Hi,
I am creating jalview alignment pictures programmatically.
Is there a way to add a title to the pictures?
Maybe modifying the jalview properties file?
Thanks in advance!
Alessandra
Hi,
I am creating jalview alignment pictures programmatically.
Is there a way to add a title to the pictures?
Maybe modifying the jalview properties file?
Thanks in advance!
Alessandra
Hello Alessandra,
I’m afraid it’s not possible at the moment.
Jalview’s image export is designed to reproduce (as exactly as possible) the alignment that you have generated, coloured, customized, annotated etc.
Adding in ‘extras’ such as a caption, while in principle possible, raise complications such as choice of font style and placement.
There may also be an argument that image captions should be separate from images, to allow reordering, indexing for references or tables of contents etc.
I think our philosophy is that Jalview provides the alignment image, and any further customisation is best done using an image processing tool.
But we are open to persuasion - if you would like to make a case for a (simple, optional) image caption feature in Jalview we could consider adding it to our feature request list.
Best regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Alessandra Gastaldello alessandra.gastaldello@gmail.com
Sent: 07 January 2016 09:00
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Title
Hi,
I am creating jalview alignment pictures programmatically.
Is there a way to add a title to the pictures?
Maybe modifying the jalview properties file?
Thanks in advance!
Alessandra
Thanks Mungo.
I understand your philosophy
At the end I solved the “issue” in another way.
I think an optional caption feature would be useful especially if many images are generated programmatically as in my case.
Otherwise an image processor tool could be enough !
thank again
Best regards.
Alessandra
2016-01-07 11:18 GMT+01:00 Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk>:
Hello Alessandra,
I’m afraid it’s not possible at the moment.
Jalview’s image export is designed to reproduce (as exactly as possible) the alignment that you have generated, coloured, customized, annotated etc.
Adding in ‘extras’ such as a caption, while in principle possible, raise complications such as choice of font style and placement.
There may also be an argument that image captions should be separate from images, to allow reordering, indexing for references or tables of contents etc.
I think our philosophy is that Jalview provides the alignment image, and any further customisation is best done using an image processing tool.
But we are open to persuasion - if you would like to make a case for a (simple, optional) image caption feature in Jalview we could consider adding it to our feature request list.
Best regards,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Alessandra Gastaldello <alessandra.gastaldello@gmail.com>
Sent: 07 January 2016 09:00
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] TitleHi,
I am creating jalview alignment pictures programmatically.
Is there a way to add a title to the pictures?
Maybe modifying the jalview properties file?Thanks in advance!
Alessandra
The University of Dundee is a registered Scottish Charity, No: SC015096
Alessandra,
I’m glad you found a way to do this for your work.
Yes, the way we recommend people to do titling/captioning and so on is to export the alignment as an EPS file then edit in Adobe Illustrator or similar vector graphics package.
Happy Jalviewing!
Geoff.
On 08/01/2016 14:17, Alessandra Gastaldello wrote:
--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096