[Debian-med-packaging] Bug#815176: staden: Gap4 contig editor does not show sequences

[Andreas Tille]

Hi James,

just to let you know that I moved the staden packaging from Debian
SVN to Git.  You'll now find the patches we applied here:

   https://anonscm.debian.org/cgit/debian-med/staden.git/tree/debian/patches

The rationale is that we have a better documented procedure for Git when
we are doing backports ... which is what Kerstin probably will ask for
since she is running Jessie.

Kerstin, you can either download the staden packages from unstable from
here:

   https://packages.debian.org/source/unstable/staden

and install manually on your Jessie system or you add unstable to your
/etc/apt/sources.list.  ATTENTION: You need to adapt
/etc/apt/preferences to make sure you will not bump your whole system
to unstable!

As written above we will also provide a Jessie backport of staden but
this will need to wait until the current staden package will enter
testing - that's the rule we can't break.

Confirmation whether the package in unstable works would help to
craft the backport properly.

Hope this helps

       Andreas.

On Mon, Feb 22, 2016 at 05:42:38PM +0000, James Bonfield wrote:
> On Mon, Feb 22, 2016 at 04:34:13PM +0100, Andreas Tille wrote:
> > if I understand you correctly you are suggesting a further change.  Could
> > you please confirm that this patch
> > 
> >     https://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/cope_with_modern_windowmanager.patch?view=markup
> 
> Yes that's it.
> 
> The other change was an improvement to resizing. 
> 
> This is long and tedious so feel free to ignore, but if you're curious
> then here are the details.  Typically window managers treat windows as
> one of two flavours:
> 
> 1) The program set the size, so it's permitted to change it again
> itself.
> 
> 2) The user resized the window, so the application request to resize
> it will be ignored.
> 
> Tk wm geometry command allows you to programatically change the size
> of window or with the blank size (wm geometry . {} {}) it'll reset the
> window to case 1 - governed by the program rather than the user.
> 
> This is all very ICKY and it gets worse.  Gap4's contig editor is
> "courageously" setting the Y dimension itself based on how many rows
> of sequences it wants to display.  The X dimension can be controlled
> by the user, but as the user increases the size in X, more sequences
> can become visible causing the Y dimension to be resized.  In the past
> this caused massive fights between various parts of tcl/tk and window
> managers, sometimes triggering event loops with oscillating window
> dimensions.  The workaround for this was to have a 1 second delay
> between resizing the window and asking the program to recompute the
> size.
> 
> That in turn though broke all modern window managers.  Basically if
> you resized quickly and let go it'd just snap back - you had to
> resize, hold and wait for 1 sec, and then release. Bizantine...  Try
> hard as I may I couldn't recreate the strange oscillations so this
> change basically pushes it back to how it used to be with instant
> recomputation.  It seems to work much better in general, but still
> isn't perfect.
> 
> Perfection isn't possible when you start with the premise of X being
> user controlled and Y being program controlled!  With Gap5 fortunately
> we had an attack of sanity and chose a more traditional strategy.
> 
> James
> 
> PS. Kerstin if you're still reading this, if set -x doesn't work then
> just editing the first #! line to be "#!/bin/sh -x" (without the
> quotes) should do the same thing, or simpler still typing in
> 
>   sh -x `which pregap4`
> 
> -- 
> James Bonfield (jkb at sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
>                                   | Plurima gyrabant gymbolitare vabo;
>   A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
> https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 
> 
> 
> -- 
>  The Wellcome Trust Sanger Institute is operated by Genome Research 
>  Limited, a charity registered in England with number 1021457 and a 
>  company registered in England with number 2742969, whose registered 
>  office is 215 Euston Road, London, NW1 2BE. 
> 
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