Jalview properties file : documentation ?

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... :wink:

Thanks for help,
Martin

路路路

--
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

Hi Martin.

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 :wink: ). 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... :wink:

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

路路路

On 20/02/2018 12:54, Martin Raden wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

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

Hah..

.. now you got me. I eventually never opened the GUI so far! :wink: 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. :slight_smile:

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. :slight_smile:

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

Thanks,
Martin

路路路

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 :wink: ). 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... :wink:

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.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@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

鈥 now you got me. I eventually never opened the GUI so far! :wink: the whole setup is done by a colleague and I am 鈥渙nly鈥 responsible to get a backend pipeline working with his ideas.

That鈥檚 enough of a use case for us to run with! We do plan to have Jalview document its properties file鈥 and CLI only access is something we should factor in (鈥損ropertieshelp ?). 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.

:smiley:

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. :slight_smile:

Absolutely ! In the properties GUI鈥檚 鈥極utput鈥 pane there鈥檚 an 鈥楢utomatically adjust ID Width鈥 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 :slight_smile:

Hope it helps !
Jim.

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

路路路

On 20/02/2018 20:27, Martin Raden wrote:

Though I notice another gui Preference, to specify a fixed id width, doesn鈥檛 work: it is saved against 鈥淔IGURE_USERIDWIDTH鈥, but the code looks for 鈥淔IGURE_FIXEDIDWIDTH鈥 :disappointed:.

mungo

路路路

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g.m.carstairs@dundee.ac.uk

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

On 20/02/2018 20:27, Martin Raden wrote:

鈥 now you got me. I eventually never opened the GUI so far! :wink: the whole setup is done by a colleague and I am 鈥渙nly鈥 responsible to get a backend pipeline working with his ideas.

That鈥檚 enough of a use case for us to run with! We do plan to have Jalview document its properties file鈥 and CLI only access is something we should factor in (鈥損ropertieshelp ?). 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.

:smiley:

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. :slight_smile:

Absolutely ! In the properties GUI鈥檚 鈥極utput鈥 pane there鈥檚 an 鈥楢utomatically adjust ID Width鈥 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 :slight_smile:

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

Though I notice another gui Preference, to specify a fixed id width, doesn鈥檛 work: it is saved against 鈥淔IGURE_USERIDWIDTH鈥, but the code looks for 鈥淔IGURE_FIXEDIDWIDTH鈥 :disappointed:.

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

Jim

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

路路路

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