[Jalview-discuss] Jalview properties file : documentation ?

[Martin Raden]

Hi Jalview team,

is there some (online) documentation about the "properties file" that
can be set via the commandline arguments?

There is no link (on the CLI page) and Google didnt provided any hit
neither... ;)

Thanks for help,
Martin


--
Dr. Martin Raden, nee Mann, Postdoc

Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

[James Procter]

Hi Martin.

On 20/02/2018 12:54, Martin Raden wrote:
> is there some (online) documentation about the "properties file" that
> can be set via the commandline arguments?

Not exactly (I feel like I've written this before ;) ). There is source
level documentation for what gets written to/read from the properties
file, but our working model with Jalview has always been that users
would configure defaults for opening/viewing alignment data via the
Preferences GUI, and copy their .jalview_properties file and pass it in
via the -props argument if they want to run Jalview from the CLI in a
reproducible way.

>
> There is no link (on the CLI page) and Google didnt provided any hit
> neither... ;)

there are lots of hints and tips that ought to be aggregated somewhere,
but some of those are version specific.

Is there something you'd like to configure that isn't available via
Preferences ?

Jim

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
[phone] | www.jalview.org | www.compbio.dundee.ac.uk


The University of Dundee is a registered Scottish Charity, No: SC015096

[Martin Raden]

Hah..

.. now you got me. I eventually never opened the GUI so far! ;) the
whole setup is done by a colleague and I am "only" responsible to get a
backend pipeline working with his ideas.

and since I am always intrigued, I was wondering what might be
customizable, since he just mentioned this properties file today, and
didnt find any documentation.

therefore my question. :)

so far no direct questions.

maybe one: is there a possibility to increase the width of the leftmost
region in which the alignment/plot labels are plotted? our labels are
cut of to suffixes in the svg output. :)


http://rna.informatik.uni-freiburg.de/trunk/DownloadFile.jsp?jobID=6038639&toolName=CopraRNA&fileNameOrType=evo_align_img/1_mRNA.svg

Thanks,
Martin


Am 20.02.2018 um 14:17 schrieb James Procter:
> Hi Martin.
>
> On 20/02/2018 12:54, Martin Raden wrote:
>> is there some (online) documentation about the "properties file" that
>> can be set via the commandline arguments?
>
> Not exactly (I feel like I've written this before ;) ). There is source
> level documentation for what gets written to/read from the properties
> file, but our working model with Jalview has always been that users
> would configure defaults for opening/viewing alignment data via the
> Preferences GUI, and copy their .jalview_properties file and pass it in
> via the -props argument if they want to run Jalview from the CLI in a
> reproducible way.
>
>>
>> There is no link (on the CLI page) and Google didnt provided any hit
>> neither... ;)
>
> there are lots of hints and tips that ought to be aggregated somewhere,
> but some of those are version specific.
>
> Is there something you'd like to configure that isn't available via
> Preferences ?
>
> Jim
>
> --
> -------------------------------------------------------------------
> Dr JB Procter, Jalview Coordinator, The Barton Group
> Division of Computational Biology, School of Life Sciences
> University of Dundee, Dundee DD1 5EH, UK.
> [phone] | www.jalview.org | www.compbio.dundee.ac.uk
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-***@jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>


--
Dr. Martin Raden, nee Mann, Postdoc

Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

[James Procter]

On 20/02/2018 20:27, Martin Raden wrote:
.. now you got me. I eventually never opened the GUI so far! ;) the whole setup is done by a colleague and I am "only" responsible to get a backend pipeline working with his ideas.
That's enough of a use case for us to run with! We do plan to have Jalview document its properties file.. and CLI only access is something we should factor in (--propertieshelp ?). I guess we could also embed comments in the properties file.

and since I am always intrigued, I was wondering what might be customizable, since he just mentioned this properties file today, and didnt find any documentation.
:D
maybe one: is there a possibility to increase the width of the leftmost region in which the alignment/plot labels are plotted? our labels are cut of to suffixes in the svg output. :)
Absolutely ! In the properties GUI's 'Output' pane there's an 'Automatically adjust ID Width' checkbox. That translates to
FIGURE_AUTOIDWIDTH=true
http://rna.informatik.uni-freiburg.de/trunk/DownloadFile.jsp?jobID=6038639&toolName=CopraRNA&fileNameOrType=evo_align_img/1_mRNA.svg
You might find:
RIGHT_ALIGN_IDS=true

Also useful :)

Hope it helps !
Jim.


The University of Dundee is a registered Scottish Charity, No: SC015096

[Mungo Carstairs (Staff)]

Though I notice another gui Preference, to specify a fixed id width, doesn't work: it is saved against "FIGURE_USERIDWIDTH", but the code looks for "FIGURE_FIXEDIDWIDTH" 😞.


mungo



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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

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________________________________
From: jalview-discuss-***@jalview.org <jalview-discuss-***@jalview.org> on behalf of James Procter <***@dundee.ac.uk>
Sent: 21 February 2018 09:06:06
To: Martin Raden; jalview-***@jalview.org
Subject: Re: [Jalview-discuss] Jalview properties file : documentation ?



On 20/02/2018 20:27, Martin Raden wrote:
.. now you got me. I eventually never opened the GUI so far! ;) the whole setup is done by a colleague and I am "only" responsible to get a backend pipeline working with his ideas.
That's enough of a use case for us to run with! We do plan to have Jalview document its properties file.. and CLI only access is something we should factor in (--propertieshelp ?). I guess we could also embed comments in the properties file.

and since I am always intrigued, I was wondering what might be customizable, since he just mentioned this properties file today, and didnt find any documentation.
:D
maybe one: is there a possibility to increase the width of the leftmost region in which the alignment/plot labels are plotted? our labels are cut of to suffixes in the svg output. :)
Absolutely ! In the properties GUI's 'Output' pane there's an 'Automatically adjust ID Width' checkbox. That translates to
FIGURE_AUTOIDWIDTH=true
http://rna.informatik.uni-freiburg.de/trunk/DownloadFile.jsp?jobID=6038639&toolName=CopraRNA&fileNameOrType=evo_align_img/1_mRNA.svg
You might find:
RIGHT_ALIGN_IDS=true

Also useful :)

Hope it helps !
Jim.


The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

[James Procter]

On 21/02/2018 09:15, Mungo Carstairs (Staff) wrote:

Though I notice another gui Preference, to specify a fixed id width, doesn't work: it is saved against "FIGURE_USERIDWIDTH", but the code looks for "FIGURE_FIXEDIDWIDTH" 😞.

Sigh - thanks for lodging the bug https://issues.jalview.org/browse/JAL-2913 - we'll have it fixed for 2.10.4!
Jim

The University of Dundee is a registered Scottish Charity, No: SC015096