From: Ian H. <ih...@be...> - 2010-03-17 23:44:40
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Mitch drew my attention to this recently-submitted lighthouse ticket: http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries In JBrowse we draw the arrowheads outside the feature. Robert Olson protests that they should be inside. Is there an established convention for this? How does GBrowse handle it? I. |
From: Scott C. <sc...@sc...> - 2010-03-18 03:40:57
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Without double checking, I'd say I'm reasonably sure that the arrowheads are drawn inside the feature, such that the very point of the arrowhead is at the edge of the feature. Scott On Wed, Mar 17, 2010 at 7:43 PM, Ian Holmes <ih...@be...> wrote: > Mitch drew my attention to this recently-submitted lighthouse ticket: > > http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries > > In JBrowse we draw the arrowheads outside the feature. Robert Olson > protests that they should be inside. Is there an established convention > for this? How does GBrowse handle it? > > I. > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2010-03-18 03:34:51
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Err, in case it wasn't obvious, I was referring to how GBrowse does it :-) On Wed, Mar 17, 2010 at 11:34 PM, Scott Cain <sc...@sc...> wrote: > Without double checking, I'd say I'm reasonably sure that the > arrowheads are drawn inside the feature, such that the very point of > the arrowhead is at the edge of the feature. > > Scott > > > On Wed, Mar 17, 2010 at 7:43 PM, Ian Holmes <ih...@be...> wrote: >> Mitch drew my attention to this recently-submitted lighthouse ticket: >> >> http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries >> >> In JBrowse we draw the arrowheads outside the feature. Robert Olson >> protests that they should be inside. Is there an established convention >> for this? How does GBrowse handle it? >> >> I. >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Mitch S. <mit...@be...> - 2010-03-18 19:19:57
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On 03/17/2010 08:34 PM, Scott Cain wrote: > Without double checking, I'd say I'm reasonably sure that the > arrowheads are drawn inside the feature, such that the very point of > the arrowhead is at the edge of the feature. > I did some looking, and my current understanding is that in GBrowse it depends on the glyph. For example, it looks like the transcript glyph draws them outside the feature (is this the latest code? It's the Bio::Graphics SVN HEAD): http://gmod.svn.sourceforge.net/viewvc/gmod/Bio-Graphics/trunk/lib/Bio/Graphics/Glyph/transcript.pm?view=markup#l_38 It looks to me like the $self->arrow calls are drawing outside the glyph bounds; also, the pad_left and pad_right subs take into account the arrow length. It's a little complicated to follow because of the "flip" logic, though. For the transcript2 glyph, it looks like it draws the arrowhead inside the feature unless the feature is too small for the arrowhead, in which case it draws it outside. http://gmod.svn.sourceforge.net/viewvc/gmod/Bio-Graphics/trunk/lib/Bio/Graphics/Glyph/transcript2.pm?view=markup Mitch |