Re: Arc Glyph not visible when "Link to Image"

[Lincoln Stein-3]

Hi Steve,

I tracked the problem down to the call in setAntiAliased() in your draw_component() method. The GD::SVG library, which is used for the high-res images, doesn't support this method, because antialiasing is performed automatically by SVG renderers. I have corrected this in the development version of GD::SVG, and am attaching it as a tar file.

Your glyph looks nice, but I notice that when you attach labels to it, the arcs overlap the labels. I guess this is intentional so that the glyph attaches to the feature above it?

Lincoln

On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...> wrote:

Hi Steve,

Can you send me some sample data to use with this glyph?  I doubt I'll find anything just peering at the code, but trying to use it should help in the debugging process.

Thanks,
Scott

On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:

Hi Lincoln/Scott,

I sent this to the GBrowse list but didn't get a response. I am re emailing it to you in the hope of some enlightenment:-). I also attach the pm so you can check this into Bio::Graphics if you think it is potentially useful.<arc.pm>

The above is a new glyph called "arc" which can be used to plot cis genome interactions. You can see an example here at:

https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc

My problem is I can't see the track if I click on [Link to Image] or [Hi-Res Image]. Can anyone explain why this might be happening and what I need to do to get this functionaility to work?
I am using GBrowse 1.69.

Thanks,

Steve

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

--
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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[Stephen Taylor-5]

Hi Lincoln,

Hi Steve,

I tracked the problem down to the call in setAntiAliased() in your draw_component() method. The GD::SVG library, which is used for the high-res images, doesn't support this method, because antialiasing is performed automatically by SVG renderers. I have corrected this in the development version of GD::SVG, and am attaching it as a tar file.

Though It's not quite working right for me. For the SVG the glyph overlays the other features and ruler (at least in our 1.69 instance). See this link:

https://gbrowsedev.molbiol.ox.ac.uk/cgi-bin/gbrowse_img/coli_demo/?name=U00096:1..10000;type=Genes+arc;width=1200;id=cba7180d9b68429b5efe75149731f5c6;format=GD::SVG;keystyle=between;grid=on

It looks ok on the link for the non SVG image for the coli_demo database, though. However, on another database I get this when viewing in GBrowse

and this when I link to the image (ie the glyph is not visible).

Your glyph looks nice, but I notice that when you attach labels to it, the arcs overlap the labels. I guess this is intentional so that the glyph attaches to the feature above it?

Yes that's correct. It's not noticeable when you are in GBrowse since the label is drawn on top but looks not so good when doing a link to image. I can maybe move the arc terminations slightly down.

Thanks for your help so far,

Steve

Lincoln

On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...> wrote:

Hi Steve,

Can you send me some sample data to use with this glyph?  I doubt I'll find anything just peering at the code, but trying to use it should help in the debugging process.

Thanks,
Scott

On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:

Hi Lincoln/Scott,

I sent this to the GBrowse list but didn't get a response. I am re emailing it to you in the hope of some enlightenment:-). I also attach the pm so you can check this into Bio::Graphics if you think it is potentially useful.<arc.pm>

The above is a new glyph called "arc" which can be used to plot cis genome interactions. You can see an example here at:

https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc

My problem is I can't see the track if I click on [Link to Image] or [Hi-Res Image]. Can anyone explain why this might be happening and what I need to do to get this functionaility to work?
I am using GBrowse 1.69.

Thanks,

Steve

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[Lincoln Stein-3]

Sorry, but please summarize what is and isn't working. I am interested in the three cases:

1. standard browse view
2. link to low-resolution (PNG) image
3. lilnk to high-resolution (SVG) image

Lincoln

On Fri, Sep 4, 2009 at 7:34 AM, Stephen Taylor <stephen.taylor@...> wrote:

Hi Lincoln,

Hi Steve,

I tracked the problem down to the call in setAntiAliased() in your draw_component() method. The GD::SVG library, which is used for the high-res images, doesn't support this method, because antialiasing is performed automatically by SVG renderers. I have corrected this in the development version of GD::SVG, and am attaching it as a tar file.

Though It's not quite working right for me. For the SVG the glyph overlays the other features and ruler (at least in our 1.69 instance). See this link:

https://gbrowsedev.molbiol.ox.ac.uk/cgi-bin/gbrowse_img/coli_demo/?name=U00096:1..10000;type=Genes+arc;width=1200;id=cba7180d9b68429b5efe75149731f5c6;format=GD::SVG;keystyle=between;grid=on

It looks ok on the link for the non SVG image for the coli_demo database, though. However, on another database I get this when viewing in GBrowse

and this when I link to the image (ie the glyph is not visible).

Your glyph looks nice, but I notice that when you attach labels to it, the arcs overlap the labels. I guess this is intentional so that the glyph attaches to the feature above it?

Yes that's correct. It's not noticeable when you are in GBrowse since the label is drawn on top but looks not so good when doing a link to image. I can maybe move the arc terminations slightly down.

Thanks for your help so far,

Steve

Lincoln

On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...> wrote:

Hi Steve,

Can you send me some sample data to use with this glyph?  I doubt I'll find anything just peering at the code, but trying to use it should help in the debugging process.

Thanks,
Scott

On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:

Hi Lincoln/Scott,

I sent this to the GBrowse list but didn't get a response. I am re emailing it to you in the hope of some enlightenment:-). I also attach the pm so you can check this into Bio::Graphics if you think it is potentially useful.<arc.pm>

The above is a new glyph called "arc" which can be used to plot cis genome interactions. You can see an example here at:

https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc

My problem is I can't see the track if I click on [Link to Image] or [Hi-Res Image]. Can anyone explain why this might be happening and what I need to do to get this functionaility to work?
I am using GBrowse 1.69.

Thanks,

Steve

--
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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[Stephen Taylor-5]

Hi Lincoln,

> Sorry, but please summarize what is and isn't working. I am interested
> in the three cases:
>
>    1. standard browse view

Working.

>    2. link to low-resolution (PNG) image

Working on coli_demo (one of our demo public dbs) but not on our
internal database (see images below)

>    3. lilnk to high-resolution (SVG) image
>

Working on coli_demo but incorrect. See attached svg.png.

Thanks,

Steve

> Lincoln
>
> On Fri, Sep 4, 2009 at 7:34 AM, Stephen Taylor
> <stephen.taylor@... <mailto:stephen.taylor@...>> wrote:
>
>     Hi Lincoln,
>
>>     Hi Steve,
>>
>>     I tracked the problem down to the call in setAntiAliased() in your
>>     draw_component() method. The GD::SVG library, which is used for
>>     the high-res images, doesn't support this method, because
>>     antialiasing is performed automatically by SVG renderers. I have
>>     corrected this in the development version of GD::SVG, and am
>>     attaching it as a tar file.
>
>     Though It's not quite working right for me. For the SVG the glyph
>     overlays the other features and ruler (at least in our 1.69
>     instance). See this link:
>
>     https://gbrowsedev.molbiol.ox.ac.uk/cgi-bin/gbrowse_img/coli_demo/?name=U00096:1..10000;type=Genes+arc;width=1200;id=cba7180d9b68429b5efe75149731f5c6;format=GD::SVG;keystyle=between;grid=on
>
>     It looks ok on the link for the non SVG image for the coli_demo
>     database, though. However, on another database I get this when
>     viewing in GBrowse
>
>
>     and this when I link to the image (ie the glyph is not visible).
>
>>
>>
>>     Your glyph looks nice, but I notice that when you attach labels to
>>     it, the arcs overlap the labels. I guess this is intentional so
>>     that the glyph attaches to the feature above it?
>>
>
>     Yes that's correct. It's not noticeable when you are in GBrowse
>     since the label is drawn on top but looks not so good when doing a
>     link to image. I can maybe move the arc terminations slightly down.
>
>     Thanks for your help so far,
>
>     Steve
>
>
>>     Lincoln
>>
>>     On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...
>>     <mailto:scott@...>> wrote:
>>
>>         Hi Steve,
>>
>>         Can you send me some sample data to use with this glyph?  I
>>         doubt I'll find anything just peering at the code, but trying
>>         to use it should help in the debugging process.
>>
>>         Thanks,
>>         Scott
>>
>>
>>
>>         On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:
>>
>>             Hi Lincoln/Scott,
>>
>>             I sent this to the GBrowse list but didn't get a response.
>>             I am re emailing it to you in the hope of some
>>             enlightenment:-). I also attach the pm so you can check
>>             this into Bio::Graphics if you think it is potentially
>>             useful.<arc.pm <http://arc.pm>>
>>
>>             The above is a new glyph called "arc" which can be used to
>>             plot cis genome interactions. You can see an example here at:
>>
>>             https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc
>>
>>             My problem is I can't see the track if I click on [Link to
>>             Image] or [Hi-Res Image]. Can anyone explain why this
>>             might be happening and what I need to do to get this
>>             functionaility to work?
>>             I am using GBrowse 1.69.
>>
>>             Thanks,
>>
>>             Steve
>>
>
>
>
>
> --
> 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@...
> <mailto:Renata.Musa@...>>
>
>
> ------------------------------------------------------------------------
>
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> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>
>
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>
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[Lincoln Stein-3]

I'm not sure I understand why (2) is working on one database and not another. It must be a difference in the version of GD::SVG or Bio::Graphics, no?

The reason your SVG is screwed up is that you are deliberately setting the top of the glyph to start at position zero. Position zero is relative to the whole panel, not the track. Perhaps you want to set the top to $dy, which is the top of the track.

Lincoln

On Fri, Sep 4, 2009 at 11:59 AM, Stephen Taylor <stephen.taylor@...> wrote:

Hi Lincoln,

Sorry, but please summarize what is and isn't working. I am interested in the three cases:

  1. standard browse view

Working.

  2. link to low-resolution (PNG) image

Working on coli_demo (one of our demo public dbs) but not on our internal database (see images below)

  3. lilnk to high-resolution (SVG) image

Working on coli_demo but incorrect. See attached svg.png.

Thanks,

Steve

Lincoln

On Fri, Sep 4, 2009 at 7:34 AM, Stephen Taylor <stephen.taylor@... <mailto:stephen.taylor@...>> wrote:

   Hi Lincoln,

   Hi Steve,

   I tracked the problem down to the call in setAntiAliased() in your
   draw_component() method. The GD::SVG library, which is used for
   the high-res images, doesn't support this method, because
   antialiasing is performed automatically by SVG renderers. I have
   corrected this in the development version of GD::SVG, and am
   attaching it as a tar file.

   Though It's not quite working right for me. For the SVG the glyph
   overlays the other features and ruler (at least in our 1.69
   instance). See this link:

   https://gbrowsedev.molbiol.ox.ac.uk/cgi-bin/gbrowse_img/coli_demo/?name=U00096:1..10000;type=Genes+arc;width=1200;id=cba7180d9b68429b5efe75149731f5c6;format=GD::SVG;keystyle=between;grid=on

   It looks ok on the link for the non SVG image for the coli_demo
   database, though. However, on another database I get this when
   viewing in GBrowse


   and this when I link to the image (ie the glyph is not visible).

   Your glyph looks nice, but I notice that when you attach labels to
   it, the arcs overlap the labels. I guess this is intentional so
   that the glyph attaches to the feature above it?

   Yes that's correct. It's not noticeable when you are in GBrowse
   since the label is drawn on top but looks not so good when doing a
   link to image. I can maybe move the arc terminations slightly down.

   Thanks for your help so far,

   Steve

   Lincoln

   On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...

   <mailto:scott@...>> wrote:

       Hi Steve,

       Can you send me some sample data to use with this glyph?  I
       doubt I'll find anything just peering at the code, but trying
       to use it should help in the debugging process.

       Thanks,
       Scott



       On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:

           Hi Lincoln/Scott,

           I sent this to the GBrowse list but didn't get a response.
           I am re emailing it to you in the hope of some
           enlightenment:-). I also attach the pm so you can check
           this into Bio::Graphics if you think it is potentially

           useful.<arc.pm <http://arc.pm>>

           The above is a new glyph called "arc" which can be used to
           plot cis genome interactions. You can see an example here at:

           https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc

           My problem is I can't see the track if I click on [Link to
           Image] or [Hi-Res Image]. Can anyone explain why this
           might be happening and what I need to do to get this
           functionaility to work?
           I am using GBrowse 1.69.

           Thanks,

           Steve

--
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@... <mailto:Renata.Musa@...>>


------------------------------------------------------------------------

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--
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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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trial. Simplify your report design, integration and deployment - and focus on
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[Stephen Taylor-5]

Hi Lincoln,

I'm not sure I understand why (2) is working on one database and not another. It must be a difference in the version of GD::SVG or Bio::Graphics, no?

Me either, but your suggestion below seemed to fix it. Just FYI I have been working/testing on our dev server so the libraries are the same for all databases.

The reason your SVG is screwed up is that you are deliberately setting the top of the glyph to start at position zero. Position zero is relative to the whole panel, not the track. Perhaps you want to set the top to $dy, which is the top of the track.

I wasn't aware of that. That seems to have fixed the label overlap problem and problem (2).

I have attached the updated glyph code.

Thanks for your help,

Steve

[arc.pm]

---

package Bio::Graphics::Glyph::arc;

use strict;
use base 'Bio::Graphics::Glyph::generic';
use constant THICKNESS => 1;

sub draw_component {
  my $self = shift;
  my ($gd,$dx,$dy) = @_;
  my ($left,$top,$right,$bottom) = $self->bounds($dx,$dy);
  #my $width;
  my $feature = $self->feature;
  ($left,$right) = $self->factory->map_no_trunc($feature->start,$feature->end);



  # clipping
  # if both ends disappear off the panel then don't show
  # perhap should be an option?
  my $panel = $self->panel;
  if ($left <= $panel->left and $right >= $panel->right) {
      return;
  }
  #return unless $left >= $panel->left and $right <= $panel->right;

  $gd->setThickness($self->thickness);
  $gd->setAntiAliased($self->bgcolor);

  # setting top =0 means it always joins the ruler
  $top=$dy;
  my $width=abs($right-$left);
  my $middle=$left+int($width/2);
  $gd->arc($middle,$top,$width,$self->height*2,0,180,$self->fgcolor);


}

 
sub thickness {
        my $self = shift;
        my $requested_thickness=$self->option('thickness');
        if (defined $requested_thickness) {
                return $requested_thickness;
        } else {
                return THICKNESS;
        }
}
 
 
1;

---

Lincoln

On Fri, Sep 4, 2009 at 11:59 AM, Stephen Taylor <stephen.taylor@...> wrote:

Hi Lincoln,

Sorry, but please summarize what is and isn't working. I am interested in the three cases:

  1. standard browse view

Working.

  2. link to low-resolution (PNG) image

Working on coli_demo (one of our demo public dbs) but not on our internal database (see images below)

  3. lilnk to high-resolution (SVG) image

Working on coli_demo but incorrect. See attached svg.png.

Thanks,

Steve

Lincoln

On Fri, Sep 4, 2009 at 7:34 AM, Stephen Taylor <stephen.taylor@... <mailto:stephen.taylor@...>> wrote:

   Hi Lincoln,

   Hi Steve,

   I tracked the problem down to the call in setAntiAliased() in your
   draw_component() method. The GD::SVG library, which is used for
   the high-res images, doesn't support this method, because
   antialiasing is performed automatically by SVG renderers. I have
   corrected this in the development version of GD::SVG, and am
   attaching it as a tar file.

   Though It's not quite working right for me. For the SVG the glyph
   overlays the other features and ruler (at least in our 1.69
   instance). See this link:

   https://gbrowsedev.molbiol.ox.ac.uk/cgi-bin/gbrowse_img/coli_demo/?name=U00096:1..10000;type=Genes+arc;width=1200;id=cba7180d9b68429b5efe75149731f5c6;format=GD::SVG;keystyle=between;grid=on

   It looks ok on the link for the non SVG image for the coli_demo
   database, though. However, on another database I get this when
   viewing in GBrowse


   and this when I link to the image (ie the glyph is not visible).

   Your glyph looks nice, but I notice that when you attach labels to
   it, the arcs overlap the labels. I guess this is intentional so
   that the glyph attaches to the feature above it?

   Yes that's correct. It's not noticeable when you are in GBrowse
   since the label is drawn on top but looks not so good when doing a
   link to image. I can maybe move the arc terminations slightly down.

   Thanks for your help so far,

   Steve

   Lincoln

   On Thu, Sep 3, 2009 at 9:17 AM, Scott Cain <scott@...

   <mailto:scott@...>> wrote:

       Hi Steve,

       Can you send me some sample data to use with this glyph?  I
       doubt I'll find anything just peering at the code, but trying
       to use it should help in the debugging process.

       Thanks,
       Scott



       On Sep 3, 2009, at 8:14 AM, Stephen Taylor wrote:

           Hi Lincoln/Scott,

           I sent this to the GBrowse list but didn't get a response.
           I am re emailing it to you in the hope of some
           enlightenment:-). I also attach the pm so you can check
           this into Bio::Graphics if you think it is potentially

           useful.<arc.pm <http://arc.pm>>

           The above is a new glyph called "arc" which can be used to
           plot cis genome interactions. You can see an example here at:

           https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?start=1;stop=10000;ref=U00096;width=1200;version=100;cache=0;drag_and_drop=on;show_tooltips=on;grid=on;id=151a6964fec5227b03ed6c8772f6a42d;label=Genes-arc

           My problem is I can't see the track if I click on [Link to
           Image] or [Hi-Res Image]. Can anyone explain why this
           might be happening and what I need to do to get this
           functionaility to work?
           I am using GBrowse 1.69.

           Thanks,

           Steve

--
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@... <mailto:Renata.Musa@...>>


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Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now.  http://p.sf.net/sfu/bobj-july


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
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