Example program for retrieving general search information.
/* ############################################################################## # file: resfile_info.java # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2003 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Archive:: /MowseBranches/ms_mascotresfile_1.2/test_java/test_searchi $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ import java.util.Date; import matrix_science.msparser.*; public class resfile_info { static { try { System.loadLibrary("msparserj"); } catch (UnsatisfiedLinkError e) { System.err.println("Native code library failed to load. " + "Is msparserj.dll on the path?\n" + e); System.exit(0); } } public static void main(String argv[]) { // ----- Object creation ----- if(argv.length < 1) { System.out.println("Must specify results filename as parameter"); System.exit(0); } ms_mascotresfile file = new ms_mascotresfile(argv[0], 0, ""); if (file.isValid()) { searchInformation(file); } else { System.out.println("Error number: "+file.getLastError()); System.out.println("Error string: "+file.getLastErrorString()); System.exit(0); } } private static void searchInformation(ms_mascotresfile file) { Date searchDate = null; // Java.util.date object int seconds = file.getDate(); // get date of search in seconds since midnight GMT Jan 1st 1970 long milliseconds = (long) seconds * 1000; // convert to milliseconds searchDate=new Date(milliseconds); // create the date object System.out.println("Search information from ms_mascotresfile"); System.out.println("========================================"); System.out.println("Number of queries : "+file.getNumQueries()); System.out.println("Number of hits : "+file.getNumHits()); System.out.println("Number of sequences : "+file.getNumSeqs()); System.out.println("Sequences after tax : "+file.getNumSeqsAfterTax()); System.out.println("Number of residues : "+(int)file.getNumResidues()); System.out.println("Execution time : "+file.getExecTime()); System.out.println("Date (seconds) : "+file.getDate()); // make java output identical to perl output System.out.print("Date : "); String toPerlDate = searchDate.toString(); if(toPerlDate.indexOf("GMT ") > -1) { String beforeGMT = toPerlDate.substring(0,toPerlDate.indexOf("GMT")); String afterGMT = toPerlDate.substring(toPerlDate.indexOf("GMT ")+4,toPerlDate.length()); System.out.println(beforeGMT+afterGMT); } else { System.out.println(searchDate); } System.out.println("Mascot version : "+file.getMascotVer()); System.out.println("Fasta version : "+file.getFastaVer()); // make java output identical to perl output System.out.println("Is PMF? : "+toBinary(file.isPMF())); System.out.println("Is MSMS? : "+toBinary(file.isMSMS())); System.out.println("Is SQ? : "+toBinary(file.isSQ())); System.out.println("Is Error tolerant : "+toBinary(file.isErrorTolerant())); System.out.println("Any PMF? : "+toBinary(file.anyPMF())); System.out.println("Any MSMS? : "+toBinary(file.anyMSMS())); System.out.println("Any SQ? : "+toBinary(file.anySQ())); System.out.println("Any peptides section: "+toBinary(file.doesSectionExist(ms_mascotresfile.SEC_PEPTIDES))); System.out.println("Any peptide matches : "+toBinary(file.anyPeptideSummaryMatches())); System.out.println(); } private static int toBinary(boolean bool) { if(bool) return 1; return 0; } } /* will give the output: C:>java -classpath .;../java/msparser.jar resfile_info F981123.dat Search information from ms_mascotresfile ======================================== Number of queries : 4 Number of hits : 50 Number of sequences : 820227 Sequences after tax : 820227 Number of residues : 255696937 Execution time : 14 Date (seconds) : 1014568786 Date : Sun Feb 24 16:39:46 2002 Mascot version : 1.7.17 Fasta version : MSDB_20020121.fasta Is PMF? : 0 Is MSMS? : 1 Is SQ? : 0 Is Error tolerant : 0 Any PMF? : 0 Any MSMS? : 1 Any SQ? : 0 Any peptides section: 1 Any peptide matches : 1 */
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