gmod-cmap — Discussion of the CMAP comparative map viewer

Re: [gmod-cmap] Help: Error at Name-based Correspondence

[Scott C. <cai...@gm...>]

Hi Amy,

Could your server have been running out of memory?  It is possible
that the operating system killed MySQL to keep the whole computer from
crashing.  You should check your syslog for messages about mysql.

Scott


On Thu, Oct 9, 2008 at 2:54 AM, Lee Amy <ope...@gm...> wrote:
> Hello,
>
> I encountered an error while I'm doing name-based correspondence, it's about
> MySQL. This error occurred suddenly and after running a long time.
>
> The error is:
>
> DBD::mysql::db selectall_arrayref failed: MySQL server has gone away at
> /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 3008,
> <STDIN> line 16.
> DBD::mysql::db selectall_arrayref failed: MySQL server has gone away at
> /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 3008,
> <STDIN> line 16.
>
> Could you tell me how to fix that?
>
> Huge thanks to you.
>
> Best Regards,
>
> Amy Lee
>
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>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cai...@gm...
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[gmod-cmap] Help: Error at Name-based Correspondence

[Lee A. <ope...@gm...>]

Hello,

I encountered an error while I'm doing name-based correspondence, it's about
MySQL. This error occurred suddenly and after running a long time.

The error is:

DBD::mysql::db selectall_arrayref failed: MySQL server has gone away at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 3008,
<STDIN> line 16.
DBD::mysql::db selectall_arrayref failed: MySQL server has gone away at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 3008,
<STDIN> line 16.

Could you tell me how to fix that?

Huge thanks to you.

Best Regards,

Amy Lee

Re: [gmod-cmap] Controlling label_features default//Solution

[John M. <McC...@cr...>]

Hi Ben,
I have managed to reproduce the behaviour I don't like in Firefox & IE
like so:
-select a map in VIEWER
-click on a marker
-select VIEW MAP DETAILS

This sets view to SHOW LANDMARKS as it is coded in feature_detail.tmpl
and seems to affect this setting via cookies,as deleting cookies
resents to SHOW ALL

So...I have just deleted the SHOW FEATURES string from the URL in the
template file to get the behaviour I want.

Regards
John


>>> Ben Faga <fag...@gm...> 9:01 a.m. 05-Oct-08 >>>
Hi John,

Without looking at code, I can tell you how this is supposed to work.

If you have never been to the site, the config option should set the
labels to "all".

Since you have visited the site, your cookie remembers which option
you
selected.

Try deleting the cookie with your browser and then visiting again.  If
there isn't a bug, then it should be fine.

If there is a bug then let Ken know.

Ben

On Mon, 2008-09-29 at 14:13 +1300, John McCallum wrote:
> Im struggling to work out how to better control the default genetic
map
> drawing behaviour in terms of showing ALL feature labels vs Landmark
> features only.
> 
> In my database config file the option set is 'label_features all'
> 
> but on first selecting a map the behaviour is to just show landmark
> feature labels.
> 
> I definitely don't want new users getting this (and having to
manually
> change this themselves)
> 
> Im sure I can change this by hacking the templates but that seems a
> little extreme!
> 
> 
> 
> 
> 
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
> Christchurch
> New Zealand
> Work Ph 64 3 325 6400
> Home 64 3 328 7420
> Mobile 027 443 9033
> Fax 64 3 325 2074
> Email MCC...@CR... 
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 
> 
>
-------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
> Build the coolest Linux based applications with Moblin SDK & win
great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/ 
> _______________________________________________
> gmod-cmap mailing list
> gmo...@li... 
> https://lists.sourceforge.net/lists/listinfo/gmod-cmap 



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Re: [gmod-cmap] CMap-1.01 Map.pm issue

[Ben F. <fag...@gm...>]

Hi Anil,

I'm cc'ing to the list since I've moved on to a different job.

My guess is that you have maps of zero length (although, I thought we
had a fix for that).  If so, you need to set the map_start and map_stop
for the map in the database.

Ben

On Sat, 2008-10-04 at 13:01 -0400, as...@CL... wrote:
> Hi Ben,
> 
> This is Anil, graduate student from Clemson University. I had interacted
> with you during the CMap-1.01 installation. Currently, I am running into
> few issues with it, so please help me out if you have some time for this.
> 
> - CMap is in: http://www.cottonmarker.org/cmap/
> - Issue is that, in the recently uploaded data, when I try to compare
> maps(left or right), I get an error saying:
> Illegal division by zero at
> /gnb/blenda/sites/www.cottonmarker.org/cmap-1.01/lib/Bio/GMOD/CMap/Drawer/Map.pm
> line 2451.
> 
> - The URL for this data is:
> http://www.cottonmarker.org/cgi-bin/cmap/viewer?ref_map_set_acc=11;ref_map_accs=359
> 
> - This is the first set of data I uploaded after installing CMap.
> 
> I was not sure what was going wrong in Map.pm module. Please let me know
> if you can figure out the issue here.
> 
> Thanks a lot.
> Anil

Re: [gmod-cmap] Controlling label_features default

[Ben F. <fag...@gm...>]

Hi John,

Without looking at code, I can tell you how this is supposed to work.

If you have never been to the site, the config option should set the
labels to "all".

Since you have visited the site, your cookie remembers which option you
selected.

Try deleting the cookie with your browser and then visiting again.  If
there isn't a bug, then it should be fine.

If there is a bug then let Ken know.

Ben

On Mon, 2008-09-29 at 14:13 +1300, John McCallum wrote:
> Im struggling to work out how to better control the default genetic map
> drawing behaviour in terms of showing ALL feature labels vs Landmark
> features only.
> 
> In my database config file the option set is 'label_features all'
> 
> but on first selecting a map the behaviour is to just show landmark
> feature labels.
> 
> I definitely don't want new users getting this (and having to manually
> change this themselves)
> 
> Im sure I can change this by hacking the templates but that seems a
> little extreme!
> 
> 
> 
> 
> 
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
> Christchurch
> New Zealand
> Work Ph 64 3 325 6400
> Home 64 3 328 7420
> Mobile 027 443 9033
> Fax 64 3 325 2074
> Email MCC...@CR...
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> gmod-cmap mailing list
> gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-cmap

Re: [gmod-cmap] How to enable 'EVAL_PERL' ?

[Ben F. <fag...@gm...>]

Hi John,

Thanks for testing this for me.  I've sent the patch out to the list.

You might still want to patch your bin/cmap_validate_config.pl script so
you don't get a warning when testing your config files.

http://sourceforge.net/tracker/index.php?func=detail&aid=2138364&group_id=27707&atid=391293

Ben

On Tue, 2008-09-23 at 10:04 +1200, John McCallum wrote:
> Thanks a lot Ben!
> I suspected this might be the case.
> 
> Do you mean that it is already possible to do this (ie set TT flags in
> cmap.conf or other )  or we need to edit the configuration modules to do
> this?
>  (and pass back coee to the project,...)
> 
> Regards
> John
> 
> 
> 
> >>> Ben Faga <fag...@gm...> 1:25 a.m. 23-Sep-08-08 >>>
> Hi John,
> 
> This is untested but I think you set the EVAL_PERL flag when creating
> the template toolkit object.  
> 
> In CMap's case this is located in the module Bio/GMOD/CMap.pm, line
> 1555
> (in the "template" subroutine).
> 
> Although, hacking the code isn't really the best solution (since you
> are
> essentially creating a local fork which you will have to port all your
> changes).  It should be possible to add TT configuration flags to the
> CMap config file.
> 
> Thoughts?
> 
> Ben
> 
> On Mon, 2008-09-22 at 11:36 +1200, John McCallum wrote:
> > I have been delving into the template toolkit to enable some
> > customization of our cmap installation and finding it very
> > straightforward EXCEPT the following..
> > 
> > We want to enable some custom inclusion and the simplest is to
> enable
> > some PERL....However I can't for the life of me work out how or where
> to
> > enable the 'EVAL_PERL' flag.
> > 
> > Could anyone point me to how this is done?
> > 
> > Regards
> > John
> > 
> > 
> > Visit our website at http://www.crop.cri.nz 
> > ______________________________________________________
> > CAUTION: The information contained in this email is privileged 
> > and confidential.  If you read this message and you are not the 
> > intended recipient, you are hereby notified that any use, 
> > dissemination, distribution or reproduction of all or part of the 
> > contents is prohibited. If you receive this message in error, 
> > please notify the sender immediately.
> > 
> > Any opinions or views expressed in this message are those of the 
> > individual sender and may not represent those of their employer.
> > 
> > 
> >
> -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ 
> > _______________________________________________
> > gmod-cmap mailing list
> > gmo...@li... 
> > https://lists.sourceforge.net/lists/listinfo/gmod-cmap
> 
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 

[gmod-cmap] Template Toolkit Flags (patch)

[Ben F. <fag...@gm...>]

Hi everyone,

I've released a patch which adds some obscure functionality to the
configuration.

You will only need this patch if you want to add flags during the
creation of the Template Toolkit object.  John McCallum needed it to
enable 'EVAL_PERL' for the templates that he was creating.

Ben

The patch is at:

http://sourceforge.net/tracker/index.php?func=detail&aid=2138364&group_id=27707&atid=391293

README:

NOTE: This patch adds obscure functionality to CMap.  It is not needed for normal use of CMap.

This patch adds a configuration option that can set flags during the creation
of the Template Toolkit object.  This allows for more powerful use of Template
Toolkit.  The flags are passed into the Template->new() method.

The following is an example of how to use this new configuration option.  It
will only take strings as values (no complicated objects).

  <template_toolkit_flags>
    EVAL_PERL 1
    SOMETHING else
  </template_toolkit_flags>

These patches will work for CMap version 1.01.

Apply these patches to the CMap.pm perl module and the cmap_validate_config.pl script.

  $ patch /path/to/Bio/GMOD/CMap.pm CMap.080924.v1.01.patch
  $ patch /path/to/bin/cmap_validate_config.pl cmap_validate_config.080924.v1.01.patch

[gmod-cmap] Controlling label_features default

[John M. <McC...@cr...>]

Im struggling to work out how to better control the default genetic map
drawing behaviour in terms of showing ALL feature labels vs Landmark
features only.

In my database config file the option set is 'label_features all'

but on first selecting a map the behaviour is to just show landmark
feature labels.

I definitely don't want new users getting this (and having to manually
change this themselves)

Im sure I can change this by hacking the templates but that seems a
little extreme!





Dr. John A. McCallum
Crop & Food Research
Private Bag 4704
Christchurch
New Zealand
Work Ph 64 3 325 6400
Home 64 3 328 7420
Mobile 027 443 9033
Fax 64 3 325 2074
Email MCC...@CR...


Visit our website at http://www.crop.cri.nz 
______________________________________________________
CAUTION: The information contained in this email is privileged 
and confidential.  If you read this message and you are not the 
intended recipient, you are hereby notified that any use, 
dissemination, distribution or reproduction of all or part of the 
contents is prohibited. If you receive this message in error, 
please notify the sender immediately.

Any opinions or views expressed in this message are those of the 
individual sender and may not represent those of their employer.

Re: [gmod-cmap] Patch: Negative Numbers Bug

[David H. <dav...@gm...>]

Thanks Ben! Works perfectly now. Our fresh install now look beautiful :)

On Tue, Sep 23, 2008 at 8:26 AM, Ben Faga <fag...@gm...> wrote:

> Hello everyone,
>
> It has come to my attention that there is a bug when CMap displays
> negative numbers on the map tick marks.  This bug has existed in the
> code since the 0.13 release (I don't know how it has slipped by this
> long).
>
> Note: This bug only affects maps that have a negative start value.
>
> The bug causes negative numbers on the tick marks to be off by one (in
> the last significant digit.  For example:
>
> -30   -20  -10     0    10
>  |    |     |     |     |
> ----------------------------
>
> Is being displayed as:
>
> -20   -10    0     0    10
>  |    |     |     |     |
> ----------------------------
>
> I have attached a patch that will work with versions 0.15 to the current
> release.
>
> To apply the patch, find the Bio/GMOD/CMap/Utils.pm file and patch it
> like so:
>
>  $ patch Bio/GMOD/CMap/Utils.pm Utils.080923.v1.01.patch
>
> This should fix the problem.
>
>
> If you are using versions 0.13 or 0.14, then you will have to make the
> patch by hand.  Simply open the Bio/GMOD/CMap/Utils.pm file.  Find the
> "presentable_number" subroutine and replace the line:
>
>    my $rounded_temp   = int( ( $num / ( 10**$rounding_power ) ) + .5 );
>
> with:
>
>    my $half = ($num >= 0)? 0.5: -0.5;
>    my $rounded_temp = int( ( $num / ( 10**$rounding_power ) ) + $half );
>
> I'm sorry for the inconvenience.  My thanks goes to David Hane for
> reporting this bug.
>
> Ben
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> gmod-cmap mailing list
> gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-cmap
>
>

Re: [gmod-cmap] How to enable 'EVAL_PERL' ?

[Ben F. <fag...@gm...>]

Hi John,

No, it isn't possible to set TT flags without hacking the code yet.  I
probably won't be able to get to it today but hopefully tomorrow I'll
have a patch for you to allow this.

Ben

On Tue, 2008-09-23 at 10:04 +1200, John McCallum wrote:
> Thanks a lot Ben!
> I suspected this might be the case.
> 
> Do you mean that it is already possible to do this (ie set TT flags in
> cmap.conf or other )  or we need to edit the configuration modules to do
> this?
>  (and pass back coee to the project,...)
> 
> Regards
> John
> 
> 
> 
> >>> Ben Faga <fag...@gm...> 1:25 a.m. 23-Sep-08-08 >>>
> Hi John,
> 
> This is untested but I think you set the EVAL_PERL flag when creating
> the template toolkit object.  
> 
> In CMap's case this is located in the module Bio/GMOD/CMap.pm, line
> 1555
> (in the "template" subroutine).
> 
> Although, hacking the code isn't really the best solution (since you
> are
> essentially creating a local fork which you will have to port all your
> changes).  It should be possible to add TT configuration flags to the
> CMap config file.
> 
> Thoughts?
> 
> Ben
> 
> On Mon, 2008-09-22 at 11:36 +1200, John McCallum wrote:
> > I have been delving into the template toolkit to enable some
> > customization of our cmap installation and finding it very
> > straightforward EXCEPT the following..
> > 
> > We want to enable some custom inclusion and the simplest is to
> enable
> > some PERL....However I can't for the life of me work out how or where
> to
> > enable the 'EVAL_PERL' flag.
> > 
> > Could anyone point me to how this is done?
> > 
> > Regards
> > John
> > 
> > 
> > Visit our website at http://www.crop.cri.nz 
> > ______________________________________________________
> > CAUTION: The information contained in this email is privileged 
> > and confidential.  If you read this message and you are not the 
> > intended recipient, you are hereby notified that any use, 
> > dissemination, distribution or reproduction of all or part of the 
> > contents is prohibited. If you receive this message in error, 
> > please notify the sender immediately.
> > 
> > Any opinions or views expressed in this message are those of the 
> > individual sender and may not represent those of their employer.
> > 
> > 
> >
> -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > Build the coolest Linux based applications with Moblin SDK & win
> great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ 
> > _______________________________________________
> > gmod-cmap mailing list
> > gmo...@li... 
> > https://lists.sourceforge.net/lists/listinfo/gmod-cmap
> 
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 

[gmod-cmap] Patch: Negative Numbers Bug

[Ben F. <fag...@gm...>]

Hello everyone,

It has come to my attention that there is a bug when CMap displays
negative numbers on the map tick marks.  This bug has existed in the
code since the 0.13 release (I don't know how it has slipped by this
long).

Note: This bug only affects maps that have a negative start value.

The bug causes negative numbers on the tick marks to be off by one (in
the last significant digit.  For example:

-30   -20  -10     0    10
  |    |     |     |     |
----------------------------

Is being displayed as:

-20   -10    0     0    10
  |    |     |     |     |
----------------------------

I have attached a patch that will work with versions 0.15 to the current
release.

To apply the patch, find the Bio/GMOD/CMap/Utils.pm file and patch it
like so:

  $ patch Bio/GMOD/CMap/Utils.pm Utils.080923.v1.01.patch

This should fix the problem.


If you are using versions 0.13 or 0.14, then you will have to make the
patch by hand.  Simply open the Bio/GMOD/CMap/Utils.pm file.  Find the
"presentable_number" subroutine and replace the line:

    my $rounded_temp   = int( ( $num / ( 10**$rounding_power ) ) + .5 );  

with:

    my $half = ($num >= 0)? 0.5: -0.5;
    my $rounded_temp = int( ( $num / ( 10**$rounding_power ) ) + $half );

I'm sorry for the inconvenience.  My thanks goes to David Hane for
reporting this bug.

Ben

Re: [gmod-cmap] How to enable 'EVAL_PERL' ?

[John M. <McC...@cr...>]

Thanks a lot Ben!
I suspected this might be the case.

Do you mean that it is already possible to do this (ie set TT flags in
cmap.conf or other )  or we need to edit the configuration modules to do
this?
 (and pass back coee to the project,...)

Regards
John



>>> Ben Faga <fag...@gm...> 1:25 a.m. 23-Sep-08-08 >>>
Hi John,

This is untested but I think you set the EVAL_PERL flag when creating
the template toolkit object.  

In CMap's case this is located in the module Bio/GMOD/CMap.pm, line
1555
(in the "template" subroutine).

Although, hacking the code isn't really the best solution (since you
are
essentially creating a local fork which you will have to port all your
changes).  It should be possible to add TT configuration flags to the
CMap config file.

Thoughts?

Ben

On Mon, 2008-09-22 at 11:36 +1200, John McCallum wrote:
> I have been delving into the template toolkit to enable some
> customization of our cmap installation and finding it very
> straightforward EXCEPT the following..
> 
> We want to enable some custom inclusion and the simplest is to
enable
> some PERL....However I can't for the life of me work out how or where
to
> enable the 'EVAL_PERL' flag.
> 
> Could anyone point me to how this is done?
> 
> Regards
> John
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 
> 
>
-------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
> Build the coolest Linux based applications with Moblin SDK & win
great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/ 
> _______________________________________________
> gmod-cmap mailing list
> gmo...@li... 
> https://lists.sourceforge.net/lists/listinfo/gmod-cmap



Visit our website at http://www.crop.cri.nz 
______________________________________________________
CAUTION: The information contained in this email is privileged 
and confidential.  If you read this message and you are not the 
intended recipient, you are hereby notified that any use, 
dissemination, distribution or reproduction of all or part of the 
contents is prohibited. If you receive this message in error, 
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Any opinions or views expressed in this message are those of the 
individual sender and may not represent those of their employer.

Re: [gmod-cmap] Double Zero maps

[Ben F. <fag...@gm...>]

Just wanted to let you know of my progress with this bug.  I've figured
out where it's happening.  It *is* just a labeling problem
(specifically, it's in the math that turns the tick mark into a short,
readable number (4000000 into 4M etc).  

I'm surprised that no one has noticed this before since any negative
numbers seem to be off by 1 (at the first significant digit).

I need to work on the math.  Hopefully, I can get this worked out
tomorrow morning.

Ben

On Mon, 2008-09-22 at 09:22 -0700, David Hane wrote:
> I'm having some issues with maps being drawn with 2 entries for the
> zero position. An example can be found at my devel database:
> 
> http://feline.pw.usda.gov/cgi-bin/cmap/viewer?data_source=CMAP;saved_link_id=1;
> 

Re: [gmod-cmap] Announcement: Returning CMap Development Ken

[David H. <dav...@gm...>]

Wow, I missed the announcement.

Best of luck to you Ben. You were, and always will be, a great asset to the
project.

Hip-Hip-Hooray!

On Mon, Sep 22, 2008 at 10:57 AM, Ken Youens-Clark <kc...@cs...> wrote:

> On Sep 22, 2008, at 9:17 AM, Ben Faga wrote:
>
> > Ken Youens-Clark will be returning to the role of lead developer for
> > CMap.  As the original author of CMap, he is well suited for the task.
> >
> > I am leaving my current position in Lincoln Stein's lab (four and a
> > half
> > years of telecommuting is enough for me to want to work in person with
> > other people).  I will still watch the mailing list for a time but I
> > will not be doing any large scale work.
> >
> > CMap is a stable project and Ken is a brilliant developer.  I have no
> > concerns over the future of CMap.
> >
> > It has been wonderful working with this community over the years.
> > Thank
> > you for 4.5+ years of interesting work.
>
> Three cheers for Ben!
>
> I'll miss Ben's work on CMap and his support on this list.  I will
> endeavor to be as helpful and responsive as he has been lo these many
> years.
>
> ky
>
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Re: [gmod-cmap] Announcement: Returning CMap Development Ken

[Ken Youens-C. <kc...@cs...>]

On Sep 22, 2008, at 9:17 AM, Ben Faga wrote:

> Ken Youens-Clark will be returning to the role of lead developer for
> CMap.  As the original author of CMap, he is well suited for the task.
>
> I am leaving my current position in Lincoln Stein's lab (four and a  
> half
> years of telecommuting is enough for me to want to work in person with
> other people).  I will still watch the mailing list for a time but I
> will not be doing any large scale work.
>
> CMap is a stable project and Ken is a brilliant developer.  I have no
> concerns over the future of CMap.
>
> It has been wonderful working with this community over the years.  
> Thank
> you for 4.5+ years of interesting work.

Three cheers for Ben!

I'll miss Ben's work on CMap and his support on this list.  I will  
endeavor to be as helpful and responsive as he has been lo these many  
years.

ky

Re: [gmod-cmap] Double Zero maps

[Ben F. <fag...@gm...>]

Yeah, that's not right.  It appears to be a problem with the tick mark
naming.

I'll work on a patch for that.

Ben

On Mon, 2008-09-22 at 09:22 -0700, David Hane wrote:
> I'm having some issues with maps being drawn with 2 entries for the
> zero position. An example can be found at my devel database:
> 
> http://feline.pw.usda.gov/cgi-bin/cmap/viewer?data_source=CMAP;saved_link_id=1;
> 

[gmod-cmap] Announcement: Returning CMap Development Ken

[Ben F. <fag...@gm...>]

Hello everyone,

Ken Youens-Clark will be returning to the role of lead developer for
CMap.  As the original author of CMap, he is well suited for the task.

I am leaving my current position in Lincoln Stein's lab (four and a half
years of telecommuting is enough for me to want to work in person with
other people).  I will still watch the mailing list for a time but I
will not be doing any large scale work.

CMap is a stable project and Ken is a brilliant developer.  I have no
concerns over the future of CMap.

It has been wonderful working with this community over the years. Thank
you for 4.5+ years of interesting work.

Ben

Re: [gmod-cmap] How to enable 'EVAL_PERL' ?

[Ben F. <fag...@gm...>]

Hi John,

This is untested but I think you set the EVAL_PERL flag when creating
the template toolkit object.  

In CMap's case this is located in the module Bio/GMOD/CMap.pm, line 1555
(in the "template" subroutine).

Although, hacking the code isn't really the best solution (since you are
essentially creating a local fork which you will have to port all your
changes).  It should be possible to add TT configuration flags to the
CMap config file.

Thoughts?

Ben

On Mon, 2008-09-22 at 11:36 +1200, John McCallum wrote:
> I have been delving into the template toolkit to enable some
> customization of our cmap installation and finding it very
> straightforward EXCEPT the following..
> 
> We want to enable some custom inclusion and the simplest is to enable
> some PERL....However I can't for the life of me work out how or where to
> enable the 'EVAL_PERL' flag.
> 
> Could anyone point me to how this is done?
> 
> Regards
> John
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
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> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 
> 
> -------------------------------------------------------------------------
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[gmod-cmap] How to enable 'EVAL_PERL' ?

[John M. <McC...@cr...>]

I have been delving into the template toolkit to enable some
customization of our cmap installation and finding it very
straightforward EXCEPT the following..

We want to enable some custom inclusion and the simplest is to enable
some PERL....However I can't for the life of me work out how or where to
enable the 'EVAL_PERL' flag.

Could anyone point me to how this is done?

Regards
John


Visit our website at http://www.crop.cri.nz 
______________________________________________________
CAUTION: The information contained in this email is privileged 
and confidential.  If you read this message and you are not the 
intended recipient, you are hereby notified that any use, 
dissemination, distribution or reproduction of all or part of the 
contents is prohibited. If you receive this message in error, 
please notify the sender immediately.

Any opinions or views expressed in this message are those of the 
individual sender and may not represent those of their employer.

Re: [gmod-cmap] Help: GFF format

[Ben F. <fag...@gm...>]

I replied to this in a thread that was off list.  For the sake of the
archive, I'll include the portion that referenced this email.

As for GFF3, assuming you have a recent version of bioperl-live, you
can run:

  perldoc Bio::DB::SeqFeature::Store::cmap

And that will give you a description of the CMap GFF3.

Ben

On Fri, 2008-09-05 at 07:55 +0800, Lee Amy wrote:
> Hi,
> 
> I'm going to import GFF format file, however, I don't know the field
> which is requirement. So could you provide me some more details?
> 
> Huge thanks!
> 
> Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: [gmod-cmap] Help: Duplicate entry problem

[Ben F. <fag...@gm...>]

Hi Amy,

My guess is that there is already a map in a different map set with the
accession "bgi2005-1".

That's the only thing that makes sense because if you were importing the
data into the same map set as the previous bgi2005-1, it would just add
the features to it.

Try the following sql query:

select map_set_name 
from cmap_map m, cmap_map_set ms
where m.map_acc="bgi2005-1" and m.map_set_id = ms.map_set_id

And see if that is the same map set as the one you are importing into.

Ben

On Fri, 2008-09-12 at 15:01 +0800, Lee Amy wrote:
> Hello,
> 
> It seems that I encounter this problem again though I have change the
> attributes and enlarge the values by using MySQL. I have enlarged
> every possible vaules as I think, but when I import data errors are
> showing by following words.
> 
> DBD::mysql::db do failed: Duplicate entry 'bgi2005-1' for key 2
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line
> 3316, <GEN5> line 2904351.
> DBD::mysql::db do failed: Duplicate entry 'bgi2005-1' for key 2
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line
> 3316, <GEN5> line 2904351.
> 
> There's a demo data I will paste here. The attachment I also provide
> the configuration file.
> 
> Could you tell me how to fix that?
> 
> Thanks in advance.
> 
> Regards,
> 
> Amy
> 
> 
> 
> -------------------------------------------------------------------------
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Re: [gmod-cmap] Help: Delete Species

[Lee A. <ope...@gm...>]

2008/9/8 Lee Amy <ope...@gm...>

> Hello,
>
> Is there any way to delete the specific species?
>
> Thank you very much~
>
> Regards,
>
> Amy
>
Sorry for that, I use Admin Home to remove them well.

Amy

[gmod-cmap] Help: Delete Species

[Lee A. <ope...@gm...>]

Hello,

Is there any way to delete the specific species?

Thank you very much~

Regards,

Amy

[gmod-cmap] Help: GFF format

[Lee A. <ope...@gm...>]

Hi,

I'm going to import GFF format file, however, I don't know the field which
is requirement. So could you provide me some more details?

Huge thanks!

Regards,

Amy Lee

Re: [gmod-cmap] Help: Cannot draw pictures

[Ben F. <fag...@gm...>]

Yeah, that's a lot of maps to view as reference maps.  If you really
want to see them all, try turning off features (in the menu just before
creating the image).  That should render and show you the folly of
trying to view that much information in one image. ;)

You can then try to add features in one at a time until it breaks again.

Ben

On Mon, 2008-09-01 at 15:27 +0800, Lee Amy wrote:
> Hello,
> 
> I have a data which contains 167 maps. And I can import it correctly
> but when I draw the all maps, it seems that I cannot see these maps. I
> suppose that whether that is too big to show, or any limitation I
> should change?
> 
> Huge thanks to you.
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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