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wilzbach / msa

Modular BioJS compoment for a multiple sequence alignment
http://msa.biojs.net
Boost Software License 1.0
168 stars 79 forks source link

integration with the phylogenetic tree viewer #3

Closed wilzbach closed 9 years ago

wilzbach commented 10 years ago

Any reordering or hide/view would need to send out notification to listeners that need to be kept in sync. In particular the tree viewer.

The MSA viewer should listen for selection events from other components e.g. a user selects a node in the tree view and the clade-members/individual leaf nodes are selected. A user would want to see those same sequences visually 'un/selected' in the MSA view.

We would also need synchronized scrolling. If a user scrolls up and down in the tree view (or other views showing rows of the same sequences), then they would want to be looking at the same region in the MSA viewer. Otherwise they have to scroll twice and with finicky position the 2nd time to get things aligned.

wilzbach commented 10 years ago

A preview can be found here http://sniper.biojs-msa.org:9090/snippets/msa_tree

wilzbach commented 9 years ago

@daviddao and I tried to write component adapters to combine different components (= global model). Here's our result (alpha):

http://workmen.biojs.net/demo/msa-tnt/first

TatyanaGoldberg commented 9 years ago

Embedding fasta and clustal files didnt work for me... My files are: https://rostlab.org/~goldberg/biojs/ssGP/ssgp/B2014122194A560KL7I.4.ids.fa and https://rostlab.org/~goldberg/biojs/ssGP/ssgp/B2014122194A560KL7I.4.ids.phylotree.txt

wilzbach commented 9 years ago

One can now asynchronously require the msa-tnt package and display the tree. Here is an example with @TatyanaGoldberg files http://workmen.biojs.net/demo/msa/tree - however importing the newick files via the drag & drop or the menu bar is possible too. At the moment there is also an option in the "extra" menu to calculate a tree from the sequences.

(this feature is alpha - please try with patience and report bugs ;-) )