config_fragrules.java

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_dat_1.2/test_java/test_searchi $ #
#     $Author: robertog@matrixscience.com $ #
#       $Date: 2022-07-21 11:07:25 +0100 $ #
#   $Revision: 11e243bdaeaabd63950eb86ad86ce3acc1116e78 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $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.
 
*/