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problem specifying gbrowse image width

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	problem specifying gbrowse image width by Marcela Karey Monaco :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Scott Cain-4 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Marcela, I don't know of hand what is going on, but the fact that those are floating numbers rather than integers strikes me as a little odd. How do those urls get generated? When I change the 200.0 to 200, it works as expected. Scott On Oct 13, 2009, at 3:24 PM, Marcela Karey Monaco wrote: > Hello developers, > > We recently transferred the hapmap web domain to a new server > (including a few software updates) and are now having problems > specifying the width on a png image generated from the browser. > Anyone had to deal with this problem before? > > Example: the following URL constructs are returning the exact same > image with no change in width, which was not the case before the > transfer... > > http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 > > http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 > > Could this be a problem in the way the new server is parsing the > arguments, a known bug, or are there recent changes in the way the > width arguments should be parsed? > Thanks on advance for any hints or suggestions, > > Marcela > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference_______________________________________________ > 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 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Zhang, Hua (NIH/NLM/NCBI) [C] :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Some parts of this message have been removed. Learn more about Nabble's security policy. Marcela, if you look closely, the two images contain different info. (pls check the rs on the left most). Not sure why. Btw, I checked the virtual image and the size of the pictures are same from there too. Hua From: Marcela Karey Monaco [mailto:mmonaco@...] Sent: Tuesday, October 13, 2009 3:25 PM To: gmod-gbrowse@... Cc: Beloslyudtsev, Dmitriy (NIH/NLM/NCBI) [E]; Zhang, Hua (NIH/NLM/NCBI) [C] Subject: problem specifying gbrowse image width Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Marcela Karey Monaco :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Scott, You're right, that does the trick! I had never tried to implement this myself, the Haploview developers use the pngs generated in this manner on their application and asked us about it. Now I know how it should work ;) Thanks so much for the quick response! Marcela On Tue, Oct 13, 2009 at 3:31 PM, Scott Cain <scott@...> wrote: Hi Marcela, I don't know of hand what is going on, but the fact that those are floating numbers rather than integers strikes me as a little odd. How do those urls get generated? When I change the 200.0 to 200, it works as expected. Scott On Oct 13, 2009, at 3:24 PM, Marcela Karey Monaco wrote: Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference_______________________________________________ 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 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Lincoln Stein-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Marcela, Try it without the decimal point. This is working ok for me. Lincoln On Tue, Oct 13, 2009 at 3:24 PM, Marcela Karey Monaco <mmonaco@...> wrote: Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Lincoln Stein-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message If haploview generates floating point numbers and it is hard for them to fix it, we may have to make a tiny patch to gbrowse to recognize and process floats. Lincoln On Tue, Oct 13, 2009 at 3:36 PM, Marcela Karey Monaco <mmonaco@...> wrote: Hi Scott, You're right, that does the trick! I had never tried to implement this myself, the Haploview developers use the pngs generated in this manner on their application and asked us about it. Now I know how it should work ;) Thanks so much for the quick response! Marcela On Tue, Oct 13, 2009 at 3:31 PM, Scott Cain <scott@...> wrote: Hi Marcela, I don't know of hand what is going on, but the fact that those are floating numbers rather than integers strikes me as a little odd. How do those urls get generated? When I change the 200.0 to 200, it works as expected. Scott On Oct 13, 2009, at 3:24 PM, Marcela Karey Monaco wrote: Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference_______________________________________________ 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 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
	Re: problem specifying gbrowse image width by Marcela Karey Monaco :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Thanks Lincoln. I will ask them and let you guys know. Marcela On Tue, Oct 13, 2009 at 3:58 PM, Lincoln Stein <lincoln.stein@...> wrote: If haploview generates floating point numbers and it is hard for them to fix it, we may have to make a tiny patch to gbrowse to recognize and process floats. Lincoln On Tue, Oct 13, 2009 at 3:36 PM, Marcela Karey Monaco <mmonaco@...> wrote: Hi Scott, You're right, that does the trick! I had never tried to implement this myself, the Haploview developers use the pngs generated in this manner on their application and asked us about it. Now I know how it should work ;) Thanks so much for the quick response! Marcela On Tue, Oct 13, 2009 at 3:31 PM, Scott Cain <scott@...> wrote: Hi Marcela, I don't know of hand what is going on, but the fact that those are floating numbers rather than integers strikes me as a little odd. How do those urls get generated? When I change the 200.0 to 200, it works as expected. Scott On Oct 13, 2009, at 3:24 PM, Marcela Karey Monaco wrote: Hello developers, We recently transferred the hapmap web domain to a new server (including a few software updates) and are now having problems specifying the width on a png image generated from the browser. Anyone had to deal with this problem before? Example: the following URL constructs are returning the exact same image with no change in width, which was not the case before the transfer... http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=200.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse_img/hapmap3r2_B36/?name=chr22:24086674..24284454;width=2000.0;type=gtsh+mRNA;options=gtsh%201+mRNA%203;nocache=1 Could this be a problem in the way the new server is parsing the arguments, a known bug, or are there recent changes in the way the width arguments should be parsed? Thanks on advance for any hints or suggestions, Marcela ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference_______________________________________________ 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 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse