Details
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Type:
Improvement
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: printing and export
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Labels:None
Description
For HTML export of an alignment, there are currently two options.
1) Jalview embedded SVG.
2) BioJS MSAViewer.
(1) Provides a vectorised and familiar looking output, though it is non-interactive. A thought to add tooltip behaviour over the alignment (e.g. features), IDs and annotations may be feasible, though with the SVG output coming from a Graphics2D object it might not be.
(2) Could be updated: the version of biojs MSAViewer uses comes from a (jalview controlled) github repo found here:
https://github.com/jalview/exporter-templates/tree/master/biojs
The latest version of MSAViewer found here is 0.2.0
The biojs MSAViewer (https://msa.biojs.net/ https://doi.org/10.1093/bioinformatics/btw474) has now stopped being actively developed, but has several tagged updates after 0.2.0 (in fact 0.2.0 is not to be found in the releases/tags): https://github.com/wilzbach/msa/tags
including a release v1.0.0
(3+) Several other standalone javascript MSA viewers are now available, and could be considered as a potential HTML output. biojs MSAViewer recommends
i) react-msa-viewer https://github.com/plotly/react-msa-viewer
Available on npm, still labelled "Work in progress - use with caution"
Others available are:
ii) MSABrowser https://thekaplanlab.github.io/
https://academic.oup.com/bioinformaticsadvances/article-abstract/1/1/vbab009/6345340
iii) ProSeqViewer https://biocomputingup.github.io/ProSeqViewer-documentation/
https://academic.oup.com/bioinformatics/article/38/4/1129/6426073
iv) react-msaview https://github.com/GMOD/react-msaview
https://gmod.github.io/react-msaview
v) AlignmentViewer2.0 (supercedes AlignmentViewer) https://github.com/sanderlab/AlignmentViewer2.0
https://fast.alignmentviewer.org/
Consideration should be given to the JSON data storage format so that the HTML file can be read back into Jalview.
1) Jalview embedded SVG.
2) BioJS MSAViewer.
(1) Provides a vectorised and familiar looking output, though it is non-interactive. A thought to add tooltip behaviour over the alignment (e.g. features), IDs and annotations may be feasible, though with the SVG output coming from a Graphics2D object it might not be.
(2) Could be updated: the version of biojs MSAViewer uses comes from a (jalview controlled) github repo found here:
https://github.com/jalview/exporter-templates/tree/master/biojs
The latest version of MSAViewer found here is 0.2.0
The biojs MSAViewer (https://msa.biojs.net/ https://doi.org/10.1093/bioinformatics/btw474) has now stopped being actively developed, but has several tagged updates after 0.2.0 (in fact 0.2.0 is not to be found in the releases/tags): https://github.com/wilzbach/msa/tags
including a release v1.0.0
(3+) Several other standalone javascript MSA viewers are now available, and could be considered as a potential HTML output. biojs MSAViewer recommends
i) react-msa-viewer https://github.com/plotly/react-msa-viewer
Available on npm, still labelled "Work in progress - use with caution"
Others available are:
ii) MSABrowser https://thekaplanlab.github.io/
https://academic.oup.com/bioinformaticsadvances/article-abstract/1/1/vbab009/6345340
iii) ProSeqViewer https://biocomputingup.github.io/ProSeqViewer-documentation/
https://academic.oup.com/bioinformatics/article/38/4/1129/6426073
iv) react-msaview https://github.com/GMOD/react-msaview
https://gmod.github.io/react-msaview
v) AlignmentViewer2.0 (supercedes AlignmentViewer) https://github.com/sanderlab/AlignmentViewer2.0
https://fast.alignmentviewer.org/
Consideration should be given to the JSON data storage format so that the HTML file can be read back into Jalview.
