Hi – I’ve just found the reason the file I was looking at was not loading (or actually is loading but extremely slowly). The bad news is it looks like it’s been in the code since Aug 2016 but the good news is it looks very fixable.
The initialisation is being held up in Alignment::resolveAndAddDatasetSeq which is in the call stack called by the AlignFrame initialisation code. The code here has a LinkedIdentityHashSet seqs containing all the sequences it has looked at so far. When it gets the next sequence it calls seqs.contains to see if the sequence is already in seqs, if not, it adds the sequence to seqs. The slow bit is the seqs.contains call: if I have 85,000 sequences in seqs it takes around 0.5 secs to do one check, so another 200,000+ is going to take a while… The reason seqs.contains is slow is because, despite the name, LinkedIdentityHashSet::contains is doing a linear search. This rather echoes what I was saying earlier about checking our data structures are appropriate. I’ll log a JIRA issue for this. It would be useful to know what the purpose of using LinkedIdentityHashSet here was though, as this is the only place it’s used in the code. Cheers Kira [cid:[email protected]]<http://uod.ac.uk/sig-home> Kira Mourão Postdoctoral Researcher The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. [email protected]<mailto:[email protected]> www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> Twitter @kiramt [cid:[email protected]]<http://uod.ac.uk/sig-fb>[cid:[email protected]]<http://uod.ac.uk/sig-tw>[cid:[email protected]]<http://uod.ac.uk/sig-li>[cid:[email protected]]<http://uod.ac.uk/sig-yt>[cid:[email protected]]<http://uod.ac.uk/sig-ig>[cid:[email protected]]<http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The University of Dundee is a registered Scottish Charity, No: SC015096
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