SequenceFeatures and dataset sequences

Jalview Developers
1

​As discussed yesterday with Jim, I’ve hit this problem:

  • currently, sequences in the Desktop version hold dataset sequences, but the applet sequences don’t

  • in the Desktop, SequenceFeatures are attached to the dataset sequence, in the applet to the sequence

  • there are about 65 calls to Sequence.getSequenceFeatures() with various flavours of how to retrieve this data

  • for cDNA/protein mapping to work in the applet, I want to create dataset sequences - breaking some of this code

Suggested solution:

  1. change method Sequence.getSequenceFeatures() so it searches the sequence or dataset sequence until it finds sequence features (or not)
  • i.e. use the same logic as currently in FeatureRendererModel.findFeaturesAtRes()
  1. track down and change any code that does this (example: AlignmentSorter.sortByFeature())

SequenceFeatures sf = seq.getSequenceFeatures();

// remove these lines:

if (sf.getDatasetSequence() != null) {

sf = sf.getDatasetSequence().getSequenceFeatures();

}

I think that’s the safest way to keep everything happy, but I’m open to objections or better suggestions.

What I haven’t explored is whether there are similar problems elsewhere triggered by creating dataset sequences in the applet. Sequence.getDBRef() might be a similar case?

Mungo

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

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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
www.compbio.dundee.ac.uk

2

This is the right time to do it! refactoring to a branch off the develop branch should lead to the maximisation of sanity…

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On 18/02/2015 09:27, Mungo Carstairs (Staff) wrote:

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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) 
The University of Dundee is registered Scottish charity: No.SC015096