error messages due to added code in the init_code

[Erick Antezana-4]

Hi,
 
if we add the following "use"s to the init_code block:

init_code =use BCS_GGB_Util;
    use BCS_ENV;
    use BcsGGBFunc;

we get the following error message in the apache log file:

[error] Odd number of elements in hash assignment at,
[error] \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/PluginSet.pm line 197 (#1),
[error]      (W misc) You specified an odd number of elements to initialize a hash,,
[error]      which is odd, because hashes come in key/value pairs.,

But ... everything is working well even though we get those error messages (If the added modules are deleted from the init_code section, the error messages disappear of course.)

Any suggestions?
Erick

------------------------------------------------------------------------------
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looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
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[Lincoln Stein-3]

Do any of these libraries call plugin library functions?

Lincoln

On Tue, Jun 2, 2009 at 11:18 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,
 
if we add the following "use"s to the init_code block:

init_code =use BCS_GGB_Util;
    use BCS_ENV;
    use BcsGGBFunc;

we get the following error message in the apache log file:

[error] Odd number of elements in hash assignment at,
[error] \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/PluginSet.pm line 197 (#1),
[error]      (W misc) You specified an odd number of elements to initialize a hash,,
[error]      which is odd, because hashes come in key/value pairs.,

But ... everything is working well even though we get those error messages (If the added modules are deleted from the init_code section, the error messages disappear of course.)

Any suggestions?
Erick

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
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[Erick Antezana-4]

No. They are pretty simple implementations. Please find below one of them (BCS_GGB_Util.pm)

package BCS_GGB_Util;
use strict;
use warnings;
use diagnostics;

use vars qw(@ISA @EXPORT);

require Exporter;
@ISA = 'Exporter';
@EXPORT = qw(
    gene_bgcolor
    gene_fgcolor
    codon_bgcolor
        );

use constant DEBUG => 0;

sub codon_bgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('Charge');
    if (grep(/(acidic)/i, @name)) {
        return 'red';
    }
    elsif (grep(/(basic)/i, @name)) {
        return 'blue';
    }
    elsif (grep(/(nonpolar_neutral)/i, @name)) {
        return 'green';
    }
     elsif (grep(/(polar_neutral)/i, @name)) {
        return 'yellow';
    }
    else {
        return 'black';
    }
}

sub gene_bgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('SubjectDescription');
    if (grep(/(transpos)|(repeat)|(repeti)/i, @name)) {
        return 'red';
    }
    elsif (grep(/(hypotheti)|(putative)|(probable)/i, @name)) {
        return 'orange';
    }
    elsif (grep(/(unknown)|(no annot)/i, @name)) {
        return 'yellow';
    }
    elsif (grep(/(express)/i, @name)) {
        return 'green';
    }
    else {
        return 'greenyellow';
    }
}

sub gene_fgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('SubjectDescription');
    if (grep(/(transpos)|(repeat)|(repeti)/i, @name)) {
        return 'darkred';
    }
    elsif (grep(/(hypotheti)|(putative)|(probable)/i, @name)) {
        return 'orangered';
    }
    elsif (grep(/(unknown)|(no annot)/i, @name)) {
        return 'orange';
    }
    elsif (grep(/(express)/i, @name)) {
        return 'darkgreen';
    }
    else {
           return 'forestgreen';
    }
}

1;


Erick

2009/6/2 Lincoln Stein <lincoln.stein@...>

Do any of these libraries call plugin library functions?

Lincoln

On Tue, Jun 2, 2009 at 11:18 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,
 
if we add the following "use"s to the init_code block:

init_code =use BCS_GGB_Util;
    use BCS_ENV;
    use BcsGGBFunc;

we get the following error message in the apache log file:

[error] Odd number of elements in hash assignment at,
[error] \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/PluginSet.pm line 197 (#1),
[error]      (W misc) You specified an odd number of elements to initialize a hash,,
[error]      which is odd, because hashes come in key/value pairs.,

But ... everything is working well even though we get those error messages (If the added modules are deleted from the init_code section, the error messages disappear of course.)

Any suggestions?
Erick

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse