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Re: [Gmod-ajax] Feature Mark Up
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From: Andrew U. <and...@gm...> - 2006-11-15 19:04:35
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Hi Steve...
Yep, it works and looks good, you should check it in. The only issue
I see is that the window scrolls back to top whenever the pop up menu
fires... maybe it has to do with its positioning in the DOM, I'm not
sure... it should be a child of outerDivMain, I think, not the entire
document. But I'd have to play with it to figure it out.
We were thinking about having the pop up menu behave a little
differently - it shoud pop up after hovering over a feature for a
fraction of a second or so, then disappear when dragging starts. The
reason for this is that single-clicking should be reserved for other
things, such as dragging or maybe drawing a little box or something to
select features, etc. (this will come later, it's not well-defined at
the moment). Also, double-clicking to center should be unhindered by
a menu popping up after the first click, but I think that can be taken
care of by cancelling the results of a single-click event if a
double-click comes in... somehow.
I also see that double-clicking to center (on the main view cell, not
the ruler cell) is broken now, but I think I know why and I can fix it
when the code is in CVS.
Next comes the figuring out how to populate the pop up menu with
relevant info...
Thanks!
Andrew
On 11/15/06, Steve Taylor <st...@mo...> wrote:
> Hi Andrew,
>
> > I found the problem. Everywhere, including "prototype_gbrowse.html",
> > your URLs should be "https", not "http"... on a whim I portscanned
> > {slave,gbrowse}.molbiol.ox.ac.uk and noticed port 80 is closed, but
> > 443 is open... or at least for U.S.-originating packets.
> >
> > So this one:
> >
> > https://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=3DU000=
96%3A1..10000
> >
> > works just fine. This one:
> >
> > https://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrow=
se.html
> >
> > seems to load the XHTML, but nothing else. The problem seems to be
> > that the XHTML has "http" instead of "https" for the JavaScript
> > library URLs, so I can't load the JavaScript libraries. If the URLs
> > for libraries were changed to something like:
> >
> > https://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/client/View.js
> >
> > then they would load.
> >
> > I guess there is some firewall config causing this problem... although
> > I'm puzzled why it works for someone from Australia but not the U.S.
> >
>
> We have worked out what the problem is and it is down to some configurati=
on issues set up by the Oxford IT service which I won't go into since it's =
so bizarre (unless you're *really* interested :-)).
> http will work in a day or so but in the meantime have a look on our test=
server. This *should* work...
>
> http://jenna.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.=
html
>
> I have also added a js pop-up based on one that was originally developed =
by Sylvain Gaillard and Ga=EBtan Droc.
>
> If it all works your end I will check it in.
>
> Cheers,
>
> Steve
> >
> >
> > On 11/14/06, Steve Taylor <st...@mo...> wrote:
> >
> >>Hi Andrew,
> >>
> >>>This sounds like excellent news, thanks! But, I'm getting timed-out
> >>>loading both pages you linked to... can you let us know when they're
> >>>back up? I would love to take a look.
> >>>
> >>
> >>Hmmm. I have tested both here and they work reasonably quickly although=
are more slow to load than the original AjaxGBrowse...I also got a got som=
eone to test in Australia and he said it loaded ok
> >>though slightly more slowly.
> >>
> >>Can you try again please? Has anyone else on the list had time out prob=
lems? Again the URLs to try are:
> >>
> >>Ajax Gbrowse
> >>http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrows=
e.html
> >>
> >>Original Gbrowse
> >>http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=3DU0009=
6%3A1..10000
> >>
> >>
> >>>You should commit the code to CVS... I've also made a few changes
> >>>across the server-side code (including generate-tiles) to test
> >>>on-demand tile rendering, which will be useful for large genomes, and
> >>>to fix some stupid bugs left in TiledImage, etc. from back in the day
> >>>(e.g. database connections not hanging up), which you probably noticed
> >>>and fixed by now also. Once your code is in, I'll merge in my
> >>>changes.
> >>>
> >>>Just to let everyone know about the "render on demand" stuff... the
> >>>idea is that we still fill a database with primitives, but only render
> >>>tiles as they are request by user (they are also saved, so no need to
> >>>re-render unless the underlying data changes, so we'll have some sort
> >>>of "dirty tile" flag or some such).
> >>>
> >>>This will enable people to put up large genomes without pre-rendering
> >>>all the tiles. Currently, the rendering step is the major limiting
> >>>factor (my benchmarks show around 90% of the actual generate-tiles.pl
> >>>time is spent on database lookup of primitives). For example, Dmel
> >>>arm 4 takes a full day to render on our 24-CPU cluster, but only an
> >>>hour of that time is spent filling the database.
> >>>
> >>>I'm trying a few things to optimize this right now, including the
> >>>on-demand rendering, and I'll keep the list updated once I get
> >>>somewhere (the things I'm trying can be found on
> >>>http://biowiki.org/view/GBrowse/WishList under the "rendering
> >>>optimizations" sublist). I think we could seriously reduce the
> >>>fill/access time, but until then, on-demand rendering will at least
> >>>make large genomes feasible.
> >>>
> >>
> >>Sounds good. Look forward to seeing that!
> >>
> >>Steve
> >>
> >>>
> >>>On 11/13/06, Steve Taylor <st...@mo...> wrote:
> >>>
> >>>
> >>>>Hi,
> >>>>
> >>>>I thought I'd send this to open up the discussions on the new list!:-=
)
> >>>>
> >>>>I haven't checked in this code yet but I have modified generate-tiles=
.pm and BatchTilesImage.pm to allow marking up of the features in each of t=
he tiles using client side image maps. We may want to
> >>>>change this later to do CSS maps but that would be only a small code =
modification. It basically generates an html file per tile with an inlined =
image and the appropriate map coordinates. The browser
> >>>>XMLHttpRequests the data over when it needs to using Ajax.Updater (fr=
om the js library Prototype).
> >>>>
> >>>>You can see what it looks like on:
> >>>>
> >>>>http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbro=
wse.html
> >>>>
> >>>>Try dragging and clicking on features.
> >>>>
> >>>>Advantages of current implementation
> >>>>-----------------------------------
> >>>>- should work on all browsers and doesn't require any fancy javascrip=
t
> >>>>- will support polygons, ellipses etc
> >>>>- allows distribution on different servers for tiles
> >>>>
> >>>>Disadvantages of implementation
> >>>>-------------------------------
> >>>>- all html per tile currently generated server side (not sure if this=
is an advantage or disadvantage at this stage) but may be a pain to do upd=
ates
> >>>>
> >>>>Obviously where javascript:alert('Active image map') you should have =
the relevant details of the feature and a nicer pop up. The js alerts are p=
retty annoying at the moment when dragging! I intend to
> >>>>put js pop ups similar to the ones we have at http://gbrowse.molbiol.=
ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=3DU00096%3A1..10000.
> >>>>
> >>>>Let me know what you think. I will check it in if people think it is =
worthwhile at this stage.
> >>>>
> >>>>Regards,
> >>>>
> >>>>Steve
> >>>>------------------------------------------------------------------
> >>>>Head of Computational Biology Research Group
> >>>>Medical Sciences Division
> >>>>Weatherall Institute of Molecular Medicine/Sir William Dunn School
> >>>>Oxford University
> >>>>Tel: +44 (0)1865 (2)22640 (WIMM - Monday to Wednesday)
> >>>>Tel: +44 (0)1865 (2)85732 (Dunn - Thursday to Friday)
> >>>>Web: http://www.compbio.ox.ac.uk
> >>>>
>
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