Apply thread to AnnotationGraphBuilder

.classpath

@@ -13,20 +13,7 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/main" path="src/main/resources">
-		<attributes>
-			<attribute name="gradle_scope" value="main"/>
-			<attribute name="gradle_used_by_scope" value="main,test"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="src/test/resources">
-		<attributes>
-			<attribute name="gradle_scope" value="test"/>
-			<attribute name="gradle_used_by_scope" value="test"/>
-			<attribute name="test" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-13/"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-12/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>
 </classpath>

src/main/java/hgu/csee/isel/alinew/szz/AGSZZ.java

@@ -3,17 +3,14 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Set;
 
 import org.apache.commons.io.FileUtils;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 
-import hgu.csee.isel.alinew.szz.exception.EmptyHunkTypeException;
 import hgu.csee.isel.alinew.szz.graph.AnnotationGraphBuilder;
 import hgu.csee.isel.alinew.szz.graph.AnnotationGraphModel;
 import hgu.csee.isel.alinew.szz.model.Line;
@@ -27,6 +24,7 @@ public class AGSZZ {
 	private List<String> BFCList = new ArrayList<>();
 	private boolean debug;
 	private File localPath;
+	public static AnnotationGraphModel agm = new AnnotationGraphModel();
 
 	public AGSZZ(String gIT_URL, List<String> bFCList, boolean debug) {
 		this.GIT_URL = gIT_URL;
@@ -38,55 +36,55 @@ public void run() throws IOException {
 		try {
 			// Clone
 			final String REMOTE_URI = GIT_URL + ".git";
-			
+
 			// prepare a new folder for the cloned repository
 			localPath = File.createTempFile("TestGitRepository", "");
 			if (!localPath.delete()) {
 				throw new IOException("Could not delete temporary file " + localPath);
 			}
-			
+
 			System.out.println("\nCloning from " + REMOTE_URI + " to " + localPath);
 
-			Git git = Git.cloneRepository()
-						 .setURI(REMOTE_URI)
-						 .setDirectory(localPath)
-						 .call();
+			Git git = Git.cloneRepository().setURI(REMOTE_URI).setDirectory(localPath).call();
 
 			System.out.println("Having repository: " + git.getRepository().getDirectory());
 
 			Repository repo = git.getRepository();
-			
+
 			List<RevCommit> revs = GitUtils.getRevs(git);
-			
+
 			List<RevCommit> bfcList = GitUtils.getBFCList(BFCList, revs);
-			
+
 			List<String> targetPaths = GitUtils.getTargetPaths(repo, bfcList);
-
-			RevsWithPath revsWithPath = GitUtils.collectRevsWithSpecificPath(GitUtils.configurePathRevisionList(repo, revs), targetPaths);
-
+
+			RevsWithPath revsWithPath = GitUtils
+					.collectRevsWithSpecificPath(GitUtils.configurePathRevisionList(repo, revs), targetPaths);
+
 			// Phase 1 : Build the annotation graph
 			final long startBuildingTime = System.currentTimeMillis();
 
 			AnnotationGraphBuilder agb = new AnnotationGraphBuilder();
-			AnnotationGraphModel agm = agb.buildAnnotationGraph(repo, revsWithPath, debug);
+			agb.buildAnnotationGraph(repo, revsWithPath, debug);
 
 			final long endBuildingTime = System.currentTimeMillis();
 			System.out.println("\nBuilding Annotation Graph takes " + (endBuildingTime - startBuildingTime) / 1000.0 + "s\n");
 
-			// Phase 2 : Trace and collect BIC candidates and filter out format changes, comments, etc among candidates
+			// Phase 2 : Trace and collect BIC candidates and filter out format changes,
+			// comments, etc among candidates
 			final long startTracingTime = System.currentTimeMillis();
-			
+
 			Tracer tracer = new Tracer();
-			//List<Line> BILines = tracer.collectBILines(repo, revs, agm, revsWithPath, BFCList, debug);
+			// List<Line> BILines = tracer.collectBILines(repo, revs, agm, revsWithPath,
+			// BFCList, debug);
 			List<Line> BILines = tracer.collectBILines(repo, bfcList, agm, revsWithPath, debug);
-			
+
 			final long endTracingTime = System.currentTimeMillis();
 			System.out.println("\nCollecting BICs takes " + (endTracingTime - startTracingTime) / 1000.0 + "s\n");
-			
+
 			// Phase 3 : store outputs
 			Utils.storeOutputFile(GIT_URL, BILines);
 
-		} catch (IOException | GitAPIException | EmptyHunkTypeException e) {
+		} catch (IOException | GitAPIException e) {
 			e.printStackTrace();
 		} finally {
 			// clean up here to not keep using more and more disk-space for these samples