Mercurial > repos > timpalpant > java_genomics_toolkit

comparison java-genomics-toolkit/src/edu/unc/genomics/AssemblyConverter.java @ 0:1daf3026d231

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Upload alpha version
author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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1 package edu.unc.genomics;
2
3 import java.io.IOException;
4 import java.nio.file.Files;
5 import java.nio.file.Path;
6 import java.nio.file.Paths;
7 import java.util.zip.DataFormatException;
8
9 import com.beust.jcommander.IStringConverter;
10 import com.beust.jcommander.ParameterException;
11
12 /**
13 * @author timpalpant
14 *
15 */
16 public class AssemblyConverter implements IStringConverter<Assembly> {
17
18 public static final Path ASSEMBLIES_DIR = Paths.get("resources", "assemblies");
19
20 @Override
21 public Assembly convert(String value) throws ParameterException {
22 // Look for the assembly in the resources/assemblies directory
23 Path p = ASSEMBLIES_DIR.resolve(value+".len");
24
25 // If it does not exist in the assemblies directory, check if it is a path to a file
26 if (!Files.isReadable(p)) {
27 PathConverter converter = new PathConverter();
28 p = converter.convert(value);
29 // If it does not exist, then throw an exception that the assembly cannot be found
30 if (!Files.isReadable(p)) {
31 throw new ParameterException("Cannot find Assembly file: " + value);
32 }
33 }
34
35 // Attempt to load the assembly from file
36 try {
37 return new Assembly(p);
38 } catch (IOException | DataFormatException e) {
39 throw new ParameterException("Error loading Assembly from file: " + p);
40 }
41 }
42
43 }