veg / flea-web-app Goto Github PK

Color nodes and their ancestor links according to the currently selected columns in the sequence alignment tab.

So the trajectory page is never shown.

If runinfo.configuration.Tasks.hyphy_analysis=false, we hide certain tabs from the template. However, their routes still get created in the router.

Also add option to render surface

For instance, an MRCA node.

Instead of selecting one of "label", "id", "motif", etc., allow turning each on and off.

prop.[] only watches for array changes (like inserting/removing elements). prop.@each should be used for observing properties of each element, like [email protected].

@each only works one level deep.

In order to seamlessly work with other applications, routes without the prefix 'api' would be appropriate.

That way dNdS can be the default, if it is available.

• trajectory plots
• gene plots
• sequence viewer
• aa trajectory
• tree viewer

It depends both on the current metric and the current timepoint. How to ensure it only changes once?

The alignment-overview component uses d3.select(window).on(event, callback) to check whether the shift key is pressed. However, these callbacks persist after navigating to a different route, and therefore try to modify a nonexistent component.

Right now the alignment viewer assumes that the amplicon includes the beginning of the gene.

Right now it is hardcoded at 0.95.

For instance, CT gets cut off.

Need to find gaps before combining selected regions, not after.

Or somehow get it out of the way.

This line fails:

var t = this.get('_threshold').trim();

with Uncaught TypeError: undefined is not a function.

onChartChange() observes multiple properties, and gets called multiple times if more than one change at once. It should use Ember.run.once() to run after all changes, but for some reason that does not work.

• updating min and max bubble size is not working
• duplicate nodes not getting cleared on first draw
• add checkbox to disable bubbles
• resize buttons do not work

They stop updating after the first click.

• fix all deprecation warnings
• fix x-select-bootstrap-max when max=1
• remove all two-way binding
• switch to pods

Make it easier to zoom out, pan, and compress the tree so the whole thing is visible without scrolling.

Also the line gets plotted on the x axis. It would be more readable in the middle of the figure.

• multiple sequence alignment
• copynumbers
• phylogenetic tree
  etc

Currently the user needs to add modifiers for "-" and "|" manually to the regexp. Instead insert them automatically.

• add a legend
• set a consistent color scale across all time points, so they are comparable
• make color gradient customizable, to fix dynamic range

Let each session specify whether an analysis tab (e.g. "Evolutionary Trajectory") should be present.

• round labels to a reasonable length
• vary the margins or label size

Highlight selected region and fade others.

Observing changes on that nested property is inefficient. Instead maintain a map from sequence id to motif.

Plot all sequences, not just averages.