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1 package edu.unc.genomics;
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2
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3 import java.io.IOException;
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4 import java.nio.file.DirectoryStream;
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5 import java.nio.file.Files;
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6 import java.nio.file.Path;
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7 import java.nio.file.Paths;
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8 import java.util.ArrayList;
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9 import java.util.List;
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10 import java.util.zip.DataFormatException;
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11
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12 import org.apache.log4j.Logger;
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13
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14 /**
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15 * Suite of static methods for managing the built-in assemblies in the resources dir
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16 * as well as keeping track of the last used assembly
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17 *
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18 * @author timpalpant
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19 *
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20 */
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21 public class AssemblyManager {
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22
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23 private static final Logger log = Logger.getLogger(AssemblyManager.class);
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24
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25 /**
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26 * The last used Assembly
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27 */
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28 private static Assembly lastUsed;
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29
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30 /**
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31 * Returns all available assemblies in the resources directory
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32 * @return the assemblies available in the resources directory
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33 */
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34 public static List<Assembly> getAvailableAssemblies() {
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35 List<Assembly> assemblies = new ArrayList<>();
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36
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37 try (DirectoryStream<Path> stream = Files.newDirectoryStream(ResourceManager.getAssembliesDirectory(), "*.{len}")) {
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38 for (Path entry : stream) {
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39 log.debug("Loading assembly: " + entry);
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40 try {
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41 Assembly a = new Assembly(entry);
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42 assemblies.add(a);
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43 } catch (IOException | DataFormatException e1) {
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44 log.warn("Error loading assembly: " + entry);
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45 }
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46 }
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47 } catch (IOException e) {
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48 log.error("Error listing assemblies");
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49 e.printStackTrace();
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50 }
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51
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52 return assemblies;
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53 }
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54
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55 public static void deleteAssembly(Assembly a) throws IOException {
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56 Files.deleteIfExists(a.getPath());
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57 }
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58
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59 public static Assembly loadCustomAssembly(Path assemblyFile) throws IOException, DataFormatException {
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60 log.debug("Loading custom assembly from file: " + assemblyFile);
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61 Assembly a = new Assembly(assemblyFile);
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62
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63 // TODO: Warn if this assembly is already loaded
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64
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65 // Copy the assembly file into the built-in assemblies directory
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66 Files.copy(assemblyFile, ResourceManager.getAssembliesDirectory().resolve(assemblyFile.getFileName()));
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67 return a;
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68 }
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69
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70 /**
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71 * @return the lastUsed
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72 */
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73 public static Assembly getLastUsed() {
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74 return lastUsed;
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75 }
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76
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77 /**
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78 * @param lastUsed the lastUsed to set
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79 */
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80 public static void setLastUsed(Assembly lastUsed) {
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81 AssemblyManager.lastUsed = lastUsed;
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82 }
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83 }
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