Jalview Freezing

dmamartin · 11 February 2019 18:11

I’m trying to persuade Jalview to behave but it keeps freezing on me.

Windows 7 (Dundee Uni staff desktop).

I open a saved project with many windows, each containing a pair of sequences for aligning or a single sequence.

I try to load a features file which maps sequencing quality onto the sequences. There are sequences referred to in the JFF that do not exist in the alignment.

Jalview just freezes completely. Nothing on the console, no response at all to the mouse.

Any suggestiosn? Is it trying to ID match all the unattached annotations?

How can I stop it doing this?

…d

g_m_carstairs · 12 February 2019 07:48

Hello Dave,

Any errors showing in the Java console?

Does your ~/.jalview_properties file have a line

RELAXEDSEQIDMATCHING=true

if so, you try removing this. It may trigger some highly nested ‘fuzzy matching’ of sequence ids (in the features file) to ids or cross-references of sequences in the alignment. It should simply ignore any features for sequences not in the alignment.

If you can pass me your project file and features file I can look further into this.

Thanks,

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
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 11 February 2019 18:11:50
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Jalview Freezing