Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/CommandLineTool.java @ 2:e16016635b2a

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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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1:a54db233ee3d 2:e16016635b2a
1 package edu.unc.genomics;
2
3 import java.io.IOException;
4
5 import com.beust.jcommander.JCommander;
6 import com.beust.jcommander.ParameterException;
7
8 /**
9 * A command-line script
10 * @author timpalpant
11 *
12 */
13 public abstract class CommandLineTool {
14
15 /**
16 * JCommander command-line argument parser
17 */
18 private final JCommander jc = new JCommander(this);
19
20 public CommandLineTool() {
21 // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
22 jc.addConverterFactory(new PathFactory());
23 jc.addConverterFactory(new AssemblyFactory());
24 jc.addConverterFactory(new IntervalFileFactory());
25 jc.addConverterFactory(new WigFileFactory());
26
27 // Set the program name to be the class name
28 jc.setProgramName(this.getClass().getSimpleName());
29 }
30
31 /**
32 * The default bite-size to use for applications that process files in chunks
33 */
34 public static final int DEFAULT_CHUNK_SIZE = 500_000;
35
36 /**
37 * Do the main computation of this tool
38 * @throws IOException
39 */
40 public abstract void run() throws IOException;
41
42 /**
43 * Parse command-line arguments and run the tool
44 * Exit on parameter exceptions
45 * @param args
46 */
47 public void instanceMain(String[] args) throws CommandLineToolException {
48 try {
49 toolRunnerMain(args);
50 } catch (ParameterException e) {
51 System.err.println(e.getMessage());
52 jc.usage();
53 System.exit(-1);
54 }
55 }
56
57 /**
58 * Parse command-line arguments and run the tool
59 * @param args
60 * @throws ParameterException if there are invalid/missing parameters
61 * @throws CommandLineToolException if an exception occurs while running the tool
62 */
63 public void toolRunnerMain(String[] args) throws ParameterException, CommandLineToolException {
64 jc.parse(args);
65
66 try {
67 run();
68 } catch (IOException e) {
69 e.printStackTrace();
70 throw new CommandLineToolException("IO error while running tool");
71 }
72 }
73 }