--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/gui/edu/unc/genomics/AssemblyManager.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,83 @@
+package edu.unc.genomics;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.DataFormatException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Suite of static methods for managing the built-in assemblies in the resources dir
+ * as well as keeping track of the last used assembly
+ * 
+ * @author timpalpant
+ *
+ */
+public class AssemblyManager {
+	
+	private static final Logger log = Logger.getLogger(AssemblyManager.class);
+	
+	/**
+	 * The last used Assembly
+	 */
+	private static Assembly lastUsed;
+	
+	/**
+	 * Returns all available assemblies in the resources directory
+	 * @return the assemblies available in the resources directory
+	 */
+	public static List<Assembly> getAvailableAssemblies() {
+		List<Assembly> assemblies = new ArrayList<>();
+		
+		try (DirectoryStream<Path> stream = Files.newDirectoryStream(ResourceManager.getAssembliesDirectory(), "*.{len}")) {
+      for (Path entry : stream) {
+      	log.debug("Loading assembly: " + entry);
+				try {
+					Assembly a = new Assembly(entry);
+					assemblies.add(a);
+				} catch (IOException | DataFormatException e1) { 
+					log.warn("Error loading assembly: " + entry);
+				}
+      }
+		} catch (IOException e) {
+			log.error("Error listing assemblies");
+			e.printStackTrace();
+		}
+		
+		return assemblies;
+	}
+	
+	public static void deleteAssembly(Assembly a) throws IOException {
+		Files.deleteIfExists(a.getPath());
+	}
+	
+	public static Assembly loadCustomAssembly(Path assemblyFile) throws IOException, DataFormatException {
+		log.debug("Loading custom assembly from file: " + assemblyFile);
+		Assembly a = new Assembly(assemblyFile);
+		
+		// TODO: Warn if this assembly is already loaded
+		
+		// Copy the assembly file into the built-in assemblies directory
+		Files.copy(assemblyFile, ResourceManager.getAssembliesDirectory().resolve(assemblyFile.getFileName()));
+		return a;
+	}
+
+	/**
+	 * @return the lastUsed
+	 */
+	public static Assembly getLastUsed() {
+		return lastUsed;
+	}
+
+	/**
+	 * @param lastUsed the lastUsed to set
+	 */
+	public static void setLastUsed(Assembly lastUsed) {
+		AssemblyManager.lastUsed = lastUsed;
+	}
+}