Mercurial > repos > timpalpant > java_genomics_toolkit
comparison gui/edu/unc/genomics/AssemblyManager.java @ 2:e16016635b2a
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author | timpalpant |
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date | Mon, 13 Feb 2012 22:12:06 -0500 |
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1:a54db233ee3d | 2:e16016635b2a |
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1 package edu.unc.genomics; | |
2 | |
3 import java.io.IOException; | |
4 import java.nio.file.DirectoryStream; | |
5 import java.nio.file.Files; | |
6 import java.nio.file.Path; | |
7 import java.nio.file.Paths; | |
8 import java.util.ArrayList; | |
9 import java.util.List; | |
10 import java.util.zip.DataFormatException; | |
11 | |
12 import org.apache.log4j.Logger; | |
13 | |
14 /** | |
15 * Suite of static methods for managing the built-in assemblies in the resources dir | |
16 * as well as keeping track of the last used assembly | |
17 * | |
18 * @author timpalpant | |
19 * | |
20 */ | |
21 public class AssemblyManager { | |
22 | |
23 private static final Logger log = Logger.getLogger(AssemblyManager.class); | |
24 | |
25 /** | |
26 * The last used Assembly | |
27 */ | |
28 private static Assembly lastUsed; | |
29 | |
30 /** | |
31 * Returns all available assemblies in the resources directory | |
32 * @return the assemblies available in the resources directory | |
33 */ | |
34 public static List<Assembly> getAvailableAssemblies() { | |
35 List<Assembly> assemblies = new ArrayList<>(); | |
36 | |
37 try (DirectoryStream<Path> stream = Files.newDirectoryStream(ResourceManager.getAssembliesDirectory(), "*.{len}")) { | |
38 for (Path entry : stream) { | |
39 log.debug("Loading assembly: " + entry); | |
40 try { | |
41 Assembly a = new Assembly(entry); | |
42 assemblies.add(a); | |
43 } catch (IOException | DataFormatException e1) { | |
44 log.warn("Error loading assembly: " + entry); | |
45 } | |
46 } | |
47 } catch (IOException e) { | |
48 log.error("Error listing assemblies"); | |
49 e.printStackTrace(); | |
50 } | |
51 | |
52 return assemblies; | |
53 } | |
54 | |
55 public static void deleteAssembly(Assembly a) throws IOException { | |
56 Files.deleteIfExists(a.getPath()); | |
57 } | |
58 | |
59 public static Assembly loadCustomAssembly(Path assemblyFile) throws IOException, DataFormatException { | |
60 log.debug("Loading custom assembly from file: " + assemblyFile); | |
61 Assembly a = new Assembly(assemblyFile); | |
62 | |
63 // TODO: Warn if this assembly is already loaded | |
64 | |
65 // Copy the assembly file into the built-in assemblies directory | |
66 Files.copy(assemblyFile, ResourceManager.getAssembliesDirectory().resolve(assemblyFile.getFileName())); | |
67 return a; | |
68 } | |
69 | |
70 /** | |
71 * @return the lastUsed | |
72 */ | |
73 public static Assembly getLastUsed() { | |
74 return lastUsed; | |
75 } | |
76 | |
77 /** | |
78 * @param lastUsed the lastUsed to set | |
79 */ | |
80 public static void setLastUsed(Assembly lastUsed) { | |
81 AssemblyManager.lastUsed = lastUsed; | |
82 } | |
83 } |