Read in the fragmentation_rules file.
/* ############################################################################## # file: config_quantitation.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 config_fragrules { 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("The location of 'fragmentation_rules' file has to be specified as a parameter"); System.out.println("The location should either be the full path to the fragmentation_rules file"); System.out.println("or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi"); System.exit(0); } // A sessionID can optionally be passed as the second parameter // This will only be required if the 'file' is a URL ms_fragrulesfile file; if (argv.length > 1) { ms_connection_settings cs = new ms_connection_settings(); cs.setSessionID(argv[1]); file = new ms_fragrulesfile(argv[0], cs); } else { file = new ms_fragrulesfile(argv[0]); } if (!file.isValid()) { System.out.println("Error number: "+file.getLastError()); System.out.println("Error string: "+file.getLastErrorString()); System.exit(0); } int n = file.getNumberOfInstruments(); System.out.println(n + " instruments are configured:"); for(int i=0; i < n; i++) { System.out.println(file.getInstrumentName(i)); } // Now change ESI-QUAD-TOF ms_fragmentationrules instrument = file.getInstrumentByName("ESI-QUAD-TOF"); instrument.setSeriesUsed(23, true); // Add v series file.updateInstrumentByName("ESI-QUAD-TOF", instrument); // And delete MALDI-QIT-TOF file.deleteInstrumentByName("MALDI-QIT-TOF"); // Finally, save the file under a new name file.setFileName(argv[0] + ".new"); file.save_file(); System.out.println("There are now " + file.getNumberOfInstruments() + " instruments configured."); } } /* will give the output: C:>java -classpath .;../java/msparser.jar config_fragrules fragmentation_rules 12 instruments are configured: Default ESI-QUAD-TOF MALDI-TOF-PSD ESI-TRAP ESI-QUAD ESI-FTICR MALDI-TOF-TOF ESI-4SECTOR FTMS-ECD MALDI-QUAD-TOF MALDI-QIT-TOF ALL There are now 11 instruments configured. */
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