This looks a lot like JAL-207<https://issues.jalview.org/browse/JAL-207> which is closed as Fixed in 2.8.2, but I am not convinced.
If you do a pairwise alignment of a sub-selection of two sequences and then view the result as an alignment, then start/end ranges are wrong and sequence features are wrongly located. Suggest we re-open JAL-207? Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> 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<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> [email protected]<mailto:[email protected]> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: [email protected] <[email protected]> on behalf of Mungo Carstairs (Staff) <[email protected]> Sent: 23 August 2017 12:19:16 To: Jalview Development List Subject: [Jalview-dev] Fw: Pairwise alignment coordinates Had a quick look at this. The output is on screen and also in the console. Looks like it could be doable with a combination of 1) report seq.getDisplayId(true) instead of seq.getName() 2) use SelectionGroup.getSelectionAsNewSequences() instead of SelectionGroup.getSequencesInOrder() - so sub-sequences get constructed with the correct start/end ranges for a sub-selection Current sequence ids get truncated to 30 characters in the report, which might be a bit severe with the range suffix added. Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> 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<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> [email protected]<mailto:[email protected]> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: [email protected] <[email protected]> on behalf of David Martin (Staff) <[email protected]> Sent: 23 August 2017 11:28 To: [email protected] Subject: [Jalview-discuss] Piarwise alignment coordinates It would be really helpful if the start and end coordinates of the matching sequences could be displayed in the ‘calculate pairwise alignment’ results. ..d <//sig/> [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Dr David M A Martin PhD FRSB Senior Lecturer in Bioinformatics School of Life Sciences, University of Dundee +44(0)1382 388704 | [email protected]<mailto:[email protected]@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb>[University of Dundee Twitter]<http://uod.ac.uk/sig-tw>[University of Dundee LinkedIn]<http://uod.ac.uk/sig-li>[University of Dundee YouTube]<http://uod.ac.uk/sig-yt>[University of Dundee Instagram]<http://uod.ac.uk/sig-ig>[University of Dundee Snapchat]<http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096 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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