Hi-Res images of conservation tracks have the background turn blue.

[Bill Pulec]

Hi All,
I am attempting to view high-res images of conservation tracks but the background of these tracks in high-res is blue. This isn't the case when these tracks are displayed in gbrowse normally, it only happens when viewed as high-res. Also all the non-conservation tracks are fine in high res. Is there any reason why outputting these images in high-res would do this? Has anyone encountered other tracks doing this in high-res? Any insight would be appreciated. I have attached an example image of the track below.

Thanks,
Bill




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[Dave Clements, GMOD Help Desk]

Hi Bill,

I have no particular insight on why this is happening.  My guess is
that it is due some obscure interaction between the UCSC plugin and
core GBrowse, but I don't actually know.

I've CC'd Angie at UCSC to see if she may have any insight.

Dave C.



On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:

> Hi All,
> I am attempting to view high-res images of conservation tracks but the
> background of these tracks in high-res is blue. This isn't the case when
> these tracks are displayed in gbrowse normally, it only happens when viewed
> as high-res. Also all the non-conservation tracks are fine in high res. Is
> there any reason why outputting these images in high-res would do this? Has
> anyone encountered other tracks doing this in high-res? Any insight would be
> appreciated. I have attached an example image of the track below.
>
> Thanks,
> Bill
>
>
>

Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

Learn more about GMOD at:
  SMBE: http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
  Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
  AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration

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[Angie Hinrichs]

Dave - yes, that sounds likely.  

Bill, what version of GBrowse are you running?  How recently did you
grab the plugin code?  I didn't get the screenshot attachment so if
you wouldn't mind sending that to me, that would be helpful.  If your
GBrowse is on a public server, can you send the URL?

Angie

On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:

> Hi Bill,
>
> I have no particular insight on why this is happening.  My guess is
> that it is due some obscure interaction between the UCSC plugin and
> core GBrowse, but I don't actually know.
>
> I've CC'd Angie at UCSC to see if she may have any insight.
>
> Dave C.
>
>
>
> On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
> > Hi All,
> > I am attempting to view high-res images of conservation tracks but the
> > background of these tracks in high-res is blue. This isn't the case when
> > these tracks are displayed in gbrowse normally, it only happens when viewed
> > as high-res. Also all the non-conservation tracks are fine in high res. Is
> > there any reason why outputting these images in high-res would do this? Has
> > anyone encountered other tracks doing this in high-res? Any insight would be
> > appreciated. I have attached an example image of the track below.
> >
> > Thanks,
> > Bill
> >
> >
> >
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
>   SMBE: http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>   AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration
>

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[mark meyer-3]

Hi Angie,

 

Bill is out of the office today, but I can try to answer your questions.  Attached are the two screen shots, one is what the plugin looks like in the gbrowse, just fine as it looks in UCSC.  The second is what happens when you click on high-res image.

 

We are running gbrowse v1.69.  The plugin code was implemented and downloaded about 1 month ago, just recently ran into this issue since we are trying to make some publication figures from our Gbrowse data. 

 

I can access conf files, etc. if you need to see them and try to do my best to answer questions, but I may not be able to answer very detailed questions in Bill's absence since he has been the one configuring this.

 

Thanks for checking into this for us,

 

Mark

On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...> wrote:

Dave - yes, that sounds likely.

Bill, what version of GBrowse are you running?  How recently did you
grab the plugin code?  I didn't get the screenshot attachment so if
you wouldn't mind sending that to me, that would be helpful.  If your
GBrowse is on a public server, can you send the URL?

Angie

On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:

> Hi Bill,
>
> I have no particular insight on why this is happening.  My guess is
> that it is due some obscure interaction between the UCSC plugin and
> core GBrowse, but I don't actually know.
>
> I've CC'd Angie at UCSC to see if she may have any insight.
>
> Dave C.
>
>
>
> On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
> > Hi All,
> > I am attempting to view high-res images of conservation tracks but the
> > background of these tracks in high-res is blue. This isn't the case when
> > these tracks are displayed in gbrowse normally, it only happens when viewed
> > as high-res. Also all the non-conservation tracks are fine in high res. Is
> > there any reason why outputting these images in high-res would do this? Has
> > anyone encountered other tracks doing this in high-res? Any insight would be
> > appreciated. I have attached an example image of the track below.
> >
> > Thanks,
> > Bill
> >
> >
> >
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
>   SMBE: http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>   AGA Next Gen Seq in Non-Models: http://www.regonline.com/Nextgeneration
>

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[Scott Cain-4]

Hi all,

Could this be a bad interaction between the plug in and GD::SVG or
inkscape (depending on what sort of hi res image you are getting)?
For example, I think that GD::SVG has a hard time with alpha channels.

Scott


On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...> wrote:

> Hi Angie,
>
> Bill is out of the office today, but I can try to answer your questions.
> Attached are the two screen shots, one is what the plugin looks like in the
> gbrowse, just fine as it looks in UCSC.  The second is what happens when you
> click on high-res image.
>
> We are running gbrowse v1.69.  The plugin code was implemented and
> downloaded about 1 month ago, just recently ran into this issue since we are
> trying to make some publication figures from our Gbrowse data.
>
> I can access conf files, etc. if you need to see them and try to do my best
> to answer questions, but I may not be able to answer very detailed questions
> in Bill's absence since he has been the one configuring this.
>
> Thanks for checking into this for us,
>
> Mark
>
> On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...> wrote:
>>
>> Dave - yes, that sounds likely.
>>
>> Bill, what version of GBrowse are you running?  How recently did you
>> grab the plugin code?  I didn't get the screenshot attachment so if
>> you wouldn't mind sending that to me, that would be helpful.  If your
>> GBrowse is on a public server, can you send the URL?
>>
>> Angie
>>
>> On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
>>
>> > Hi Bill,
>> >
>> > I have no particular insight on why this is happening.  My guess is
>> > that it is due some obscure interaction between the UCSC plugin and
>> > core GBrowse, but I don't actually know.
>> >
>> > I've CC'd Angie at UCSC to see if she may have any insight.
>> >
>> > Dave C.
>> >
>> >
>> >
>> > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
>> > > Hi All,
>> > > I am attempting to view high-res images of conservation tracks but the
>> > > background of these tracks in high-res is blue. This isn't the case
>> > > when
>> > > these tracks are displayed in gbrowse normally, it only happens when
>> > > viewed
>> > > as high-res. Also all the non-conservation tracks are fine in high
>> > > res. Is
>> > > there any reason why outputting these images in high-res would do
>> > > this? Has
>> > > anyone encountered other tracks doing this in high-res? Any insight
>> > > would be
>> > > appreciated. I have attached an example image of the track below.
>> > >
>> > > Thanks,
>> > > Bill
>> > >
>> > >
>> > >
>> >
>> > Was this helpful?  Let us know at
>> > http://gmod.org/wiki/Help_Desk_Feedback
>> >
>> > Learn more about GMOD at:
>> >   SMBE:
>> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>> >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>> >   AGA Next Gen Seq in Non-Models:
>> > http://www.regonline.com/Nextgeneration
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
>> is a gathering of tech-side developers & brand creativity professionals.
>> Meet
>> the minds behind Google Creative Lab, Visual Complexity, Processing, &
>> iPhoneDevCamp as they present alongside digital heavyweights like
>> Barbarian
>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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[mark meyer-3]

We use the GD::SVG and was never able to get the inkscape (pdf generation) operational, if that helps any.

On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...> wrote:

Hi all,

Could this be a bad interaction between the plug in and GD::SVG or
inkscape (depending on what sort of hi res image you are getting)?
For example, I think that GD::SVG has a hard time with alpha channels.

Scott

On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...> wrote:
> Hi Angie,
>
> Bill is out of the office today, but I can try to answer your questions.
> Attached are the two screen shots, one is what the plugin looks like in the
> gbrowse, just fine as it looks in UCSC.  The second is what happens when you
> click on high-res image.
>
> We are running gbrowse v1.69.  The plugin code was implemented and
> downloaded about 1 month ago, just recently ran into this issue since we are
> trying to make some publication figures from our Gbrowse data.
>
> I can access conf files, etc. if you need to see them and try to do my best
> to answer questions, but I may not be able to answer very detailed questions
> in Bill's absence since he has been the one configuring this.
>
> Thanks for checking into this for us,
>
> Mark
>
> On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...> wrote:
>>
>> Dave - yes, that sounds likely.
>>
>> Bill, what version of GBrowse are you running?  How recently did you
>> grab the plugin code?  I didn't get the screenshot attachment so if
>> you wouldn't mind sending that to me, that would be helpful.  If your
>> GBrowse is on a public server, can you send the URL?
>>
>> Angie
>>
>> On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
>>
>> > Hi Bill,
>> >
>> > I have no particular insight on why this is happening.  My guess is
>> > that it is due some obscure interaction between the UCSC plugin and
>> > core GBrowse, but I don't actually know.
>> >
>> > I've CC'd Angie at UCSC to see if she may have any insight.
>> >
>> > Dave C.
>> >
>> >
>> >
>> > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
>> > > Hi All,
>> > > I am attempting to view high-res images of conservation tracks but the
>> > > background of these tracks in high-res is blue. This isn't the case
>> > > when
>> > > these tracks are displayed in gbrowse normally, it only happens when
>> > > viewed
>> > > as high-res. Also all the non-conservation tracks are fine in high
>> > > res. Is
>> > > there any reason why outputting these images in high-res would do
>> > > this? Has
>> > > anyone encountered other tracks doing this in high-res? Any insight
>> > > would be
>> > > appreciated. I have attached an example image of the track below.
>> > >
>> > > Thanks,
>> > > Bill
>> > >
>> > >
>> > >
>> >
>> > Was this helpful?  Let us know at
>> > http://gmod.org/wiki/Help_Desk_Feedback
>> >
>> > Learn more about GMOD at:
>> >   SMBE:
>> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>> >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>> >   AGA Next Gen Seq in Non-Models:
>> > http://www.regonline.com/Nextgeneration
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
>> is a gathering of tech-side developers & brand creativity professionals.
>> Meet
>> the minds behind Google Creative Lab, Visual Complexity, Processing, &
>> iPhoneDevCamp as they present alongside digital heavyweights like
>> Barbarian
>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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[Todd Harris-3]

Mark - 

Try upgrading your GD::SVG to the most current version on CPAN.

Todd

On May 29, 2009, at 9:42 AM, mark meyer wrote:

We use the GD::SVG and was never able to get the inkscape (pdf generation) operational, if that helps any.

On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...> wrote:

Hi all,

Could this be a bad interaction between the plug in and GD::SVG or
inkscape (depending on what sort of hi res image you are getting)?
For example, I think that GD::SVG has a hard time with alpha channels.

Scott

On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...> wrote:
> Hi Angie,
>
> Bill is out of the office today, but I can try to answer your questions.
> Attached are the two screen shots, one is what the plugin looks like in the
> gbrowse, just fine as it looks in UCSC.  The second is what happens when you
> click on high-res image.
>
> We are running gbrowse v1.69.  The plugin code was implemented and
> downloaded about 1 month ago, just recently ran into this issue since we are
> trying to make some publication figures from our Gbrowse data.
>
> I can access conf files, etc. if you need to see them and try to do my best
> to answer questions, but I may not be able to answer very detailed questions
> in Bill's absence since he has been the one configuring this.
>
> Thanks for checking into this for us,
>
> Mark
>
> On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...> wrote:
>>
>> Dave - yes, that sounds likely.
>>
>> Bill, what version of GBrowse are you running?  How recently did you
>> grab the plugin code?  I didn't get the screenshot attachment so if
>> you wouldn't mind sending that to me, that would be helpful.  If your
>> GBrowse is on a public server, can you send the URL?
>>
>> Angie
>>
>> On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
>>
>> > Hi Bill,
>> >
>> > I have no particular insight on why this is happening.  My guess is
>> > that it is due some obscure interaction between the UCSC plugin and
>> > core GBrowse, but I don't actually know.
>> >
>> > I've CC'd Angie at UCSC to see if she may have any insight.
>> >
>> > Dave C.
>> >
>> >
>> >
>> > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
>> > > Hi All,
>> > > I am attempting to view high-res images of conservation tracks but the
>> > > background of these tracks in high-res is blue. This isn't the case
>> > > when
>> > > these tracks are displayed in gbrowse normally, it only happens when
>> > > viewed
>> > > as high-res. Also all the non-conservation tracks are fine in high
>> > > res. Is
>> > > there any reason why outputting these images in high-res would do
>> > > this? Has
>> > > anyone encountered other tracks doing this in high-res? Any insight
>> > > would be
>> > > appreciated. I have attached an example image of the track below.
>> > >
>> > > Thanks,
>> > > Bill
>> > >
>> > >
>> > >
>> >
>> > Was this helpful?  Let us know at
>> > http://gmod.org/wiki/Help_Desk_Feedback
>> >
>> > Learn more about GMOD at:
>> >   SMBE:
>> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>> >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>> >   AGA Next Gen Seq in Non-Models:
>> > http://www.regonline.com/Nextgeneration
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
>> is a gathering of tech-side developers & brand creativity professionals.
>> Meet
>> the minds behind Google Creative Lab, Visual Complexity, Processing, &
>> iPhoneDevCamp as they present alongside digital heavyweights like
>> Barbarian
>> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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[Angie Hinrichs]

Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
be out of sync ($i --> $index)!" ?

Wherever the bad interaction is taking place, it is definitely an
alpha-channel problem.  To construct the GD::Image using the colormap
and pixelmap returned by the UCSC C code,
Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:

  my $im = GD::Image->new($width, $height);
  $im->transparent( <UCSC colormap's white index> );

... loop on UCSC colormap calls $im->colorAllocate(),
    ** hoping that calling $im->colorAllocate() in the same order
       results in same colormap indices

... loop on UCSC pixelmap calls $im->setPixel()

** Here is where something could go wrong.  It looks like I should
call $im->transparent *after* the call to $im->colorAllocate() for
white, making sure that I pass $im's actual white index to
$im->transparent.  However, when I call transparent after
colorAllocate, the white pixels are shaded light gray instead of being
transparent, even in the default display.  Calling $im->transparent
first was just a hack that worked, and then I forgot about it.  I will
try updating GD too, to see if that makes any difference.

FWIW I am constructing the GD::Image one color and pixel at a time
because when I used GD::Image->newFromGdData(), the image was created
OK but when I returned the new $im from a sub{}, perl crashed with a
'glibc detected double free or corruption'.  Does that ring a bell for
anybody?  

Angie

On Fri, 29 May 2009, Todd W. Harris wrote:

> Mark -
>
> Try upgrading your GD::SVG to the most current version on CPAN.
>
> Todd
>
>
> On May 29, 2009, at 9:42 AM, mark meyer wrote:
>
> > We use the GD::SVG and was never able to get the inkscape (pdf generation)
> > operational, if that helps any.
> >
> > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...> wrote:
> > Hi all,
> >
> > Could this be a bad interaction between the plug in and GD::SVG or
> > inkscape (depending on what sort of hi res image you are getting)?
> > For example, I think that GD::SVG has a hard time with alpha channels.
> >
> > Scott
> >
> >
> > On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...>
> > wrote:
> > > Hi Angie,
> > >
> > > Bill is out of the office today, but I can try to answer your questions.
> > > Attached are the two screen shots, one is what the plugin looks like in
> > > the
> > > gbrowse, just fine as it looks in UCSC.  The second is what happens when
> > > you
> > > click on high-res image.
> > >
> > > We are running gbrowse v1.69.  The plugin code was implemented and
> > > downloaded about 1 month ago, just recently ran into this issue since we
> > > are
> > > trying to make some publication figures from our Gbrowse data.
> > >
> > > I can access conf files, etc. if you need to see them and try to do my
> > > best
> > > to answer questions, but I may not be able to answer very detailed
> > > questions
> > > in Bill's absence since he has been the one configuring this.
> > >
> > > Thanks for checking into this for us,
> > >
> > > Mark
> > >
> > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...>
> > > wrote:
> > > >
> > > > Dave - yes, that sounds likely.
> > > >
> > > > Bill, what version of GBrowse are you running?  How recently did you
> > > > grab the plugin code?  I didn't get the screenshot attachment so if
> > > > you wouldn't mind sending that to me, that would be helpful.  If your
> > > > GBrowse is on a public server, can you send the URL?
> > > >
> > > > Angie
> > > >
> > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > >
> > > > > Hi Bill,
> > > > >
> > > > > I have no particular insight on why this is happening.  My guess is
> > > > > that it is due some obscure interaction between the UCSC plugin and
> > > > > core GBrowse, but I don't actually know.
> > > > >
> > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > >
> > > > > Dave C.
> > > > >
> > > > >
> > > > >
> > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
> > > > > > Hi All,
> > > > > > I am attempting to view high-res images of conservation tracks but
> > > > the
> > > > > > background of these tracks in high-res is blue. This isn't the case
> > > > > > when
> > > > > > these tracks are displayed in gbrowse normally, it only happens when
> > > > > > viewed
> > > > > > as high-res. Also all the non-conservation tracks are fine in high
> > > > > > res. Is
> > > > > > there any reason why outputting these images in high-res would do
> > > > > > this? Has
> > > > > > anyone encountered other tracks doing this in high-res? Any insight
> > > > > > would be
> > > > > > appreciated. I have attached an example image of the track below.
> > > > > >
> > > > > > Thanks,
> > > > > > Bill
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > Was this helpful?  Let us know at
> > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > >
> > > > > Learn more about GMOD at:
> > > > >   SMBE:
> > > > > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
> > > > >   AGA Next Gen Seq in Non-Models:
> > > > > http://www.regonline.com/Nextgeneration
> > > > >
> > > >
> > > >
> > > >
> > > > ------------------------------------------------------------------------------
> > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > > > is a gathering of tech-side developers & brand creativity professionals.
> > > > Meet
> > > > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > Barbarian
> > > > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > > > _______________________________________________
> > > > Gmod-gbrowse mailing list
> > > > Gmod-gbrowse@...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> > >
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot
> > net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> > ------------------------------------------------------------------------------
> > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > is a gathering of tech-side developers & brand creativity professionals.
> > Meet
> > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse@...
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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[Lincoln Stein]

Angie, is there any reason to call transparent()? The other tracks render their background in a solid color.

Lincoln

On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...> wrote:

Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
be out of sync ($i --> $index)!" ?

Wherever the bad interaction is taking place, it is definitely an
alpha-channel problem.  To construct the GD::Image using the colormap
and pixelmap returned by the UCSC C code,
Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:

 my $im = GD::Image->new($width, $height);
 $im->transparent( <UCSC colormap's white index> );

... loop on UCSC colormap calls $im->colorAllocate(),
   ** hoping that calling $im->colorAllocate() in the same order
      results in same colormap indices

... loop on UCSC pixelmap calls $im->setPixel()

** Here is where something could go wrong.  It looks like I should
call $im->transparent *after* the call to $im->colorAllocate() for
white, making sure that I pass $im's actual white index to
$im->transparent.  However, when I call transparent after
colorAllocate, the white pixels are shaded light gray instead of being
transparent, even in the default display.  Calling $im->transparent
first was just a hack that worked, and then I forgot about it.  I will
try updating GD too, to see if that makes any difference.

FWIW I am constructing the GD::Image one color and pixel at a time
because when I used GD::Image->newFromGdData(), the image was created
OK but when I returned the new $im from a sub{}, perl crashed with a
'glibc detected double free or corruption'.  Does that ring a bell for
anybody?

Angie

On Fri, 29 May 2009, Todd W. Harris wrote:

> Mark -
>
> Try upgrading your GD::SVG to the most current version on CPAN.
>
> Todd
>
>
> On May 29, 2009, at 9:42 AM, mark meyer wrote:
>
> > We use the GD::SVG and was never able to get the inkscape (pdf generation)
> > operational, if that helps any.
> >
> > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...> wrote:
> > Hi all,
> >
> > Could this be a bad interaction between the plug in and GD::SVG or
> > inkscape (depending on what sort of hi res image you are getting)?
> > For example, I think that GD::SVG has a hard time with alpha channels.
> >
> > Scott
> >
> >
> > On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...>
> > wrote:
> > > Hi Angie,
> > >
> > > Bill is out of the office today, but I can try to answer your questions.
> > > Attached are the two screen shots, one is what the plugin looks like in
> > > the
> > > gbrowse, just fine as it looks in UCSC.  The second is what happens when
> > > you
> > > click on high-res image.
> > >
> > > We are running gbrowse v1.69.  The plugin code was implemented and
> > > downloaded about 1 month ago, just recently ran into this issue since we
> > > are
> > > trying to make some publication figures from our Gbrowse data.
> > >
> > > I can access conf files, etc. if you need to see them and try to do my
> > > best
> > > to answer questions, but I may not be able to answer very detailed
> > > questions
> > > in Bill's absence since he has been the one configuring this.
> > >
> > > Thanks for checking into this for us,
> > >
> > > Mark
> > >
> > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...>
> > > wrote:
> > > >
> > > > Dave - yes, that sounds likely.
> > > >
> > > > Bill, what version of GBrowse are you running?  How recently did you
> > > > grab the plugin code?  I didn't get the screenshot attachment so if
> > > > you wouldn't mind sending that to me, that would be helpful.  If your
> > > > GBrowse is on a public server, can you send the URL?
> > > >
> > > > Angie
> > > >
> > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > >
> > > > > Hi Bill,
> > > > >
> > > > > I have no particular insight on why this is happening.  My guess is
> > > > > that it is due some obscure interaction between the UCSC plugin and
> > > > > core GBrowse, but I don't actually know.
> > > > >
> > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > >
> > > > > Dave C.
> > > > >
> > > > >
> > > > >
> > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...> wrote:
> > > > > > Hi All,
> > > > > > I am attempting to view high-res images of conservation tracks but
> > > > the
> > > > > > background of these tracks in high-res is blue. This isn't the case
> > > > > > when
> > > > > > these tracks are displayed in gbrowse normally, it only happens when
> > > > > > viewed
> > > > > > as high-res. Also all the non-conservation tracks are fine in high
> > > > > > res. Is
> > > > > > there any reason why outputting these images in high-res would do
> > > > > > this? Has
> > > > > > anyone encountered other tracks doing this in high-res? Any insight
> > > > > > would be
> > > > > > appreciated. I have attached an example image of the track below.
> > > > > >
> > > > > > Thanks,
> > > > > > Bill
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > Was this helpful?  Let us know at
> > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > >
> > > > > Learn more about GMOD at:
> > > > >   SMBE:
> > > > > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > >   Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
> > > > >   AGA Next Gen Seq in Non-Models:
> > > > > http://www.regonline.com/Nextgeneration
> > > > >
> > > >
> > > >
> > > >
> > > > ------------------------------------------------------------------------------
> > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > > > is a gathering of tech-side developers & brand creativity professionals.
> > > > Meet
> > > > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > Barbarian
> > > > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > > > _______________________________________________
> > > > Gmod-gbrowse mailing list
> > > > Gmod-gbrowse@...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> > >
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot
> > net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> > ------------------------------------------------------------------------------
> > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > is a gathering of tech-side developers & brand creativity professionals.
> > Meet
> > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > _______________________________________________
> > 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@...>

------------------------------------------------------------------------------
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is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
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[Angie Hinrichs]

> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.

In a nutshell, to avoid hiding the vertical light blue ruler lines in
the background by drawing white on top of them.  

Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
an image with a white background (from UCSC C code by way of
UcscConservation plugin), creates a GD::Image $im as described below
and uses $gd->copy to plop that on top of the GBrowse image:

  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);

-- so it bypasses all of the usual glyph draw() infrastructure, and
renders the entire allocated space in the main image.  Using
transparency preserves the light blue lines and whatever else might be
in the background... is it not worth the trouble?  Is there a better
way?

Thanks,
Angie

On Fri, 29 May 2009, Lincoln Stein wrote:

> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.
>
> Lincoln
>
> On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...> wrote:
>
> > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > be out of sync ($i --> $index)!" ?
> >
> > Wherever the bad interaction is taking place, it is definitely an
> > alpha-channel problem.  To construct the GD::Image using the colormap
> > and pixelmap returned by the UCSC C code,
> > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> >
> >  my $im = GD::Image->new($width, $height);
> >  $im->transparent( <UCSC colormap's white index> );
> >
> > ... loop on UCSC colormap calls $im->colorAllocate(),
> >    ** hoping that calling $im->colorAllocate() in the same order
> >       results in same colormap indices
> >
> > ... loop on UCSC pixelmap calls $im->setPixel()
> >
> > ** Here is where something could go wrong.  It looks like I should
> > call $im->transparent *after* the call to $im->colorAllocate() for
> > white, making sure that I pass $im's actual white index to
> > $im->transparent.  However, when I call transparent after
> > colorAllocate, the white pixels are shaded light gray instead of being
> > transparent, even in the default display.  Calling $im->transparent
> > first was just a hack that worked, and then I forgot about it.  I will
> > try updating GD too, to see if that makes any difference.
> >
> > FWIW I am constructing the GD::Image one color and pixel at a time
> > because when I used GD::Image->newFromGdData(), the image was created
> > OK but when I returned the new $im from a sub{}, perl crashed with a
> > 'glibc detected double free or corruption'.  Does that ring a bell for
> > anybody?
> >
> > Angie
> >
> > On Fri, 29 May 2009, Todd W. Harris wrote:
> >
> > > Mark -
> > >
> > > Try upgrading your GD::SVG to the most current version on CPAN.
> > >
> > > Todd
> > >
> > >
> > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > >
> > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > generation)
> > > > operational, if that helps any.
> > > >
> > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...>
> > wrote:
> > > > Hi all,
> > > >
> > > > Could this be a bad interaction between the plug in and GD::SVG or
> > > > inkscape (depending on what sort of hi res image you are getting)?
> > > > For example, I think that GD::SVG has a hard time with alpha channels.
> > > >
> > > > Scott
> > > >
> > > >
> > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...>
> > > > wrote:
> > > > > Hi Angie,
> > > > >
> > > > > Bill is out of the office today, but I can try to answer your
> > questions.
> > > > > Attached are the two screen shots, one is what the plugin looks like
> > in
> > > > > the
> > > > > gbrowse, just fine as it looks in UCSC.  The second is what happens
> > when
> > > > > you
> > > > > click on high-res image.
> > > > >
> > > > > We are running gbrowse v1.69.  The plugin code was implemented and
> > > > > downloaded about 1 month ago, just recently ran into this issue since
> > we
> > > > > are
> > > > > trying to make some publication figures from our Gbrowse data.
> > > > >
> > > > > I can access conf files, etc. if you need to see them and try to do
> > my
> > > > > best
> > > > > to answer questions, but I may not be able to answer very detailed
> > > > > questions
> > > > > in Bill's absence since he has been the one configuring this.
> > > > >
> > > > > Thanks for checking into this for us,
> > > > >
> > > > > Mark
> > > > >
> > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...>
> > > > > wrote:
> > > > > >
> > > > > > Dave - yes, that sounds likely.
> > > > > >
> > > > > > Bill, what version of GBrowse are you running?  How recently did
> > you
> > > > > > grab the plugin code?  I didn't get the screenshot attachment so if
> > > > > > you wouldn't mind sending that to me, that would be helpful.  If
> > your
> > > > > > GBrowse is on a public server, can you send the URL?
> > > > > >
> > > > > > Angie
> > > > > >
> > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > >
> > > > > > > Hi Bill,
> > > > > > >
> > > > > > > I have no particular insight on why this is happening.  My guess
> > is
> > > > > > > that it is due some obscure interaction between the UCSC plugin
> > and
> > > > > > > core GBrowse, but I don't actually know.
> > > > > > >
> > > > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > > > >
> > > > > > > Dave C.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...>
> > wrote:
> > > > > > > > Hi All,
> > > > > > > > I am attempting to view high-res images of conservation tracks
> > but
> > > > > > the
> > > > > > > > background of these tracks in high-res is blue. This isn't the
> > case
> > > > > > > > when
> > > > > > > > these tracks are displayed in gbrowse normally, it only happens
> > when
> > > > > > > > viewed
> > > > > > > > as high-res. Also all the non-conservation tracks are fine in
> > high
> > > > > > > > res. Is
> > > > > > > > there any reason why outputting these images in high-res would
> > do
> > > > > > > > this? Has
> > > > > > > > anyone encountered other tracks doing this in high-res? Any
> > insight
> > > > > > > > would be
> > > > > > > > appreciated. I have attached an example image of the track
> > below.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Bill
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > Was this helpful?  Let us know at
> > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > >
> > > > > > > Learn more about GMOD at:
> > > > > > >   SMBE:
> > > > > > >
> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > >   Arthropod Genomics:
> > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > ------------------------------------------------------------------------------
> > > > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC.
> > CaT
> > > > > > is a gathering of tech-side developers & brand creativity
> > professionals.
> > > > > > Meet
> > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > Processing, &
> > > > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > > > Barbarian
> > > > > > Group, R/GA, & Big Spaceship.
> > http://p.sf.net/sfu/creativitycat-com
> > > > > > _______________________________________________
> > > > > > Gmod-gbrowse mailing list
> > > > > > Gmod-gbrowse@...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
> > ------------------------------------------------------------------------
> > > > Scott Cain, Ph. D.                                   scott at scottcain
> > dot
> > > > net
> > > > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > > > Ontario Institute for Cancer Research
> > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > > > is a gathering of tech-side developers & brand creativity
> > professionals.
> > > > Meet
> > > > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > Barbarian
> > > > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > > > _______________________________________________
> > > > Gmod-gbrowse mailing list
> > > > Gmod-gbrowse@...
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > >
> >
>
>
>
>

------------------------------------------------------------------------------
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is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
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[Lincoln Stein]

Ok. I'll poke around in GD::SVG to see what might be the problem with this strategy. It ought to be ok.

Lincoln

On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...> wrote:

> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.

In a nutshell, to avoid hiding the vertical light blue ruler lines in
the background by drawing white on top of them.

Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
an image with a white background (from UCSC C code by way of
UcscConservation plugin), creates a GD::Image $im as described below
and uses $gd->copy to plop that on top of the GBrowse image:

 $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);

-- so it bypasses all of the usual glyph draw() infrastructure, and
renders the entire allocated space in the main image.  Using
transparency preserves the light blue lines and whatever else might be
in the background... is it not worth the trouble?  Is there a better
way?

Thanks,
Angie

On Fri, 29 May 2009, Lincoln Stein wrote:

> Angie, is there any reason to call transparent()? The other tracks render
> their background in a solid color.
>
> Lincoln
>
> On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...> wrote:
>
> > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > be out of sync ($i --> $index)!" ?
> >
> > Wherever the bad interaction is taking place, it is definitely an
> > alpha-channel problem.  To construct the GD::Image using the colormap
> > and pixelmap returned by the UCSC C code,
> > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> >
> >  my $im = GD::Image->new($width, $height);
> >  $im->transparent( <UCSC colormap's white index> );
> >
> > ... loop on UCSC colormap calls $im->colorAllocate(),
> >    ** hoping that calling $im->colorAllocate() in the same order
> >       results in same colormap indices
> >
> > ... loop on UCSC pixelmap calls $im->setPixel()
> >
> > ** Here is where something could go wrong.  It looks like I should
> > call $im->transparent *after* the call to $im->colorAllocate() for
> > white, making sure that I pass $im's actual white index to
> > $im->transparent.  However, when I call transparent after
> > colorAllocate, the white pixels are shaded light gray instead of being
> > transparent, even in the default display.  Calling $im->transparent
> > first was just a hack that worked, and then I forgot about it.  I will
> > try updating GD too, to see if that makes any difference.
> >
> > FWIW I am constructing the GD::Image one color and pixel at a time
> > because when I used GD::Image->newFromGdData(), the image was created
> > OK but when I returned the new $im from a sub{}, perl crashed with a
> > 'glibc detected double free or corruption'.  Does that ring a bell for
> > anybody?
> >
> > Angie
> >
> > On Fri, 29 May 2009, Todd W. Harris wrote:
> >
> > > Mark -
> > >
> > > Try upgrading your GD::SVG to the most current version on CPAN.
> > >
> > > Todd
> > >
> > >
> > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > >
> > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > generation)
> > > > operational, if that helps any.
> > > >
> > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...>
> > wrote:
> > > > Hi all,
> > > >
> > > > Could this be a bad interaction between the plug in and GD::SVG or
> > > > inkscape (depending on what sort of hi res image you are getting)?
> > > > For example, I think that GD::SVG has a hard time with alpha channels.
> > > >
> > > > Scott
> > > >
> > > >
> > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <mmeyerposting@...>
> > > > wrote:
> > > > > Hi Angie,
> > > > >
> > > > > Bill is out of the office today, but I can try to answer your
> > questions.
> > > > > Attached are the two screen shots, one is what the plugin looks like
> > in
> > > > > the
> > > > > gbrowse, just fine as it looks in UCSC.  The second is what happens
> > when
> > > > > you
> > > > > click on high-res image.
> > > > >
> > > > > We are running gbrowse v1.69.  The plugin code was implemented and
> > > > > downloaded about 1 month ago, just recently ran into this issue since
> > we
> > > > > are
> > > > > trying to make some publication figures from our Gbrowse data.
> > > > >
> > > > > I can access conf files, etc. if you need to see them and try to do
> > my
> > > > > best
> > > > > to answer questions, but I may not be able to answer very detailed
> > > > > questions
> > > > > in Bill's absence since he has been the one configuring this.
> > > > >
> > > > > Thanks for checking into this for us,
> > > > >
> > > > > Mark
> > > > >
> > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <angie@...>
> > > > > wrote:
> > > > > >
> > > > > > Dave - yes, that sounds likely.
> > > > > >
> > > > > > Bill, what version of GBrowse are you running?  How recently did
> > you
> > > > > > grab the plugin code?  I didn't get the screenshot attachment so if
> > > > > > you wouldn't mind sending that to me, that would be helpful.  If
> > your
> > > > > > GBrowse is on a public server, can you send the URL?
> > > > > >
> > > > > > Angie
> > > > > >
> > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > >
> > > > > > > Hi Bill,
> > > > > > >
> > > > > > > I have no particular insight on why this is happening.  My guess
> > is
> > > > > > > that it is due some obscure interaction between the UCSC plugin
> > and
> > > > > > > core GBrowse, but I don't actually know.
> > > > > > >
> > > > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > > > >
> > > > > > > Dave C.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <wpulec@...>
> > wrote:
> > > > > > > > Hi All,
> > > > > > > > I am attempting to view high-res images of conservation tracks
> > but
> > > > > > the
> > > > > > > > background of these tracks in high-res is blue. This isn't the
> > case
> > > > > > > > when
> > > > > > > > these tracks are displayed in gbrowse normally, it only happens
> > when
> > > > > > > > viewed
> > > > > > > > as high-res. Also all the non-conservation tracks are fine in
> > high
> > > > > > > > res. Is
> > > > > > > > there any reason why outputting these images in high-res would
> > do
> > > > > > > > this? Has
> > > > > > > > anyone encountered other tracks doing this in high-res? Any
> > insight
> > > > > > > > would be
> > > > > > > > appreciated. I have attached an example image of the track
> > below.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Bill
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > > Was this helpful?  Let us know at
> > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > >
> > > > > > > Learn more about GMOD at:
> > > > > > >   SMBE:
> > > > > > >
> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > >   Arthropod Genomics:
> > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > ------------------------------------------------------------------------------
> > > > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC.
> > CaT
> > > > > > is a gathering of tech-side developers & brand creativity
> > professionals.
> > > > > > Meet
> > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > Processing, &
> > > > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > > > Barbarian
> > > > > > Group, R/GA, & Big Spaceship.
> > http://p.sf.net/sfu/creativitycat-com
> > > > > > _______________________________________________
> > > > > > Gmod-gbrowse mailing list
> > > > > > Gmod-gbrowse@...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
> > ------------------------------------------------------------------------
> > > > Scott Cain, Ph. D.                                   scott at scottcain
> > dot
> > > > net
> > > > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > > > Ontario Institute for Cancer Research
> > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> > > > is a gathering of tech-side developers & brand creativity
> > professionals.
> > > > Meet
> > > > the minds behind Google Creative Lab, Visual Complexity, Processing, &
> > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > Barbarian
> > > > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> > > > _______________________________________________
> > > > 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@...>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
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Gmod-gbrowse@...
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[Angie Hinrichs]

I took a look at the latest C source code for gdImageCopy()
(http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup)
and it looks like since gd version 2.0.10, if a pixel is transparent
in the source, it is not copied to the destination.  I can see how
that might interact badly when copying into something other than
another pixellated image.

Is there a hook in GBrowse by which a plugin or glyph can tell that it
is in high-res mode, so it can avoid using transparency?

Thanks,
Angie

On Fri, 29 May 2009, Lincoln Stein wrote:

> Ok. I'll poke around in GD::SVG to see what might be the problem with this
> strategy. It ought to be ok.
>
> Lincoln
>
> On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...> wrote:
>
> > > Angie, is there any reason to call transparent()? The other tracks render
> > > their background in a solid color.
> >
> > In a nutshell, to avoid hiding the vertical light blue ruler lines in
> > the background by drawing white on top of them.
> >
> > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
> > an image with a white background (from UCSC C code by way of
> > UcscConservation plugin), creates a GD::Image $im as described below
> > and uses $gd->copy to plop that on top of the GBrowse image:
> >
> >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> >
> > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > renders the entire allocated space in the main image.  Using
> > transparency preserves the light blue lines and whatever else might be
> > in the background... is it not worth the trouble?  Is there a better
> > way?
> >
> > Thanks,
> > Angie
> >
> > On Fri, 29 May 2009, Lincoln Stein wrote:
> >
> > > Angie, is there any reason to call transparent()? The other tracks render
> > > their background in a solid color.
> > >
> > > Lincoln
> > >
> > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...>
> > wrote:
> > >
> > > > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > > > be out of sync ($i --> $index)!" ?
> > > >
> > > > Wherever the bad interaction is taking place, it is definitely an
> > > > alpha-channel problem.  To construct the GD::Image using the colormap
> > > > and pixelmap returned by the UCSC C code,
> > > > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> > > >
> > > >  my $im = GD::Image->new($width, $height);
> > > >  $im->transparent( <UCSC colormap's white index> );
> > > >
> > > > ... loop on UCSC colormap calls $im->colorAllocate(),
> > > >    ** hoping that calling $im->colorAllocate() in the same order
> > > >       results in same colormap indices
> > > >
> > > > ... loop on UCSC pixelmap calls $im->setPixel()
> > > >
> > > > ** Here is where something could go wrong.  It looks like I should
> > > > call $im->transparent *after* the call to $im->colorAllocate() for
> > > > white, making sure that I pass $im's actual white index to
> > > > $im->transparent.  However, when I call transparent after
> > > > colorAllocate, the white pixels are shaded light gray instead of being
> > > > transparent, even in the default display.  Calling $im->transparent
> > > > first was just a hack that worked, and then I forgot about it.  I will
> > > > try updating GD too, to see if that makes any difference.
> > > >
> > > > FWIW I am constructing the GD::Image one color and pixel at a time
> > > > because when I used GD::Image->newFromGdData(), the image was created
> > > > OK but when I returned the new $im from a sub{}, perl crashed with a
> > > > 'glibc detected double free or corruption'.  Does that ring a bell for
> > > > anybody?
> > > >
> > > > Angie
> > > >
> > > > On Fri, 29 May 2009, Todd W. Harris wrote:
> > > >
> > > > > Mark -
> > > > >
> > > > > Try upgrading your GD::SVG to the most current version on CPAN.
> > > > >
> > > > > Todd
> > > > >
> > > > >
> > > > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > > > >
> > > > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > > > generation)
> > > > > > operational, if that helps any.
> > > > > >
> > > > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...>
> > > > wrote:
> > > > > > Hi all,
> > > > > >
> > > > > > Could this be a bad interaction between the plug in and GD::SVG or
> > > > > > inkscape (depending on what sort of hi res image you are getting)?
> > > > > > For example, I think that GD::SVG has a hard time with alpha
> > channels.
> > > > > >
> > > > > > Scott
> > > > > >
> > > > > >
> > > > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <
> > mmeyerposting@...>
> > > > > > wrote:
> > > > > > > Hi Angie,
> > > > > > >
> > > > > > > Bill is out of the office today, but I can try to answer your
> > > > questions.
> > > > > > > Attached are the two screen shots, one is what the plugin looks
> > like
> > > > in
> > > > > > > the
> > > > > > > gbrowse, just fine as it looks in UCSC.  The second is what
> > happens
> > > > when
> > > > > > > you
> > > > > > > click on high-res image.
> > > > > > >
> > > > > > > We are running gbrowse v1.69.  The plugin code was implemented
> > and
> > > > > > > downloaded about 1 month ago, just recently ran into this issue
> > since
> > > > we
> > > > > > > are
> > > > > > > trying to make some publication figures from our Gbrowse data.
> > > > > > >
> > > > > > > I can access conf files, etc. if you need to see them and try to
> > do
> > > > my
> > > > > > > best
> > > > > > > to answer questions, but I may not be able to answer very
> > detailed
> > > > > > > questions
> > > > > > > in Bill's absence since he has been the one configuring this.
> > > > > > >
> > > > > > > Thanks for checking into this for us,
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <
> > angie@...>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > Dave - yes, that sounds likely.
> > > > > > > >
> > > > > > > > Bill, what version of GBrowse are you running?  How recently
> > did
> > > > you
> > > > > > > > grab the plugin code?  I didn't get the screenshot attachment
> > so if
> > > > > > > > you wouldn't mind sending that to me, that would be helpful.
> >  If
> > > > your
> > > > > > > > GBrowse is on a public server, can you send the URL?
> > > > > > > >
> > > > > > > > Angie
> > > > > > > >
> > > > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > > > >
> > > > > > > > > Hi Bill,
> > > > > > > > >
> > > > > > > > > I have no particular insight on why this is happening.  My
> > guess
> > > > is
> > > > > > > > > that it is due some obscure interaction between the UCSC
> > plugin
> > > > and
> > > > > > > > > core GBrowse, but I don't actually know.
> > > > > > > > >
> > > > > > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > > > > > >
> > > > > > > > > Dave C.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <
> > wpulec@...>
> > > > wrote:
> > > > > > > > > > Hi All,
> > > > > > > > > > I am attempting to view high-res images of conservation
> > tracks
> > > > but
> > > > > > > > the
> > > > > > > > > > background of these tracks in high-res is blue. This isn't
> > the
> > > > case
> > > > > > > > > > when
> > > > > > > > > > these tracks are displayed in gbrowse normally, it only
> > happens
> > > > when
> > > > > > > > > > viewed
> > > > > > > > > > as high-res. Also all the non-conservation tracks are fine
> > in
> > > > high
> > > > > > > > > > res. Is
> > > > > > > > > > there any reason why outputting these images in high-res
> > would
> > > > do
> > > > > > > > > > this? Has
> > > > > > > > > > anyone encountered other tracks doing this in high-res? Any
> > > > insight
> > > > > > > > > > would be
> > > > > > > > > > appreciated. I have attached an example image of the track
> > > > below.
> > > > > > > > > >
> > > > > > > > > > Thanks,
> > > > > > > > > > Bill
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > Was this helpful?  Let us know at
> > > > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > > > >
> > > > > > > > > Learn more about GMOD at:
> > > > > > > > >   SMBE:
> > > > > > > > >
> > > > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > > > >   Arthropod Genomics:
> > > > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > NYC.
> > > > CaT
> > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > professionals.
> > > > > > > > Meet
> > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > Processing, &
> > > > > > > > iPhoneDevCamp as they present alongside digital heavyweights
> > like
> > > > > > > > Barbarian
> > > > > > > > Group, R/GA, & Big Spaceship.
> > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > _______________________________________________
> > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > Gmod-gbrowse@...
> > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > Scott Cain, Ph. D.                                   scott at
> > scottcain
> > > > dot
> > > > > > net
> > > > > > GMOD Coordinator (http://gmod.org/)
> > 216-392-3087
> > > > > > Ontario Institute for Cancer Research
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC.
> > CaT
> > > > > > is a gathering of tech-side developers & brand creativity
> > > > professionals.
> > > > > > Meet
> > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > Processing, &
> > > > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > Barbarian
> > > > > > Group, R/GA, & Big Spaceship.
> > http://p.sf.net/sfu/creativitycat-com
> > > > > > _______________________________________________
> > > > > > Gmod-gbrowse mailing list
> > > > > > Gmod-gbrowse@...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > >
> > > >
> > >
> > >
> > >
> > >
> >
>
>
>
>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
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[Lincoln Stein]

Hi Angie,

Try this: if ($gd->isa('GD::SVG')) { # in high res mode }

Lincoln

On Mon, Jun 1, 2009 at 12:57 PM, Angie Hinrichs <angie@...> wrote:

I took a look at the latest C source code for gdImageCopy()
(http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup)
and it looks like since gd version 2.0.10, if a pixel is transparent
in the source, it is not copied to the destination.  I can see how
that might interact badly when copying into something other than
another pixellated image.

Is there a hook in GBrowse by which a plugin or glyph can tell that it
is in high-res mode, so it can avoid using transparency?

Thanks,
Angie

On Fri, 29 May 2009, Lincoln Stein wrote:

> Ok. I'll poke around in GD::SVG to see what might be the problem with this
> strategy. It ought to be ok.
>
> Lincoln
>
> On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...> wrote:
>
> > > Angie, is there any reason to call transparent()? The other tracks render
> > > their background in a solid color.
> >
> > In a nutshell, to avoid hiding the vertical light blue ruler lines in
> > the background by drawing white on top of them.
> >
> > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
> > an image with a white background (from UCSC C code by way of
> > UcscConservation plugin), creates a GD::Image $im as described below
> > and uses $gd->copy to plop that on top of the GBrowse image:
> >
> >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> >
> > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > renders the entire allocated space in the main image.  Using
> > transparency preserves the light blue lines and whatever else might be
> > in the background... is it not worth the trouble?  Is there a better
> > way?
> >
> > Thanks,
> > Angie
> >
> > On Fri, 29 May 2009, Lincoln Stein wrote:
> >
> > > Angie, is there any reason to call transparent()? The other tracks render
> > > their background in a solid color.
> > >
> > > Lincoln
> > >
> > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...>
> > wrote:
> > >
> > > > Mark, Do you see any error_log warnings like "ucsc_glyph: colors will
> > > > be out of sync ($i --> $index)!" ?
> > > >
> > > > Wherever the bad interaction is taking place, it is definitely an
> > > > alpha-channel problem.  To construct the GD::Image using the colormap
> > > > and pixelmap returned by the UCSC C code,
> > > > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> > > >
> > > >  my $im = GD::Image->new($width, $height);
> > > >  $im->transparent( <UCSC colormap's white index> );
> > > >
> > > > ... loop on UCSC colormap calls $im->colorAllocate(),
> > > >    ** hoping that calling $im->colorAllocate() in the same order
> > > >       results in same colormap indices
> > > >
> > > > ... loop on UCSC pixelmap calls $im->setPixel()
> > > >
> > > > ** Here is where something could go wrong.  It looks like I should
> > > > call $im->transparent *after* the call to $im->colorAllocate() for
> > > > white, making sure that I pass $im's actual white index to
> > > > $im->transparent.  However, when I call transparent after
> > > > colorAllocate, the white pixels are shaded light gray instead of being
> > > > transparent, even in the default display.  Calling $im->transparent
> > > > first was just a hack that worked, and then I forgot about it.  I will
> > > > try updating GD too, to see if that makes any difference.
> > > >
> > > > FWIW I am constructing the GD::Image one color and pixel at a time
> > > > because when I used GD::Image->newFromGdData(), the image was created
> > > > OK but when I returned the new $im from a sub{}, perl crashed with a
> > > > 'glibc detected double free or corruption'.  Does that ring a bell for
> > > > anybody?
> > > >
> > > > Angie
> > > >
> > > > On Fri, 29 May 2009, Todd W. Harris wrote:
> > > >
> > > > > Mark -
> > > > >
> > > > > Try upgrading your GD::SVG to the most current version on CPAN.
> > > > >
> > > > > Todd
> > > > >
> > > > >
> > > > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > > > >
> > > > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > > > generation)
> > > > > > operational, if that helps any.
> > > > > >
> > > > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <scott@...>
> > > > wrote:
> > > > > > Hi all,
> > > > > >
> > > > > > Could this be a bad interaction between the plug in and GD::SVG or
> > > > > > inkscape (depending on what sort of hi res image you are getting)?
> > > > > > For example, I think that GD::SVG has a hard time with alpha
> > channels.
> > > > > >
> > > > > > Scott
> > > > > >
> > > > > >
> > > > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <
> > mmeyerposting@...>
> > > > > > wrote:
> > > > > > > Hi Angie,
> > > > > > >
> > > > > > > Bill is out of the office today, but I can try to answer your
> > > > questions.
> > > > > > > Attached are the two screen shots, one is what the plugin looks
> > like
> > > > in
> > > > > > > the
> > > > > > > gbrowse, just fine as it looks in UCSC.  The second is what
> > happens
> > > > when
> > > > > > > you
> > > > > > > click on high-res image.
> > > > > > >
> > > > > > > We are running gbrowse v1.69.  The plugin code was implemented
> > and
> > > > > > > downloaded about 1 month ago, just recently ran into this issue
> > since
> > > > we
> > > > > > > are
> > > > > > > trying to make some publication figures from our Gbrowse data.
> > > > > > >
> > > > > > > I can access conf files, etc. if you need to see them and try to
> > do
> > > > my
> > > > > > > best
> > > > > > > to answer questions, but I may not be able to answer very
> > detailed
> > > > > > > questions
> > > > > > > in Bill's absence since he has been the one configuring this.
> > > > > > >
> > > > > > > Thanks for checking into this for us,
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <
> > angie@...>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > Dave - yes, that sounds likely.
> > > > > > > >
> > > > > > > > Bill, what version of GBrowse are you running?  How recently
> > did
> > > > you
> > > > > > > > grab the plugin code?  I didn't get the screenshot attachment
> > so if
> > > > > > > > you wouldn't mind sending that to me, that would be helpful.
> >  If
> > > > your
> > > > > > > > GBrowse is on a public server, can you send the URL?
> > > > > > > >
> > > > > > > > Angie
> > > > > > > >
> > > > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > > > >
> > > > > > > > > Hi Bill,
> > > > > > > > >
> > > > > > > > > I have no particular insight on why this is happening.  My
> > guess
> > > > is
> > > > > > > > > that it is due some obscure interaction between the UCSC
> > plugin
> > > > and
> > > > > > > > > core GBrowse, but I don't actually know.
> > > > > > > > >
> > > > > > > > > I've CC'd Angie at UCSC to see if she may have any insight.
> > > > > > > > >
> > > > > > > > > Dave C.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <
> > wpulec@...>
> > > > wrote:
> > > > > > > > > > Hi All,
> > > > > > > > > > I am attempting to view high-res images of conservation
> > tracks
> > > > but
> > > > > > > > the
> > > > > > > > > > background of these tracks in high-res is blue. This isn't
> > the
> > > > case
> > > > > > > > > > when
> > > > > > > > > > these tracks are displayed in gbrowse normally, it only
> > happens
> > > > when
> > > > > > > > > > viewed
> > > > > > > > > > as high-res. Also all the non-conservation tracks are fine
> > in
> > > > high
> > > > > > > > > > res. Is
> > > > > > > > > > there any reason why outputting these images in high-res
> > would
> > > > do
> > > > > > > > > > this? Has
> > > > > > > > > > anyone encountered other tracks doing this in high-res? Any
> > > > insight
> > > > > > > > > > would be
> > > > > > > > > > appreciated. I have attached an example image of the track
> > > > below.
> > > > > > > > > >
> > > > > > > > > > Thanks,
> > > > > > > > > > Bill
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > > Was this helpful?  Let us know at
> > > > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > > > >
> > > > > > > > > Learn more about GMOD at:
> > > > > > > > >   SMBE:
> > > > > > > > >
> > > > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > > > >   Arthropod Genomics:
> > > > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > NYC.
> > > > CaT
> > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > professionals.
> > > > > > > > Meet
> > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > Processing, &
> > > > > > > > iPhoneDevCamp as they present alongside digital heavyweights
> > like
> > > > > > > > Barbarian
> > > > > > > > Group, R/GA, & Big Spaceship.
> > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > _______________________________________________
> > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > Gmod-gbrowse@...
> > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > Scott Cain, Ph. D.                                   scott at
> > scottcain
> > > > dot
> > > > > > net
> > > > > > GMOD Coordinator (http://gmod.org/)
> > 216-392-3087
> > > > > > Ontario Institute for Cancer Research
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC.
> > CaT
> > > > > > is a gathering of tech-side developers & brand creativity
> > > > professionals.
> > > > > > Meet
> > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > Processing, &
> > > > > > iPhoneDevCamp as they present alongside digital heavyweights like
> > > > Barbarian
> > > > > > Group, R/GA, & Big Spaceship.
> > http://p.sf.net/sfu/creativitycat-com
> > > > > > _______________________________________________
> > > > > > 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@...>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
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[Angie Hinrichs]

Thanks!  I just checked that in to CVS -- the external repository
should be updated by noon Pacific time.  The light blue lines go away
but at least the track image doesn't disappear into dark blue.  :)

Angie

On Mon, 1 Jun 2009, Lincoln Stein wrote:

> Hi Angie,
>
> Try this: if ($gd->isa('GD::SVG')) { # in high res mode }
>
> Lincoln
>
> On Mon, Jun 1, 2009 at 12:57 PM, Angie Hinrichs <angie@...> wrote:
>
> > I took a look at the latest C source code for gdImageCopy()
> > (http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup
> > )
> > and it looks like since gd version 2.0.10, if a pixel is transparent
> > in the source, it is not copied to the destination.  I can see how
> > that might interact badly when copying into something other than
> > another pixellated image.
> >
> > Is there a hook in GBrowse by which a plugin or glyph can tell that it
> > is in high-res mode, so it can avoid using transparency?
> >
> > Thanks,
> > Angie
> >
> > On Fri, 29 May 2009, Lincoln Stein wrote:
> >
> > > Ok. I'll poke around in GD::SVG to see what might be the problem with
> > this
> > > strategy. It ought to be ok.
> > >
> > > Lincoln
> > >
> > > On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...>
> > wrote:
> > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > >
> > > > In a nutshell, to avoid hiding the vertical light blue ruler lines in
> > > > the background by drawing white on top of them.
> > > >
> > > > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
> > > > an image with a white background (from UCSC C code by way of
> > > > UcscConservation plugin), creates a GD::Image $im as described below
> > > > and uses $gd->copy to plop that on top of the GBrowse image:
> > > >
> > > >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> > > >
> > > > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > > > renders the entire allocated space in the main image.  Using
> > > > transparency preserves the light blue lines and whatever else might be
> > > > in the background... is it not worth the trouble?  Is there a better
> > > > way?
> > > >
> > > > Thanks,
> > > > Angie
> > > >
> > > > On Fri, 29 May 2009, Lincoln Stein wrote:
> > > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > > >
> > > > > Lincoln
> > > > >
> > > > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...>
> > > > wrote:
> > > > >
> > > > > > Mark, Do you see any error_log warnings like "ucsc_glyph: colors
> > will
> > > > > > be out of sync ($i --> $index)!" ?
> > > > > >
> > > > > > Wherever the bad interaction is taking place, it is definitely an
> > > > > > alpha-channel problem.  To construct the GD::Image using the
> > colormap
> > > > > > and pixelmap returned by the UCSC C code,
> > > > > > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> > > > > >
> > > > > >  my $im = GD::Image->new($width, $height);
> > > > > >  $im->transparent( <UCSC colormap's white index> );
> > > > > >
> > > > > > ... loop on UCSC colormap calls $im->colorAllocate(),
> > > > > >    ** hoping that calling $im->colorAllocate() in the same order
> > > > > >       results in same colormap indices
> > > > > >
> > > > > > ... loop on UCSC pixelmap calls $im->setPixel()
> > > > > >
> > > > > > ** Here is where something could go wrong.  It looks like I should
> > > > > > call $im->transparent *after* the call to $im->colorAllocate() for
> > > > > > white, making sure that I pass $im's actual white index to
> > > > > > $im->transparent.  However, when I call transparent after
> > > > > > colorAllocate, the white pixels are shaded light gray instead of
> > being
> > > > > > transparent, even in the default display.  Calling $im->transparent
> > > > > > first was just a hack that worked, and then I forgot about it.  I
> > will
> > > > > > try updating GD too, to see if that makes any difference.
> > > > > >
> > > > > > FWIW I am constructing the GD::Image one color and pixel at a time
> > > > > > because when I used GD::Image->newFromGdData(), the image was
> > created
> > > > > > OK but when I returned the new $im from a sub{}, perl crashed with
> > a
> > > > > > 'glibc detected double free or corruption'.  Does that ring a bell
> > for
> > > > > > anybody?
> > > > > >
> > > > > > Angie
> > > > > >
> > > > > > On Fri, 29 May 2009, Todd W. Harris wrote:
> > > > > >
> > > > > > > Mark -
> > > > > > >
> > > > > > > Try upgrading your GD::SVG to the most current version on CPAN.
> > > > > > >
> > > > > > > Todd
> > > > > > >
> > > > > > >
> > > > > > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > > > > > >
> > > > > > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > > > > > generation)
> > > > > > > > operational, if that helps any.
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <
> > scott@...>
> > > > > > wrote:
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > Could this be a bad interaction between the plug in and GD::SVG
> > or
> > > > > > > > inkscape (depending on what sort of hi res image you are
> > getting)?
> > > > > > > > For example, I think that GD::SVG has a hard time with alpha
> > > > channels.
> > > > > > > >
> > > > > > > > Scott
> > > > > > > >
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <
> > > > mmeyerposting@...>
> > > > > > > > wrote:
> > > > > > > > > Hi Angie,
> > > > > > > > >
> > > > > > > > > Bill is out of the office today, but I can try to answer your
> > > > > > questions.
> > > > > > > > > Attached are the two screen shots, one is what the plugin
> > looks
> > > > like
> > > > > > in
> > > > > > > > > the
> > > > > > > > > gbrowse, just fine as it looks in UCSC.  The second is what
> > > > happens
> > > > > > when
> > > > > > > > > you
> > > > > > > > > click on high-res image.
> > > > > > > > >
> > > > > > > > > We are running gbrowse v1.69.  The plugin code was
> > implemented
> > > > and
> > > > > > > > > downloaded about 1 month ago, just recently ran into this
> > issue
> > > > since
> > > > > > we
> > > > > > > > > are
> > > > > > > > > trying to make some publication figures from our Gbrowse
> > data.
> > > > > > > > >
> > > > > > > > > I can access conf files, etc. if you need to see them and try
> > to
> > > > do
> > > > > > my
> > > > > > > > > best
> > > > > > > > > to answer questions, but I may not be able to answer very
> > > > detailed
> > > > > > > > > questions
> > > > > > > > > in Bill's absence since he has been the one configuring this.
> > > > > > > > >
> > > > > > > > > Thanks for checking into this for us,
> > > > > > > > >
> > > > > > > > > Mark
> > > > > > > > >
> > > > > > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <
> > > > angie@...>
> > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > Dave - yes, that sounds likely.
> > > > > > > > > >
> > > > > > > > > > Bill, what version of GBrowse are you running?  How
> > recently
> > > > did
> > > > > > you
> > > > > > > > > > grab the plugin code?  I didn't get the screenshot
> > attachment
> > > > so if
> > > > > > > > > > you wouldn't mind sending that to me, that would be
> > helpful.
> > > >  If
> > > > > > your
> > > > > > > > > > GBrowse is on a public server, can you send the URL?
> > > > > > > > > >
> > > > > > > > > > Angie
> > > > > > > > > >
> > > > > > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Bill,
> > > > > > > > > > >
> > > > > > > > > > > I have no particular insight on why this is happening.
> >  My
> > > > guess
> > > > > > is
> > > > > > > > > > > that it is due some obscure interaction between the UCSC
> > > > plugin
> > > > > > and
> > > > > > > > > > > core GBrowse, but I don't actually know.
> > > > > > > > > > >
> > > > > > > > > > > I've CC'd Angie at UCSC to see if she may have any
> > insight.
> > > > > > > > > > >
> > > > > > > > > > > Dave C.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <
> > > > wpulec@...>
> > > > > > wrote:
> > > > > > > > > > > > Hi All,
> > > > > > > > > > > > I am attempting to view high-res images of conservation
> > > > tracks
> > > > > > but
> > > > > > > > > > the
> > > > > > > > > > > > background of these tracks in high-res is blue. This
> > isn't
> > > > the
> > > > > > case
> > > > > > > > > > > > when
> > > > > > > > > > > > these tracks are displayed in gbrowse normally, it only
> > > > happens
> > > > > > when
> > > > > > > > > > > > viewed
> > > > > > > > > > > > as high-res. Also all the non-conservation tracks are
> > fine
> > > > in
> > > > > > high
> > > > > > > > > > > > res. Is
> > > > > > > > > > > > there any reason why outputting these images in
> > high-res
> > > > would
> > > > > > do
> > > > > > > > > > > > this? Has
> > > > > > > > > > > > anyone encountered other tracks doing this in high-res?
> > Any
> > > > > > insight
> > > > > > > > > > > > would be
> > > > > > > > > > > > appreciated. I have attached an example image of the
> > track
> > > > > > below.
> > > > > > > > > > > >
> > > > > > > > > > > > Thanks,
> > > > > > > > > > > > Bill
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Was this helpful?  Let us know at
> > > > > > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > > > > > >
> > > > > > > > > > > Learn more about GMOD at:
> > > > > > > > > > >   SMBE:
> > > > > > > > > > >
> > > > > >
> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > > > > > >   Arthropod Genomics:
> > > > > > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > > > NYC.
> > > > > > CaT
> > > > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > > > Meet
> > > > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > > > Processing, &
> > > > > > > > > > iPhoneDevCamp as they present alongside digital
> > heavyweights
> > > > like
> > > > > > > > > > Barbarian
> > > > > > > > > > Group, R/GA, & Big Spaceship.
> > > > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > > > Gmod-gbrowse@...
> > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > > > Scott Cain, Ph. D.                                   scott at
> > > > scottcain
> > > > > > dot
> > > > > > > > net
> > > > > > > > GMOD Coordinator (http://gmod.org/)
> > > > 216-392-3087
> > > > > > > > Ontario Institute for Cancer Research
> > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > NYC.
> > > > CaT
> > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > Meet
> > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > Processing, &
> > > > > > > > iPhoneDevCamp as they present alongside digital heavyweights
> > like
> > > > > > Barbarian
> > > > > > > > Group, R/GA, & Big Spaceship.
> > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > _______________________________________________
> > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > Gmod-gbrowse@...
> > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> > >
> > >
> >
>
>
>
>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
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[Lincoln Stein]

That's good news.

Lincoln

On Mon, Jun 1, 2009 at 1:57 PM, Angie Hinrichs <angie@...> wrote:

Thanks!  I just checked that in to CVS -- the external repository
should be updated by noon Pacific time.  The light blue lines go away
but at least the track image doesn't disappear into dark blue.  :)

Angie

On Mon, 1 Jun 2009, Lincoln Stein wrote:

> Hi Angie,
>
> Try this: if ($gd->isa('GD::SVG')) { # in high res mode }
>
> Lincoln
>
> On Mon, Jun 1, 2009 at 12:57 PM, Angie Hinrichs <angie@...> wrote:
>
> > I took a look at the latest C source code for gdImageCopy()
> > (http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup
> > )
> > and it looks like since gd version 2.0.10, if a pixel is transparent
> > in the source, it is not copied to the destination.  I can see how
> > that might interact badly when copying into something other than
> > another pixellated image.
> >
> > Is there a hook in GBrowse by which a plugin or glyph can tell that it
> > is in high-res mode, so it can avoid using transparency?
> >
> > Thanks,
> > Angie
> >
> > On Fri, 29 May 2009, Lincoln Stein wrote:
> >
> > > Ok. I'll poke around in GD::SVG to see what might be the problem with
> > this
> > > strategy. It ought to be ok.
> > >
> > > Lincoln
> > >
> > > On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...>
> > wrote:
> > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > >
> > > > In a nutshell, to avoid hiding the vertical light blue ruler lines in
> > > > the background by drawing white on top of them.
> > > >
> > > > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
> > > > an image with a white background (from UCSC C code by way of
> > > > UcscConservation plugin), creates a GD::Image $im as described below
> > > > and uses $gd->copy to plop that on top of the GBrowse image:
> > > >
> > > >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> > > >
> > > > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > > > renders the entire allocated space in the main image.  Using
> > > > transparency preserves the light blue lines and whatever else might be
> > > > in the background... is it not worth the trouble?  Is there a better
> > > > way?
> > > >
> > > > Thanks,
> > > > Angie
> > > >
> > > > On Fri, 29 May 2009, Lincoln Stein wrote:
> > > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > > >
> > > > > Lincoln
> > > > >
> > > > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...>
> > > > wrote:
> > > > >
> > > > > > Mark, Do you see any error_log warnings like "ucsc_glyph: colors
> > will
> > > > > > be out of sync ($i --> $index)!" ?
> > > > > >
> > > > > > Wherever the bad interaction is taking place, it is definitely an
> > > > > > alpha-channel problem.  To construct the GD::Image using the
> > colormap
> > > > > > and pixelmap returned by the UCSC C code,
> > > > > > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> > > > > >
> > > > > >  my $im = GD::Image->new($width, $height);
> > > > > >  $im->transparent( <UCSC colormap's white index> );
> > > > > >
> > > > > > ... loop on UCSC colormap calls $im->colorAllocate(),
> > > > > >    ** hoping that calling $im->colorAllocate() in the same order
> > > > > >       results in same colormap indices
> > > > > >
> > > > > > ... loop on UCSC pixelmap calls $im->setPixel()
> > > > > >
> > > > > > ** Here is where something could go wrong.  It looks like I should
> > > > > > call $im->transparent *after* the call to $im->colorAllocate() for
> > > > > > white, making sure that I pass $im's actual white index to
> > > > > > $im->transparent.  However, when I call transparent after
> > > > > > colorAllocate, the white pixels are shaded light gray instead of
> > being
> > > > > > transparent, even in the default display.  Calling $im->transparent
> > > > > > first was just a hack that worked, and then I forgot about it.  I
> > will
> > > > > > try updating GD too, to see if that makes any difference.
> > > > > >
> > > > > > FWIW I am constructing the GD::Image one color and pixel at a time
> > > > > > because when I used GD::Image->newFromGdData(), the image was
> > created
> > > > > > OK but when I returned the new $im from a sub{}, perl crashed with
> > a
> > > > > > 'glibc detected double free or corruption'.  Does that ring a bell
> > for
> > > > > > anybody?
> > > > > >
> > > > > > Angie
> > > > > >
> > > > > > On Fri, 29 May 2009, Todd W. Harris wrote:
> > > > > >
> > > > > > > Mark -
> > > > > > >
> > > > > > > Try upgrading your GD::SVG to the most current version on CPAN.
> > > > > > >
> > > > > > > Todd
> > > > > > >
> > > > > > >
> > > > > > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > > > > > >
> > > > > > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > > > > > generation)
> > > > > > > > operational, if that helps any.
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <
> > scott@...>
> > > > > > wrote:
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > Could this be a bad interaction between the plug in and GD::SVG
> > or
> > > > > > > > inkscape (depending on what sort of hi res image you are
> > getting)?
> > > > > > > > For example, I think that GD::SVG has a hard time with alpha
> > > > channels.
> > > > > > > >
> > > > > > > > Scott
> > > > > > > >
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <
> > > > mmeyerposting@...>
> > > > > > > > wrote:
> > > > > > > > > Hi Angie,
> > > > > > > > >
> > > > > > > > > Bill is out of the office today, but I can try to answer your
> > > > > > questions.
> > > > > > > > > Attached are the two screen shots, one is what the plugin
> > looks
> > > > like
> > > > > > in
> > > > > > > > > the
> > > > > > > > > gbrowse, just fine as it looks in UCSC.  The second is what
> > > > happens
> > > > > > when
> > > > > > > > > you
> > > > > > > > > click on high-res image.
> > > > > > > > >
> > > > > > > > > We are running gbrowse v1.69.  The plugin code was
> > implemented
> > > > and
> > > > > > > > > downloaded about 1 month ago, just recently ran into this
> > issue
> > > > since
> > > > > > we
> > > > > > > > > are
> > > > > > > > > trying to make some publication figures from our Gbrowse
> > data.
> > > > > > > > >
> > > > > > > > > I can access conf files, etc. if you need to see them and try
> > to
> > > > do
> > > > > > my
> > > > > > > > > best
> > > > > > > > > to answer questions, but I may not be able to answer very
> > > > detailed
> > > > > > > > > questions
> > > > > > > > > in Bill's absence since he has been the one configuring this.
> > > > > > > > >
> > > > > > > > > Thanks for checking into this for us,
> > > > > > > > >
> > > > > > > > > Mark
> > > > > > > > >
> > > > > > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <
> > > > angie@...>
> > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > Dave - yes, that sounds likely.
> > > > > > > > > >
> > > > > > > > > > Bill, what version of GBrowse are you running?  How
> > recently
> > > > did
> > > > > > you
> > > > > > > > > > grab the plugin code?  I didn't get the screenshot
> > attachment
> > > > so if
> > > > > > > > > > you wouldn't mind sending that to me, that would be
> > helpful.
> > > >  If
> > > > > > your
> > > > > > > > > > GBrowse is on a public server, can you send the URL?
> > > > > > > > > >
> > > > > > > > > > Angie
> > > > > > > > > >
> > > > > > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Bill,
> > > > > > > > > > >
> > > > > > > > > > > I have no particular insight on why this is happening.
> >  My
> > > > guess
> > > > > > is
> > > > > > > > > > > that it is due some obscure interaction between the UCSC
> > > > plugin
> > > > > > and
> > > > > > > > > > > core GBrowse, but I don't actually know.
> > > > > > > > > > >
> > > > > > > > > > > I've CC'd Angie at UCSC to see if she may have any
> > insight.
> > > > > > > > > > >
> > > > > > > > > > > Dave C.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <
> > > > wpulec@...>
> > > > > > wrote:
> > > > > > > > > > > > Hi All,
> > > > > > > > > > > > I am attempting to view high-res images of conservation
> > > > tracks
> > > > > > but
> > > > > > > > > > the
> > > > > > > > > > > > background of these tracks in high-res is blue. This
> > isn't
> > > > the
> > > > > > case
> > > > > > > > > > > > when
> > > > > > > > > > > > these tracks are displayed in gbrowse normally, it only
> > > > happens
> > > > > > when
> > > > > > > > > > > > viewed
> > > > > > > > > > > > as high-res. Also all the non-conservation tracks are
> > fine
> > > > in
> > > > > > high
> > > > > > > > > > > > res. Is
> > > > > > > > > > > > there any reason why outputting these images in
> > high-res
> > > > would
> > > > > > do
> > > > > > > > > > > > this? Has
> > > > > > > > > > > > anyone encountered other tracks doing this in high-res?
> > Any
> > > > > > insight
> > > > > > > > > > > > would be
> > > > > > > > > > > > appreciated. I have attached an example image of the
> > track
> > > > > > below.
> > > > > > > > > > > >
> > > > > > > > > > > > Thanks,
> > > > > > > > > > > > Bill
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Was this helpful?  Let us know at
> > > > > > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > > > > > >
> > > > > > > > > > > Learn more about GMOD at:
> > > > > > > > > > >   SMBE:
> > > > > > > > > > >
> > > > > >
> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > > > > > >   Arthropod Genomics:
> > > > > > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > > > NYC.
> > > > > > CaT
> > > > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > > > Meet
> > > > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > > > Processing, &
> > > > > > > > > > iPhoneDevCamp as they present alongside digital
> > heavyweights
> > > > like
> > > > > > > > > > Barbarian
> > > > > > > > > > Group, R/GA, & Big Spaceship.
> > > > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > > > Gmod-gbrowse@...
> > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > > > Scott Cain, Ph. D.                                   scott at
> > > > scottcain
> > > > > > dot
> > > > > > > > net
> > > > > > > > GMOD Coordinator (http://gmod.org/)
> > > > 216-392-3087
> > > > > > > > Ontario Institute for Cancer Research
> > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > NYC.
> > > > CaT
> > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > Meet
> > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > Processing, &
> > > > > > > > iPhoneDevCamp as they present alongside digital heavyweights
> > like
> > > > > > Barbarian
> > > > > > > > Group, R/GA, & Big Spaceship.
> > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > _______________________________________________
> > > > > > > > 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@...>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Bill Pulec]

The new CVS checkout works!

Thanks a lot,
Bill

On Mon, Jun 1, 2009 at 12:59 PM, Lincoln Stein <lstein@...> wrote:

That's good news.

Lincoln

On Mon, Jun 1, 2009 at 1:57 PM, Angie Hinrichs <angie@...> wrote:

Thanks!  I just checked that in to CVS -- the external repository
should be updated by noon Pacific time.  The light blue lines go away
but at least the track image doesn't disappear into dark blue.  :)

Angie

On Mon, 1 Jun 2009, Lincoln Stein wrote:

> Hi Angie,
>
> Try this: if ($gd->isa('GD::SVG')) { # in high res mode }
>
> Lincoln
>
> On Mon, Jun 1, 2009 at 12:57 PM, Angie Hinrichs <angie@...> wrote:
>
> > I took a look at the latest C source code for gdImageCopy()
> > (http://cvs.php.net/viewvc.cgi/gd/libgd/src/gd.c?revision=1.83&view=markup
> > )
> > and it looks like since gd version 2.0.10, if a pixel is transparent
> > in the source, it is not copied to the destination.  I can see how
> > that might interact badly when copying into something other than
> > another pixellated image.
> >
> > Is there a hook in GBrowse by which a plugin or glyph can tell that it
> > is in high-res mode, so it can avoid using transparency?
> >
> > Thanks,
> > Angie
> >
> > On Fri, 29 May 2009, Lincoln Stein wrote:
> >
> > > Ok. I'll poke around in GD::SVG to see what might be the problem with
> > this
> > > strategy. It ought to be ok.
> > >
> > > Lincoln
> > >
> > > On Fri, May 29, 2009 at 5:18 PM, Angie Hinrichs <angie@...>
> > wrote:
> > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > >
> > > > In a nutshell, to avoid hiding the vertical light blue ruler lines in
> > > > the background by drawing white on top of them.
> > > >
> > > > Currently, ucsc_glyph::draw gets a colormap+pixelmap representation of
> > > > an image with a white background (from UCSC C code by way of
> > > > UcscConservation plugin), creates a GD::Image $im as described below
> > > > and uses $gd->copy to plop that on top of the GBrowse image:
> > > >
> > > >  $gd->copy($im, $x-$leftLabelWidth, $y, 0, 0, $width, $height);
> > > >
> > > > -- so it bypasses all of the usual glyph draw() infrastructure, and
> > > > renders the entire allocated space in the main image.  Using
> > > > transparency preserves the light blue lines and whatever else might be
> > > > in the background... is it not worth the trouble?  Is there a better
> > > > way?
> > > >
> > > > Thanks,
> > > > Angie
> > > >
> > > > On Fri, 29 May 2009, Lincoln Stein wrote:
> > > >
> > > > > Angie, is there any reason to call transparent()? The other tracks
> > render
> > > > > their background in a solid color.
> > > > >
> > > > > Lincoln
> > > > >
> > > > > On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <angie@...>
> > > > wrote:
> > > > >
> > > > > > Mark, Do you see any error_log warnings like "ucsc_glyph: colors
> > will
> > > > > > be out of sync ($i --> $index)!" ?
> > > > > >
> > > > > > Wherever the bad interaction is taking place, it is definitely an
> > > > > > alpha-channel problem.  To construct the GD::Image using the
> > colormap
> > > > > > and pixelmap returned by the UCSC C code,
> > > > > > Bio/Graphics/Glyph/ucsc_glyph.pm uses these calls:
> > > > > >
> > > > > >  my $im = GD::Image->new($width, $height);
> > > > > >  $im->transparent( <UCSC colormap's white index> );
> > > > > >
> > > > > > ... loop on UCSC colormap calls $im->colorAllocate(),
> > > > > >    ** hoping that calling $im->colorAllocate() in the same order
> > > > > >       results in same colormap indices
> > > > > >
> > > > > > ... loop on UCSC pixelmap calls $im->setPixel()
> > > > > >
> > > > > > ** Here is where something could go wrong.  It looks like I should
> > > > > > call $im->transparent *after* the call to $im->colorAllocate() for
> > > > > > white, making sure that I pass $im's actual white index to
> > > > > > $im->transparent.  However, when I call transparent after
> > > > > > colorAllocate, the white pixels are shaded light gray instead of
> > being
> > > > > > transparent, even in the default display.  Calling $im->transparent
> > > > > > first was just a hack that worked, and then I forgot about it.  I
> > will
> > > > > > try updating GD too, to see if that makes any difference.
> > > > > >
> > > > > > FWIW I am constructing the GD::Image one color and pixel at a time
> > > > > > because when I used GD::Image->newFromGdData(), the image was
> > created
> > > > > > OK but when I returned the new $im from a sub{}, perl crashed with
> > a
> > > > > > 'glibc detected double free or corruption'.  Does that ring a bell
> > for
> > > > > > anybody?
> > > > > >
> > > > > > Angie
> > > > > >
> > > > > > On Fri, 29 May 2009, Todd W. Harris wrote:
> > > > > >
> > > > > > > Mark -
> > > > > > >
> > > > > > > Try upgrading your GD::SVG to the most current version on CPAN.
> > > > > > >
> > > > > > > Todd
> > > > > > >
> > > > > > >
> > > > > > > On May 29, 2009, at 9:42 AM, mark meyer wrote:
> > > > > > >
> > > > > > > > We use the GD::SVG and was never able to get the inkscape (pdf
> > > > > > generation)
> > > > > > > > operational, if that helps any.
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <
> > scott@...>
> > > > > > wrote:
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > Could this be a bad interaction between the plug in and GD::SVG
> > or
> > > > > > > > inkscape (depending on what sort of hi res image you are
> > getting)?
> > > > > > > > For example, I think that GD::SVG has a hard time with alpha
> > > > channels.
> > > > > > > >
> > > > > > > > Scott
> > > > > > > >
> > > > > > > >
> > > > > > > > On Fri, May 29, 2009 at 10:31 AM, mark meyer <
> > > > mmeyerposting@...>
> > > > > > > > wrote:
> > > > > > > > > Hi Angie,
> > > > > > > > >
> > > > > > > > > Bill is out of the office today, but I can try to answer your
> > > > > > questions.
> > > > > > > > > Attached are the two screen shots, one is what the plugin
> > looks
> > > > like
> > > > > > in
> > > > > > > > > the
> > > > > > > > > gbrowse, just fine as it looks in UCSC.  The second is what
> > > > happens
> > > > > > when
> > > > > > > > > you
> > > > > > > > > click on high-res image.
> > > > > > > > >
> > > > > > > > > We are running gbrowse v1.69.  The plugin code was
> > implemented
> > > > and
> > > > > > > > > downloaded about 1 month ago, just recently ran into this
> > issue
> > > > since
> > > > > > we
> > > > > > > > > are
> > > > > > > > > trying to make some publication figures from our Gbrowse
> > data.
> > > > > > > > >
> > > > > > > > > I can access conf files, etc. if you need to see them and try
> > to
> > > > do
> > > > > > my
> > > > > > > > > best
> > > > > > > > > to answer questions, but I may not be able to answer very
> > > > detailed
> > > > > > > > > questions
> > > > > > > > > in Bill's absence since he has been the one configuring this.
> > > > > > > > >
> > > > > > > > > Thanks for checking into this for us,
> > > > > > > > >
> > > > > > > > > Mark
> > > > > > > > >
> > > > > > > > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <
> > > > angie@...>
> > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > Dave - yes, that sounds likely.
> > > > > > > > > >
> > > > > > > > > > Bill, what version of GBrowse are you running?  How
> > recently
> > > > did
> > > > > > you
> > > > > > > > > > grab the plugin code?  I didn't get the screenshot
> > attachment
> > > > so if
> > > > > > > > > > you wouldn't mind sending that to me, that would be
> > helpful.
> > > >  If
> > > > > > your
> > > > > > > > > > GBrowse is on a public server, can you send the URL?
> > > > > > > > > >
> > > > > > > > > > Angie
> > > > > > > > > >
> > > > > > > > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Bill,
> > > > > > > > > > >
> > > > > > > > > > > I have no particular insight on why this is happening.
> >  My
> > > > guess
> > > > > > is
> > > > > > > > > > > that it is due some obscure interaction between the UCSC
> > > > plugin
> > > > > > and
> > > > > > > > > > > core GBrowse, but I don't actually know.
> > > > > > > > > > >
> > > > > > > > > > > I've CC'd Angie at UCSC to see if she may have any
> > insight.
> > > > > > > > > > >
> > > > > > > > > > > Dave C.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <
> > > > wpulec@...>
> > > > > > wrote:
> > > > > > > > > > > > Hi All,
> > > > > > > > > > > > I am attempting to view high-res images of conservation
> > > > tracks
> > > > > > but
> > > > > > > > > > the
> > > > > > > > > > > > background of these tracks in high-res is blue. This
> > isn't
> > > > the
> > > > > > case
> > > > > > > > > > > > when
> > > > > > > > > > > > these tracks are displayed in gbrowse normally, it only
> > > > happens
> > > > > > when
> > > > > > > > > > > > viewed
> > > > > > > > > > > > as high-res. Also all the non-conservation tracks are
> > fine
> > > > in
> > > > > > high
> > > > > > > > > > > > res. Is
> > > > > > > > > > > > there any reason why outputting these images in
> > high-res
> > > > would
> > > > > > do
> > > > > > > > > > > > this? Has
> > > > > > > > > > > > anyone encountered other tracks doing this in high-res?
> > Any
> > > > > > insight
> > > > > > > > > > > > would be
> > > > > > > > > > > > appreciated. I have attached an example image of the
> > track
> > > > > > below.
> > > > > > > > > > > >
> > > > > > > > > > > > Thanks,
> > > > > > > > > > > > Bill
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Was this helpful?  Let us know at
> > > > > > > > > > > http://gmod.org/wiki/Help_Desk_Feedback
> > > > > > > > > > >
> > > > > > > > > > > Learn more about GMOD at:
> > > > > > > > > > >   SMBE:
> > > > > > > > > > >
> > > > > >
> > http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > > > > > > > > > >   Arthropod Genomics:
> > > > > > http://www.k-state.edu/agc/symp2009/seminar.html
> > > > > > > > > > >   AGA Next Gen Seq in Non-Models:
> > > > > > > > > > > http://www.regonline.com/Nextgeneration
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > > > NYC.
> > > > > > CaT
> > > > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > > > Meet
> > > > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > > > Processing, &
> > > > > > > > > > iPhoneDevCamp as they present alongside digital
> > heavyweights
> > > > like
> > > > > > > > > > Barbarian
> > > > > > > > > > Group, R/GA, & Big Spaceship.
> > > > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Gmod-gbrowse mailing list
> > > > > > > > > > Gmod-gbrowse@...
> > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > > > Scott Cain, Ph. D.                                   scott at
> > > > scottcain
> > > > > > dot
> > > > > > > > net
> > > > > > > > GMOD Coordinator (http://gmod.org/)
> > > > 216-392-3087
> > > > > > > > Ontario Institute for Cancer Research
> > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > Register Now for Creativity and Technology (CaT), June 3rd,
> > NYC.
> > > > CaT
> > > > > > > > is a gathering of tech-side developers & brand creativity
> > > > > > professionals.
> > > > > > > > Meet
> > > > > > > > the minds behind Google Creative Lab, Visual Complexity,
> > > > Processing, &
> > > > > > > > iPhoneDevCamp as they present alongside digital heavyweights
> > like
> > > > > > Barbarian
> > > > > > > > Group, R/GA, & Big Spaceship.
> > > > http://p.sf.net/sfu/creativitycat-com
> > > > > > > > _______________________________________________
> > > > > > > > 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@...>

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Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
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