Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CompressFiles.java @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@68 | 1 package fileIO; |
| jpayne@68 | 2 |
| jpayne@68 | 3 import java.io.File; |
| jpayne@68 | 4 |
| jpayne@68 | 5 |
| jpayne@68 | 6 public class CompressFiles { |
| jpayne@68 | 7 |
| jpayne@68 | 8 |
| jpayne@68 | 9 public static void main(String[] args){ |
| jpayne@68 | 10 for(String s : args){ |
| jpayne@68 | 11 if(s.equalsIgnoreCase("zip")){ |
| jpayne@68 | 12 zip=true; |
| jpayne@68 | 13 gzip=false; |
| jpayne@68 | 14 }else if(s.equalsIgnoreCase("gzip") || s.equalsIgnoreCase("gz")){ |
| jpayne@68 | 15 zip=false; |
| jpayne@68 | 16 gzip=true; |
| jpayne@68 | 17 }else{ |
| jpayne@68 | 18 compressFiles(s); |
| jpayne@68 | 19 } |
| jpayne@68 | 20 } |
| jpayne@68 | 21 } |
| jpayne@68 | 22 |
| jpayne@68 | 23 |
| jpayne@68 | 24 public static void compressFiles(String path){ |
| jpayne@68 | 25 File f=new File(path); |
| jpayne@68 | 26 compressFiles(f); |
| jpayne@68 | 27 } |
| jpayne@68 | 28 |
| jpayne@68 | 29 public static void compressFiles(File path){ |
| jpayne@68 | 30 |
| jpayne@68 | 31 if(path.isDirectory()){ |
| jpayne@68 | 32 File[] array=path.listFiles(); |
| jpayne@68 | 33 for(File f : array){compressFiles(f);} |
| jpayne@68 | 34 }else{ |
| jpayne@68 | 35 compress(path); |
| jpayne@68 | 36 } |
| jpayne@68 | 37 |
| jpayne@68 | 38 } |
| jpayne@68 | 39 |
| jpayne@68 | 40 public static void compress(File in){ |
| jpayne@68 | 41 assert(in.exists()); |
| jpayne@68 | 42 assert(in.isFile()); |
| jpayne@68 | 43 String abs=in.getAbsolutePath(); |
| jpayne@68 | 44 // System.out.println("Considering "+abs); |
| jpayne@68 | 45 if(abs.endsWith(".gz") || abs.endsWith(".zip") || abs.endsWith(".bz2")){return;} |
| jpayne@68 | 46 |
| jpayne@68 | 47 // if(!abs.contains("custom_summary_") || !abs.endsWith("Gene_build36.txt")){return;} //TODO ***TEMPORARY*** |
| jpayne@68 | 48 System.err.println(abs); |
| jpayne@68 | 49 // if(!abs.endsWith(".gvla")){return;} //TODO ***TEMPORARY*** |
| jpayne@68 | 50 // if(!abs.endsWith(".gvla") || |
| jpayne@68 | 51 // !(abs.contains("seqGene") || abs.contains("refGene") || abs.contains("unionGene"))){return;} //TODO ***TEMPORARY*** |
| jpayne@68 | 52 if(abs.toLowerCase().contains("familytree")){return;} //TODO ***TEMPORARY*** |
| jpayne@68 | 53 |
| jpayne@68 | 54 if(PRINT_7Z_BATCH){ |
| jpayne@68 | 55 //-mx=4 is fast; -mx=5 or 6 is slow; 7+ is very slow. |
| jpayne@68 | 56 // System.out.println("C:"+Data.SLASH+"\"Program Files\""+Data.SLASH+"7-Zip"+Data.SLASH+"7z a -mx=4 "+abs+".zip "+abs); |
| jpayne@68 | 57 System.out.println("C:\\\"Program Files\"\\7-Zip\\7z a -mx=4 "+abs+".gz "+abs); |
| jpayne@68 | 58 }else{ |
| jpayne@68 | 59 System.out.println("Compressing "+abs+" to "+(zip ? "zip" : "gz")); |
| jpayne@68 | 60 ReadWrite.copyFile(abs, abs+(zip ? ".zip" : ".gz")); |
| jpayne@68 | 61 } |
| jpayne@68 | 62 |
| jpayne@68 | 63 } |
| jpayne@68 | 64 |
| jpayne@68 | 65 |
| jpayne@68 | 66 public static boolean zip=true; |
| jpayne@68 | 67 public static boolean gzip=!zip; |
| jpayne@68 | 68 |
| jpayne@68 | 69 public static boolean PRINT_7Z_BATCH=true; |
| jpayne@68 | 70 |
| jpayne@68 | 71 } |