Angie, is there any reason to call transparent()? The other tracks render their background in a solid color.<br><br>Lincoln<br><br><div class="gmail_quote">On Fri, May 29, 2009 at 3:56 PM, Angie Hinrichs <span dir="ltr"><<a href="mailto:angie@soe.ucsc.edu">angie@soe.ucsc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Mark, Do you see any error_log warnings like "ucsc_glyph: colors will<br>
be out of sync ($i --> $index)!" ?<br>
<br>
Wherever the bad interaction is taking place, it is definitely an<br>
alpha-channel problem. To construct the GD::Image using the colormap<br>
and pixelmap returned by the UCSC C code,<br>
Bio/Graphics/Glyph/<a href="http://ucsc_glyph.pm" target="_blank">ucsc_glyph.pm</a> uses these calls:<br>
<br>
my $im = GD::Image->new($width, $height);<br>
$im->transparent( <UCSC colormap's white index> );<br>
<br>
... loop on UCSC colormap calls $im->colorAllocate(),<br>
** hoping that calling $im->colorAllocate() in the same order<br>
results in same colormap indices<br>
<br>
... loop on UCSC pixelmap calls $im->setPixel()<br>
<br>
** Here is where something could go wrong. It looks like I should<br>
call $im->transparent *after* the call to $im->colorAllocate() for<br>
white, making sure that I pass $im's actual white index to<br>
$im->transparent. However, when I call transparent after<br>
colorAllocate, the white pixels are shaded light gray instead of being<br>
transparent, even in the default display. Calling $im->transparent<br>
first was just a hack that worked, and then I forgot about it. I will<br>
try updating GD too, to see if that makes any difference.<br>
<br>
FWIW I am constructing the GD::Image one color and pixel at a time<br>
because when I used GD::Image->newFromGdData(), the image was created<br>
OK but when I returned the new $im from a sub{}, perl crashed with a<br>
'glibc detected double free or corruption'. Does that ring a bell for<br>
anybody?<br>
<font color="#888888"><br>
Angie<br>
</font><div><div></div><div class="h5"><br>
On Fri, 29 May 2009, Todd W. Harris wrote:<br>
<br>
> Mark -<br>
><br>
> Try upgrading your GD::SVG to the most current version on CPAN.<br>
><br>
> Todd<br>
><br>
><br>
> On May 29, 2009, at 9:42 AM, mark meyer wrote:<br>
><br>
> > We use the GD::SVG and was never able to get the inkscape (pdf generation)<br>
> > operational, if that helps any.<br>
> ><br>
> > On Fri, May 29, 2009 at 9:52 AM, Scott Cain <<a href="mailto:scott@scottcain.net">scott@scottcain.net</a>> wrote:<br>
> > Hi all,<br>
> ><br>
> > Could this be a bad interaction between the plug in and GD::SVG or<br>
> > inkscape (depending on what sort of hi res image you are getting)?<br>
> > For example, I think that GD::SVG has a hard time with alpha channels.<br>
> ><br>
> > Scott<br>
> ><br>
> ><br>
> > On Fri, May 29, 2009 at 10:31 AM, mark meyer <<a href="mailto:mmeyerposting@gmail.com">mmeyerposting@gmail.com</a>><br>
> > wrote:<br>
> > > Hi Angie,<br>
> > ><br>
> > > Bill is out of the office today, but I can try to answer your questions.<br>
> > > Attached are the two screen shots, one is what the plugin looks like in<br>
> > > the<br>
> > > gbrowse, just fine as it looks in UCSC. The second is what happens when<br>
> > > you<br>
> > > click on high-res image.<br>
> > ><br>
> > > We are running gbrowse v1.69. The plugin code was implemented and<br>
> > > downloaded about 1 month ago, just recently ran into this issue since we<br>
> > > are<br>
> > > trying to make some publication figures from our Gbrowse data.<br>
> > ><br>
> > > I can access conf files, etc. if you need to see them and try to do my<br>
> > > best<br>
> > > to answer questions, but I may not be able to answer very detailed<br>
> > > questions<br>
> > > in Bill's absence since he has been the one configuring this.<br>
> > ><br>
> > > Thanks for checking into this for us,<br>
> > ><br>
> > > Mark<br>
> > ><br>
> > > On Thu, May 28, 2009 at 5:29 PM, Angie Hinrichs <<a href="mailto:angie@soe.ucsc.edu">angie@soe.ucsc.edu</a>><br>
> > > wrote:<br>
> > > ><br>
> > > > Dave - yes, that sounds likely.<br>
> > > ><br>
> > > > Bill, what version of GBrowse are you running? How recently did you<br>
> > > > grab the plugin code? I didn't get the screenshot attachment so if<br>
> > > > you wouldn't mind sending that to me, that would be helpful. If your<br>
> > > > GBrowse is on a public server, can you send the URL?<br>
> > > ><br>
> > > > Angie<br>
> > > ><br>
> > > > On Thu, 28 May 2009, Dave Clements, GMOD Help Desk wrote:<br>
> > > ><br>
> > > > > Hi Bill,<br>
> > > > ><br>
> > > > > I have no particular insight on why this is happening. My guess is<br>
> > > > > that it is due some obscure interaction between the UCSC plugin and<br>
> > > > > core GBrowse, but I don't actually know.<br>
> > > > ><br>
> > > > > I've CC'd Angie at UCSC to see if she may have any insight.<br>
> > > > ><br>
> > > > > Dave C.<br>
> > > > ><br>
> > > > ><br>
> > > > ><br>
> > > > > On Tue, May 26, 2009 at 2:25 PM, Bill Pulec <<a href="mailto:wpulec@gmail.com">wpulec@gmail.com</a>> wrote:<br>
> > > > > > Hi All,<br>
> > > > > > I am attempting to view high-res images of conservation tracks but<br>
> > > > the<br>
> > > > > > background of these tracks in high-res is blue. This isn't the case<br>
> > > > > > when<br>
> > > > > > these tracks are displayed in gbrowse normally, it only happens when<br>
> > > > > > viewed<br>
> > > > > > as high-res. Also all the non-conservation tracks are fine in high<br>
> > > > > > res. Is<br>
> > > > > > there any reason why outputting these images in high-res would do<br>
> > > > > > this? Has<br>
> > > > > > anyone encountered other tracks doing this in high-res? Any insight<br>
> > > > > > would be<br>
> > > > > > appreciated. I have attached an example image of the track below.<br>
> > > > > ><br>
> > > > > > Thanks,<br>
> > > > > > Bill<br>
> > > > > ><br>
> > > > > ><br>
> > > > > ><br>
> > > > ><br>
> > > > > Was this helpful? Let us know at<br>
> > > > > <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
> > > > ><br>
> > > > > Learn more about GMOD at:<br>
> > > > > SMBE:<br>
> > > > > <a href="http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27" target="_blank">http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27</a><br>
> > > > > Arthropod Genomics: <a href="http://www.k-state.edu/agc/symp2009/seminar.html" target="_blank">http://www.k-state.edu/agc/symp2009/seminar.html</a><br>
> > > > > AGA Next Gen Seq in Non-Models:<br>
> > > > > <a href="http://www.regonline.com/Nextgeneration" target="_blank">http://www.regonline.com/Nextgeneration</a><br>
> > > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > ------------------------------------------------------------------------------<br>
> > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT<br>
> > > > is a gathering of tech-side developers & brand creativity professionals.<br>
> > > > Meet<br>
> > > > the minds behind Google Creative Lab, Visual Complexity, Processing, &<br>
> > > > iPhoneDevCamp as they present alongside digital heavyweights like<br>
> > > > Barbarian<br>
> > > > Group, R/GA, & Big Spaceship. <a href="http://p.sf.net/sfu/creativitycat-com" target="_blank">http://p.sf.net/sfu/creativitycat-com</a><br>
> > > > _______________________________________________<br>
> > > > Gmod-gbrowse mailing list<br>
> > > > <a href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</a><br>
> > > > <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
> > ><br>
> > ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > ------------------------------------------------------------------------<br>
> > Scott Cain, Ph. D. scott at scottcain dot<br>
> > net<br>
> > GMOD Coordinator (<a href="http://gmod.org/" target="_blank">http://gmod.org/</a>) 216-392-3087<br>
> > Ontario Institute for Cancer Research<br>
> ><br>
> > ------------------------------------------------------------------------------<br>
> > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT<br>
> > is a gathering of tech-side developers & brand creativity professionals.<br>
> > Meet<br>
> > the minds behind Google Creative Lab, Visual Complexity, Processing, &<br>
> > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian<br>
> > Group, R/GA, & Big Spaceship. <a href="http://p.sf.net/sfu/creativitycat-com" target="_blank">http://p.sf.net/sfu/creativitycat-com</a><br>
> > _______________________________________________<br>
> > Gmod-gbrowse mailing list<br>
> > <a href="mailto:Gmod-gbrowse@lists.sourceforge.net">Gmod-gbrowse@lists.sourceforge.net</a><br>
> > <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>