?Update: The time is all spent in
AAFrequency.completeConsensus() so this would be the place to put any optimisation effort in if wanted. mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> ________________________________ From: [email protected] <[email protected]> on behalf of Mungo Carstairs (Staff) <[email protected]> Sent: 03 March 2015 11:34 To: Jalview Development List Subject: [Jalview-dev] Group by Tree - performance notes I drilled down into the Group by Tree function to see why it seems slow. With an alignment of 50 sequences x 1800 (I'm using Mikk Puustusmaa's DNA data), if you click 'deep' in the tree (so creating many groups), the refresh with group colouring takes over a second (Jalview desktop 2.8.2). It turns out most of the time is spent in SequenceGroup.recalcConservation(). This takes around 13ms but is done for each group. For example: - 82 groups formed - time in recalcConservation: 82 * 13ms = 1066ms approx - total time in colourGroups: 1111ms This gets more noticeable in a split frame view when there are two alignments performing this action. Not sure if there are any easy optimisations here. ? It still happens with no annotations displayed, and Puridine/Pyrimidine colour scheme, which feels unnecessary...? Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096
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