = run_similaritySearch.runBlastSearch(true);
+           
+       System.out.println("BLAST PERFORMED!!");
+		
+	}
+       
+       /**
+   	 * 
+   	 * @param url
+   	 * @return
+   	 * @throws Exception
+   	 */
+   	public static Map<String, AbstractSequence<?>> getTcdbInMapFormat() throws Exception {
+           
+           InputStream tcdbInputStream = (new URL(TcdbExplorer.TCDB_FASTA_URL)).openStream();
+           BufferedReader br= new BufferedReader(new InputStreamReader(tcdbInputStream));
+           StringBuilder sb = new StringBuilder();
+           String line;
+           
+           
+           while ((line = br.readLine()) != null)
+               sb.append(line.concat("\n"));
+           
+           String theString = sb.toString().replace("</p>", "").replace("<p>", "").replace(">gnl|TC-DB|xxxxxx 3.A.1.205.14 \ndsfgdfg", "");
+           byte[] bytes = theString.getBytes("utf-8");
+           tcdbInputStream =  new ByteArrayInputStream(bytes);
+           
+           FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence,AminoAcidCompound>(
+                   tcdbInputStream, 
+                   //tcdbFile,
+                   new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), 
+                   new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+           
+//           System.out.println("CHECK3---->"+LocalDateTime.now().getHour()+":"+LocalDateTime.now().getMinute()+":"+LocalDateTime.now().getSecond());
+
+           
+           Map<String, AbstractSequence<?>> tcdb  =  new HashMap<>();
+           tcdb.putAll(fastaReader.process());
+           
+           return tcdb;
+       }
+
+	@Override
+	public void update(Observable arg0, Object arg1) {
+		// TODO Auto-generated method stub
+		
+	}
+	
+}

src/main/java/tcdb/comparison/Compare.java

@@ -348,6 +348,8 @@ public class Compare {
 			workbook.write(fileOut);
 			fileOut.flush();
 			fileOut.close();
+			
+			workbook.close();
 
 			System.out.println("xlsx containing the comparison results created");
 

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

@@ -26,13 +26,18 @@ public class GenerateTransportReactions {
 	 * @param tcdbMetabolites
 	 * @return
 	 */
-	public static Map<String, Map<String, TcNumberContainer>> generateReactions(Map<String, TcNumberContainer> data, Map<String, TcdbMetabolitesContainer> tcdbMetabolites) {
+	public static Map<String, Map<String, TcNumberContainer>> generateReactions(Map<String, TcNumberContainer> data,
+			Map<String, TcdbMetabolitesContainer> tcdbMetabolites, Map<String, String> proteinFamilyDescription) {
 
 		Map<String, Map<String, TcNumberContainer>> mainMap = new HashMap<>();
 
 		Synonyms dictionary = new Synonyms();
 		
 		int noMetabolitesNoReactionsCounter = 0;
+		
+//		Map<String, TcdbMetabolitesContainer> tcdbMetabolites = new HashMap<>();
+//		
+//		tcdbMetabolites.put("O51918", tcdbMetabolitessss.get("O51918"));
 
 		for(String accession : tcdbMetabolites.keySet()) {
 
@@ -61,9 +66,12 @@ public class GenerateTransportReactions {
 							for(int id : tcNumberContainer.getAllReactionsIds()) {
 
 								ReactionContainer reactionContainer = tcNumberContainer.getReactionContainer(id);
-
+								
 								TypeOfTransporter evidence = checkForEvidenceOfTransport(tcdbMetContainer.getDescription(tcNumber), tcNumber);
-
+								
+								if(evidence == null && proteinFamilyDescription.containsKey(tcNumber.replaceAll("(\\.\\d+)$", ""))) 
+										evidence = checkForEvidenceOfTransport(proteinFamilyDescription.get(tcNumber.replaceAll("(\\.\\d+)$", "")), tcNumber);
+								
 								//							System.out.println(accession);
 
 								Boolean antiportOrSymport = selectMethodOfMetabolitesDistribution(reactionContainer.getReaction(), reactionContainer.getTransportType(), dictionary);
@@ -83,8 +91,6 @@ public class GenerateTransportReactions {
 
 									//							Set<String> metabolites = tcdbMetContainer.getMetabolites(tcNumber);	
 
-
-
 									if(evidence == null) {
 
 										if(reactionContainer.getTransportType().equals(TypeOfTransporter.Uniport) || reactionContainer.getTransportType().equals(TypeOfTransporter.Symport))
@@ -109,7 +115,7 @@ public class GenerateTransportReactions {
 
 										newTcContainer = processAntiportReactions(reactionContainer, newTcContainer, metabolites, dictionary, tcNumber+" "+accession);
 									//																}
-									else
+									else if(!tcNumberContainer.evidenceTransportTypeExists(evidence))
 										newTcContainer = correctReaction(tcNumber, reactionContainer.getReaction(), "C-1" ,evidence, reactionContainer.getProperties(), metabolites, newTcContainer);
 
 									//									System.out.println(tcNumber+" "+accession + " " + evidence + " " + reactionContainer.getTransportType() + " " + reactionContainer.getReaction() + "\t" + metabolites);
@@ -133,7 +139,8 @@ public class GenerateTransportReactions {
 						
 						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
-							
+						
+						newTcContainer = filterUnwantedReactions(tcNumber, newTcContainer);
 
 						newContainers.put(tcNumber, newTcContainer);
 					} 
@@ -155,6 +162,24 @@ public class GenerateTransportReactions {
 
 	}
 
+	private static TcNumberContainer filterUnwantedReactions(String tcNumber, TcNumberContainer newTcContainer) {
+		
+		Set<TypeOfTransporter> set = newTcContainer.getAllTransportTypesAssociated();
+		
+		if(set.size() > 1) {
+			
+			for(int id : newTcContainer.getAllReactionsIds()) {
+				
+				ReactionContainer container = newTcContainer.getReactionContainer(id);
+				
+				if(!container.getTransportType().equals(TypeOfTransporter.Uniport))
+					newTcContainer.removeReaction(id);
+			}
+		}
+		
+		return newTcContainer;
+	}
+
 	/**
 	 * Process metabolites associated to the wrong transport types. 
 	 * 
@@ -256,18 +281,26 @@ public class GenerateTransportReactions {
 	 * @return
 	 */
 	private static TypeOfTransporter checkForEvidenceOfTransport(String description, String tcNumber) {
-
-		if(tcNumber.equals("2.A.1.4.8"))
-			return TypeOfTransporter.Uniport;
-
-		if(description.matches("(?i).*uniporte*r*[\\s*\\.*].*"))
-			return TypeOfTransporter.Uniport;
-
-		else if(description.matches("(?i).*symporte*r*[\\s*\\.*].*"))
-			return TypeOfTransporter.Symport;
-
-		else if(description.matches("(?i).*antiporte*r*[\\s*\\.*]"))
-			return TypeOfTransporter.Antiport;
+		
+		try {
+			if(tcNumber.equals("2.A.1.4.8"))
+				return TypeOfTransporter.Uniport;
+
+			if(description.matches("(?i).*uniporte*r*[\\s*\\.*]*.*"))
+				return TypeOfTransporter.Uniport;
+
+			else if(description.matches("(?i).*symporte*r*[\\s*\\.*]*.*"))
+				return TypeOfTransporter.Symport;
+
+			else if(description.matches("(?i).*antiporte*r*[\\s*\\.*]*.*"))
+				return TypeOfTransporter.Antiport;
+		} 
+		catch (Exception e) {
+			System.out.println(tcNumber);
+			System.out.println(description);
+			
+			e.printStackTrace();
+		}
 
 		return null;
 	}
@@ -745,7 +778,7 @@ public class GenerateTransportReactions {
 		reactant = aux[1];
 		product = aux[2];
 
-		Set<String> reactions = getAllPossibleReactions(originalReaction, reactant, product, reactionContainer.getReversible(), tc);
+		Set<String> reactions = getAllPossibleReactions(originalReaction, reactant, product, reactionContainer.isReversible(), tc);
 
 		//		if(tc.equals("2.A.20.1.2 P43676")) {
 		//			System.out.println("Areactions " + reactions);
@@ -757,7 +790,7 @@ public class GenerateTransportReactions {
 			//			System.out.println(react);
 			String[] newReaction;
 
-			if(reactionContainer.getReversible())
+			if(reactionContainer.isReversible())
 				newReaction = react.split(ReactionContainer.REV_TOKEN);
 			else
 				newReaction = react.split(ReactionContainer.IRREV_TOKEN);
@@ -785,7 +818,7 @@ public class GenerateTransportReactions {
 				//					System.out.println();
 				//				}
 
-				ReactionContainer newReactContainer = new ReactionContainer(result[0], result[1], reactionContainer.getReversible());
+				ReactionContainer newReactContainer = new ReactionContainer(result[0], result[1], reactionContainer.isReversible());
 
 				newReactContainer.setTransportType(reactionContainer.getTransportType());
 				newReactContainer.setProperties(reactionContainer.getProperties());
@@ -1667,7 +1700,7 @@ public class GenerateTransportReactions {
 				//					System.out.println();
 				//				}
 
-				ReactionContainer newReactContainer = new ReactionContainer(result[0], result[1], reactionContainer.getReversible());
+				ReactionContainer newReactContainer = new ReactionContainer(result[0], result[1], reactionContainer.isReversible());
 
 				newReactContainer.setTransportType(reactionContainer.getTransportType());
 				newReactContainer.setProperties(reactionContainer.getProperties());

src/main/java/tcdb/tcdbTransportTypesRetriever/FindTransportTypes.java

@@ -39,15 +39,15 @@ public class FindTransportTypes {
 	 * @throws IOException
 	 * @throws Exception
 	 */
-	public static Map<String, TcNumberContainer> getAllTCNumbersInformation() throws IOException, Exception{
+	public static Map<String, TcNumberContainer> getAllTCNumbersInformation(Set<String> toSearch) throws IOException, Exception{
 
 		Map<String, TcNumberContainer> data = new HashMap<>();
 
-		//				Set<String> toSearch = TcdbExplorer.getTcNumbers();
-
-		Set<String> toSearch = new HashSet<>();
-
-		toSearch.add("2.A.37");
+//		Set<String> toSearch = TcdbExplorer.getTcNumbers();
+//
+////		Set<String> toSearch = new HashSet<>();
+//
+////		toSearch.add("2.A.37");
 
 		List<String> searched = new ArrayList<>();
 

src/main/java/tcdb/tcdbTransportTypesRetriever/FindTransporters.java

@@ -30,7 +30,7 @@ import tcdb.capsules.TcNumberContainer;
 public class FindTransporters {
 
 	public static final int LIMIT = 10;
-	private static final String URL = "http://www.tcdb.org/search/result.php?tc=";
+	
 	public static final List<String> REVERSIBLES =  List.of ("⇌", "⇌&nbsp;", "&harr;", "&#8652;", "⇋");  
 	public static final List<String> IRREVERSIBLES =  List.of ("&rarr;", "%u21CC", "%u2192", "--&gt;", "&rightarrow;", "&AElig;", 
 			"&agrave;");
@@ -90,7 +90,7 @@ public class FindTransporters {
 
 			while(attempt < LIMIT && !found) {
 
-				if(conn.getCodeConnection(URL.concat(tc)) == 200){
+				if(conn.getCodeConnection(TcdbExplorer.TCDB_TCNUMBER_URL.concat(tc)) == 200){
 					
 					FilesUtils.webPageSaver(conn.getPageOpenStream(), out);
 
@@ -122,7 +122,7 @@ public class FindTransporters {
 
 			if(attempt == LIMIT && !found){
 
-				System.out.println("results not found for query: " + URL.concat(tc));
+				System.out.println("results not found for query: " + TcdbExplorer.TCDB_TCNUMBER_URL.concat(tc));
 				failed.add(tc);
 			}
 
@@ -973,5 +973,5 @@ public class FindTransporters {
 
 		return null;
 	}
-
+	
 }

src/main/java/tcdb/tcdbTransportTypesRetriever/ReadFastaTcdb.java

@@ -50,10 +50,10 @@ public class ReadFastaTcdb {
 
 			String accession = "", tcNumber = "", organism = "", description = "";
 
-			Map<String, Integer> distributions1 = new TreeMap<>();
-			Map<String, Integer> distributions2 = new TreeMap<>();
-			Map<String, Integer> distributions3 = new TreeMap<>();
-			Map<String, Integer> distributions4 = new TreeMap<>();
+//			Map<String, Integer> distributions1 = new TreeMap<>();
+//			Map<String, Integer> distributions2 = new TreeMap<>();
+//			Map<String, Integer> distributions3 = new TreeMap<>();
+//			Map<String, Integer> distributions4 = new TreeMap<>();
 			Map<String, Integer> distributions5 = new TreeMap<>();
 
 
@@ -115,53 +115,53 @@ public class ReadFastaTcdb {
 
 					//						System.out.println("tc--" + tcNumber);
 
-					String[] newTcNumber = tcNumber.split("\\."); 
-
-					//						System.out.println(newTcNumber.length);
-
-					String newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]).concat(".").concat(newTcNumber[3]);
-
-					if(distributions4.containsKey(newTc)) {
-
-						int count = distributions4.get(newTc);
-						distributions4.put(newTc, count+1);
-					}
-
-					else
-						distributions4.put(newTc, 1);
-
-					newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]);
-
-					if(distributions3.containsKey(newTc)) {
-
-						int count = distributions3.get(newTc);
-						distributions3.put(newTc, count+1);
-					}
-
-					else
-						distributions3.put(newTc, 1);
-
-					newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]);
-
-					if(distributions2.containsKey(newTc)) {
-
-						int count = distributions2.get(newTc);
-						distributions2.put(newTc, count+1);
-					}
-
-					else
-						distributions2.put(newTc, 1);
-
-					newTc = newTcNumber[0];
-
-					if(distributions1.containsKey(newTc)) {
-
-						int count = distributions1.get(newTc);
-						distributions1.put(newTc, count+1);
-					}
-
-					else
-						distributions1.put(newTc, 1);
+//					String[] newTcNumber = tcNumber.split("\\."); 
+//
+//					//						System.out.println(newTcNumber.length);
+//
+//					String newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]).concat(".").concat(newTcNumber[3]);
+//
+//					if(distributions4.containsKey(newTc)) {
+//
+//						int count = distributions4.get(newTc);
+//						distributions4.put(newTc, count+1);
+//					}
+//
+//					else
+//						distributions4.put(newTc, 1);
+//
+//					newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]).concat(".").concat(newTcNumber[2]);
+//
+//					if(distributions3.containsKey(newTc)) {
+//
+//						int count = distributions3.get(newTc);
+//						distributions3.put(newTc, count+1);
+//					}
+//
+//					else
+//						distributions3.put(newTc, 1);
+//
+//					newTc = newTcNumber[0].concat(".").concat(newTcNumber[1]);
+//
+//					if(distributions2.containsKey(newTc)) {
+//
+//						int count = distributions2.get(newTc);
+//						distributions2.put(newTc, count+1);
+//					}
+//
+//					else
+//						distributions2.put(newTc, 1);
+//
+//					newTc = newTcNumber[0];
+//
+//					if(distributions1.containsKey(newTc)) {
+//
+//						int count = distributions1.get(newTc);
+//						distributions1.put(newTc, count+1);
+//					}
+//
+//					else
+//						distributions1.put(newTc, 1);
 
 
 					description = "";
@@ -187,7 +187,7 @@ public class ReadFastaTcdb {
 
 			System.out.println("Number of different accessions: " + accessions.size());
 
-			return distributions3.keySet();
+			return distributions5.keySet();
 		} 
 		catch (IOException e) {
 			e.printStackTrace();
@@ -213,7 +213,7 @@ public class ReadFastaTcdb {
 
 			LinkConnection conn = new LinkConnection();
 
-			if(conn.getCodeConnection("http://www.tcdb.org/public/tcdb") == 200) {
+			if(conn.getCodeConnection(TcdbExplorer.TCDB_FASTA_URL) == 200) {
 
 				webPageSaver(conn.getPageOpenStream(), out);
 

src/main/java/tcdb/tcdbTransportTypesRetriever/Retriever.java

@@ -6,6 +6,7 @@ import java.util.Map;
 import java.util.Scanner;
 import java.util.Set;
 
+import files.FilesUtils;
 import files.JSONFilesUtils;
 import files.ReadExcelFile;
 import tcdb.capsules.TcNumberContainer;
@@ -26,16 +27,24 @@ public class Retriever {
 			@SuppressWarnings("resource")
 			Scanner reader = new Scanner(System.in);
 			
-//			Set<String> toSearch = new HashSet<>();
-//			
-//			toSearch = TcdbExplorer.getTcNumbers();
+			System.out.println("Retrieving TCDB FASTA file...");
+			
+			Set<String> tcNumbers = TcdbExplorer.getTcNumbers();
+			
+			Set<String> toSearch = TcdbExplorer.generateTCsFamily(tcNumbers);
 			
 //			toSearch.add("2.A.75");
 ////			
 //			System.out.println("Retrieving data from TCDB...");
 //			Map<String, TcNumberContainer> data = FindTransporters.getAllTCNumbersInformation(toSearch);
+			
+//			Map<String, String> proteinFamilyDescription = TcdbExplorer.getProteinsBelongingToFamilyDescription(tcNumbers);
 //			
-//			System.out.println("COMPLETE...");
+//			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;
 			
@@ -52,7 +61,7 @@ public class Retriever {
 				
 //				
 				
-				
+//				///////////////DESCOMENTAR
 				
 				Map<String, TcNumberContainer> data = JSONFilesUtils.readJSONExceptionsFile();		//the reader that reads exceptios can also read normal data
 				
@@ -64,10 +73,15 @@ public class Retriever {
 				
 				Map<String, TcdbMetabolitesContainer> tcdbMetabolites = ProcessTcdbMetabolitesExcel.processData(excel);
 				
-				Map<String, Map<String, TcNumberContainer>> transportReactions = GenerateTransportReactions.generateReactions(data, tcdbMetabolites);
+				Map<String, Map<String, TcNumberContainer>> transportReactions = GenerateTransportReactions.generateReactions(data, tcdbMetabolites, proteinFamilyDescription);
 				
 				JSONFilesUtils.writeJSONtcReactions(transportReactions);
 				
+			///////////////DESCOMENTAR
+				
+				
+				
+				
 //				checkDescriptions(tcdbMetabolites);
 				
 				

src/main/java/tcdb/tcdbTransportTypesRetriever/TcdbExplorer.java

 package tcdb.tcdbTransportTypesRetriever;
 
 import java.io.BufferedReader;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.TimeUnit;
 import java.util.regex.Matcher;