resfile_error.java

Example program for handling errors in the Mascot results files.

/*
##############################################################################
# file: resfile_error.java                                                   #
# 'msparser' toolkit                                                         #
# Test harness / example code                                                #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2004 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /MowseBranches/ms_mascotresfile_dat_1.2/test_java/test_errorha $ #
#     $Author: robertog@matrixscience.com $ #
#       $Date: 2024-09-04 10:23:46 +0100 $ #
#   $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_1_0-2025-07-27-0-gea47708fac $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
import java.util.Date;
import matrix_science.msparser.*;
 
public class resfile_error {
    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_mascotresfilebase file = ms_mascotresfilebase.createResfile(argv[0], 0, "");
        if (file.isValid()) {
            checkErrorHandler(file);
        } else {
            System.out.println("Error number: "+file.getLastError());
            System.out.println("Error string: "+file.getLastErrorString());
            System.exit(0);
        }
    }
  
      
  
    private static void checkErrorHandler(ms_mascotresfilebase file) {
        int numberOfQueries;
        int loop;
        int loopTwo;
 
        System.out.println("Testing the error handling...            ");
        System.out.println("=========================================");
 
        numberOfQueries = file.getNumQueries();
        file.getObservedCharge(numberOfQueries+40);                // should fail
        System.out.println("Error number: "+file.getLastError());
        System.out.println("Error string: "+file.getLastErrorString());
 
        file.clearAllErrors();
        System.out.print("Cleared all errors - should have no errors left: "+file.getNumberOfErrors());
        System.out.println(" errors left\n");
 
        for(loop=1; loop <= 20; loop++) {
            file.getObservedCharge(numberOfQueries+loop);          // should fail
        }
 
        // Now, the best way, print out all errors.
        System.out.println("More errors added - there are now "+file.getNumberOfErrors()+" errors");
 
        for(loopTwo=1; loopTwo <= file.getNumberOfErrors(); loopTwo++) {
            System.out.print("Error number: "+file.getErrorNumber(loopTwo));
            System.out.print(" : "+file.getErrorString(loopTwo));
            System.out.println("");
        }
 
        System.out.println("");
        file.clearAllErrors();  
    }   
}
 
/*
 
 
will give the output: 
 
 
 
C:>java -classpath .;../java/msparser.jar test_errorhandler F981123.dat
Testing the error handling...
=========================================
Error number: 4
Error string: Query out of range. In function getObservedCharge. Request query 44, num queries: 4
Cleared all errors - should have no errors left: 0 errors left
 
More errors added - there are now 2 errors
Error number: 4 : Query out of range. In function getObservedCharge. Request query 5, num queries: 4
Error number: 4 : Query out of range. In function getObservedCharge. Request query 6, num queries: 4 (Error repeated 19 times)
 
*/