1 /*=========================================================================== 2 * * 3 * * PUBLIC DOMAIN NOTICE 4 * * National Center for Biotechnology Information 5 * * 6 * * This software/database is a "United States Government Work" under the 7 * * terms of the United States Copyright Act. It was written as part of 8 * * the author's official duties as a United States Government employee and 9 * * thus cannot be copyrighted. This software/database is freely available 10 * * to the public for use. The National Library of Medicine and the U.S. 11 * * Government have not placed any restriction on its use or reproduction. 12 * * 13 * * Although all reasonable efforts have been taken to ensure the accuracy 14 * * and reliability of the software and data, the NLM and the U.S. 15 * * Government do not and cannot warrant the performance or results that 16 * * may be obtained by using this software or data. The NLM and the U.S. 17 * * Government disclaim all warranties, express or implied, including 18 * * warranties of performance, merchantability or fitness for any particular 19 * * purpose. 20 * * 21 * * Please cite the author in any work or product based on this material. 22 * * 23 * * =========================================================================== 24 * * 25 * */ 26 27 package examples; 28 import ngs.ErrorMsg; 29 import ngs.ReadCollection; 30 import ngs.ReadGroup; 31 import ngs.ReadGroupIterator; 32 import ngs.Statistics; 33 34 public class ReadGroupTest 35 { run(String acc)36 static void run (String acc) 37 throws ErrorMsg, Exception 38 { 39 long i; 40 //open requested accession using SRA implementation of the API 41 ReadCollection run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc); 42 String run_name = run.getName(); 43 44 //get requested reference 45 ReadGroupIterator it = run.getReadGroups(); 46 47 for (i = 0; it . nextReadGroup (); ++ i ) 48 { 49 Statistics s = it.getStatistics(); 50 System.out.println("Statistics for group <" + it.getName() + ">"); 51 for(String p=s.nextPath("");!p.equals("");p=s.nextPath(p)){ 52 System.out.println("\t"+p+": "+s.getAsString(p)); 53 } 54 } 55 System . err . println ( "Read " + i + " ReadGroups for " + run_name); 56 } main( String [] args )57 public static void main ( String [] args ) 58 { 59 if ( args.length != 1 ) 60 { 61 System.out.print("Usage: ReadGroupTest accession\n"); 62 } 63 else try 64 { 65 run (args[0]); 66 } 67 catch ( ErrorMsg x ) 68 { 69 System . err . println ( x . toString () ); 70 x . printStackTrace (); 71 } 72 catch ( Exception x ) 73 { 74 System . err . println ( x . toString () ); 75 x . printStackTrace (); 76 } 77 } 78 } 79