resfile_error.pl

Example program for handling errors in the Mascot results files.

#!/usr/local/bin/perl
##############################################################################
# file: resfile_error_handling.pl                                            #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: parser/examples/test_perl/resfile_error.pl $ #
#     $Author: robertog@matrixscience.com $                                                      #
#       $Date: 2024-09-04 10:23:46 +0100 $                                         #
#   $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
use strict;
##############################################################################
 
use msparser;
 
if (!defined($ARGV[0])) { die "Must specify results filename as parameter"; }
 
my $file = msparser::ms_mascotresfilebase::createResfile($ARGV[0]);
 
if ($file->isValid) {
    checkErrorHandler($file);
}
 
 
##############################################################################
# checkErrorHandler                                                          #
#  - parameter 0  ms_mascotresfilebase                                       #
# Calls a couple of functions with invalid arguments                         #
##############################################################################
sub checkErrorHandler {
    my ($resfile) = @_;
 
    print "Testing the error handling...            \n";
    print "=========================================\n";
 
    my $numQueries = $resfile->getNumQueries();
    $resfile->getObservedCharge($numQueries + 40);  # Should fail
 
    print "Error number: ", $resfile->getLastError(), "\n";
    print "Error string: ", $resfile->getLastErrorString(), "\n";
 
    $resfile->clearAllErrors();
    print "Cleared all errors - should have no errors left: ", $resfile->getNumberOfErrors();
    print " errors left\n\n";
 
    for my $x (1 .. 20) {
        $resfile->getObservedCharge($numQueries + $x);  # Should fail
    }
 
    # Now, the best way, print out all errors.
    print "More errors added - there are now ", $resfile->getNumberOfErrors();
    print " errors\n";
 
    for my $i (1 .. $resfile->getNumberOfErrors) {
        print "Error number: ", $resfile->getErrorNumber($i);
        print " : ", $resfile->getErrorString($i);
        print "\n";
    }
 
    print "\n";
    $resfile->clearAllErrors();
}
 
 
=pod 
 
Running the program as 'perl resfile_error.pl ../data/F981123.dat' will
give the following output under Mascot Server 2.3:
 
 
Testing the error handling...            
=========================================
Error number: 4
Error string: Query out of range. In function getObservedCharge. Request query 107, num queries: 67
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 68, num queries: 67
Error number: 4 : Query out of range. In function getObservedCharge. Request query 69, num queries: 67 (Error repeated 19 times)
 
 
=cut