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revision 1.3, Mon Sep 12 00:25:22 2005 UTC revision 1.5, Mon Dec 5 18:56:37 2005 UTC
# Line 1  Line 1 
1  #!/usr/bin/perl -w  #!/usr/bin/perl -w
2    #
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    #
18    
19    
20  =head1 Packager  =head1 Packager
21    
# Line 740  Line 757 
757  one end record.  one end record.
758    
759  To prevent file system compatibility problems, the name is automatically cleaned  To prevent file system compatibility problems, the name is automatically cleaned
760  before the file is created: all spaces and colons are converted to underscores.  before the file is created: all spaces and colons are converted to underscores,
761    and question marks are converted to the double letter C<QQ>.
762    
763  Text files are open in text mode and binary files in binary mode. As a result, the  Text files are open in text mode and binary files in binary mode. As a result, the
764  line-end characters in a text file are automatically translated to the line-end  line-end characters in a text file are automatically translated to the line-end
# Line 945  Line 963 
963    
964  sub CreateFile {  sub CreateFile {
965      my ($fileName, $mode, $directory, $compObject) = @_;      my ($fileName, $mode, $directory, $compObject) = @_;
966      # Clear the file name.      # Clean the file name.
967      $fileName =~ tr/: /__/;      $fileName =~ tr/: /__/;
968        $fileName =~ s/\?/QQ/g;
969      # Add the file name to the directory to get the fully-qualified file name.      # Add the file name to the directory to get the fully-qualified file name.
970      my $fullName = "$directory/$fileName";      my $fullName = "$directory/$fileName";
971      # Extract the path.      # Extract the path.

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