Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CopyFile.java @ 68:5028fdace37b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 68:5028fdace37b
1 package fileIO;
2
3 import java.io.File;
4 import java.io.FileNotFoundException;
5 import java.io.IOException;
6 import java.io.InputStream;
7 import java.io.OutputStream;
8 import java.util.Locale;
9 import java.util.zip.ZipOutputStream;
10
11 import shared.Parse;
12 import shared.Parser;
13 import shared.PreParser;
14 import shared.ReadStats;
15 import shared.Timer;
16
17
18 /**
19 * Unlike ReadWrite's version, this one forces compression and decompression even with same extensions.
20 * Mainly for benchmarking.
21 * @author Brian Bushnell
22 * @date Jan 23, 2013
23 *
24 */
25 public class CopyFile {
26
27 public static void main(String[] args){
28
29 {//Preparse block for help, config files, and outstream
30 PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
31 args=pp.args;
32 //outstream=pp.outstream;
33 }
34
35 String in=null, out=null;
36 boolean overwrite=true;
37 boolean append=false;
38
39 for(int i=0; i<args.length; i++){
40 final String arg=args[i];
41 final String[] split=arg.split("=");
42 String a=split[0].toLowerCase();
43 String b=split.length>1 ? split[1] : null;
44
45 if(Parser.parseCommonStatic(arg, a, b)){
46 //do nothing
47 }else if(Parser.parseZip(arg, a, b)){
48 //do nothing
49 }else if(a.equals("in")){
50 in=b;
51 }else if(a.equals("out")){
52 out=b;
53 }else if(a.equals("append") || a.equals("app")){
54 append=ReadStats.append=Parse.parseBoolean(b);
55 }else if(a.equals("overwrite") || a.equals("ow")){
56 overwrite=Parse.parseBoolean(b);
57 }else if(in==null && i==0 && !args[i].contains("=")){
58 in=args[i];
59 }else if(out==null && i==1 && !args[i].contains("=")){
60 out=args[i];
61 }
62 }
63 assert(in!=null && out!=null);
64 long bytes=new File(in).length();
65 Timer t=new Timer();
66 copyFile(in, out, false, overwrite);
67 t.stop();
68 double mbps1=bytes*1000d/t.elapsed;
69 System.err.println("Time: \t"+t);
70 System.err.println(String.format(Locale.ROOT, "Speed: \t%.2f MB/s", mbps1));
71 }
72
73
74 public static synchronized void copyFile(String source, String dest, boolean createPathIfNeeded, boolean overwrite){
75
76 assert(overwrite || !new File(dest).exists()) : "Destination file already exists: "+dest;
77 if(createPathIfNeeded){
78 File parent=new File(dest).getParentFile();
79 if(parent!=null && !parent.exists()){
80 parent.mkdirs();
81 }
82 }
83
84 try{
85 InputStream in=ReadWrite.getInputStream(source, false, true);
86 OutputStream out=ReadWrite.getOutputStream(dest, false, false, true);
87
88 final byte[] buffer=new byte[16384];
89 int len;
90
91 while((len = in.read(buffer)) > 0){
92 out.write(buffer, 0, len);
93 }
94
95 in.close();
96 out.flush();
97 if(out.getClass()==ZipOutputStream.class){
98 ZipOutputStream zos=(ZipOutputStream)out;
99 zos.closeEntry();
100 zos.finish();
101 }
102 // else if(PROCESS_XZ && out.getClass()==org.tukaani.xz.XZOutputStream.class){
103 // org.tukaani.xz.XZOutputStream zos=(org.tukaani.xz.XZOutputStream)out;
104 // zos.finish();
105 // }
106 out.close();
107
108 }catch(FileNotFoundException e){
109 throw new RuntimeException(e);
110 }catch(IOException e){
111 throw new RuntimeException(e);
112 }
113 }
114
115 }