Glitchy pinning of annotation popup.

[jamiewaese]

Sometimes the popup doesn't disappear, even when you change views back to the Select Species page. Perhaps we should add a "close window" (X) in the corner?

[yuzhenmi]

Yes. Right now, if you pin the annotation popup from gene list without pinning the gene list first, a click on the outside first pins the gene list, and a second click unpins them both. I am planning to fix this by switching to a more sophisticated method for determining whether to pin or unpin. As for the popup remaining after switching view, I forgot to remove the annotation popup when the view becomes inactive. It should be fixed now. I think the X won't be necessary as long as these glitches are fixed.

[jamiewaese]

Just confirming this is still on your radar?

I love click to pin, and I think a lot of people will intuitively use it this way. But I notice that it takes two clicks outside the box to make the popup disappear.

On 2013-10-13, at 3:05 PM, Hans Yu notifications@github.com wrote:

Yes. Right now, if you pin the annotation popup from gene list without pinning the gene list first, a click on the outside first pins the gene list, and a second click unpins them both. I am planning to fix this by switching to a more sophisticated method for determining whether to pin or unpin. As for the popup remaining after switching view, I forgot to remove the annotation popup when the view becomes inactive. It should be fixed now. I think the X won't be necessary as long as these glitches are fixed.

— Reply to this email directly or view it on GitHub.

[yuzhenmi]

Yep, this is still on my to-do list. I am planning to do some code clean-up for the chromosome view and make the changes that Nick requested, starting tomorrow. I feel that the chromosome view is mature enough to have a more-or-less finalized code structure now. I will fix this as I clean up the code.

[yuzhenmi]

I am cleaning up the chromosome view, so the ePlant page probably won't work for a while.

Edit: I've created a backup for the chromosome view which is being used for the page for now. Edit again: I've switched out the backup and replaced it with the incomplete but cleaned version of chromosome view.

Current progress: Oct 17 -Created Eplant namespace for ePlant-specific global properties. -Defined class structures for ePlant-relevant data such as Species, Chromosomes, Genes, etc. -Created userAnnotations property for ChromosomeView, which keeps track of user annotations. This is a list that will be synchronized with GenesOfInterest, but with properties specific for ChromosomeView such as the width and color of the annotation marker. The rationale is to keep GenesOfInterest as clean and view-non-specific as possible. -Cleaned up ChromosomeView class constructor for readability and maintainability. -In the process of implementing chromosome loading by JSON files. -In the process of creating a globally-accessible list of GenesOfInterest, where each item in the list is associated with a gene and views for that gene. This is the list of to-be-loaded or loaded genes. -In the process of moving the annotation popup class to the Eplant namespace, and modifying it so that it can be used by any view.

Oct 18 -Still in the process of moving/rewriting/cleaning annotation popup class under the Eplant namespace. -In the progress of moving the gene list popup class to the Eplant namespace (similar to the annotation popup class). -Lots of code left to clean and redesign...

Oct 19 -Finished implementing chromosome loading by JSON files. This is done with REST: http://bar.utoronto.ca/~eplant/cgi-bin/chromosomeinfo.cgi?species=Arabidopsis_thaliana -Still cleaning up...

Oct 20 -Cleaned up most of the draw function. -User annotation is redesigned and cleaned up. Still need testing (see below). -Gene list and annotation popups are mostly redesigned and cleaned up. They are not yet implemented due to unavailability of gene data. Web services still have to be written for retrieving a list of genes from chromosome positions and for retrieving gene data (waiting for Asher to provide relevant database information). -Cleaning up of mouseMove event handler is postponed because it deals with gene list and annotation popups (see above). -Removed camera dampening for consistency with plugins and to avoid subtle camera movements after HTML-based UIs are generated. -ChromosomeView entry and exit zooming animations are now modeled after an exponential function f(x) = A * B^(x), where A is a constant, B is a constant less than 1, and x is derived from the frame (x = frame, if zooming in; x = lastFrame - frame, if zooming out). -Renamed views: geneSelector to chromosome, worldEFP to world, plantEFP to plant, cellEFP to cell, cytoscape to interaction, reactome to pathway, JSmol to molecule, and tracks to sequence.

[jamiewaese]

Thanks for the heads up.

You doing the icon dock too?

Can you centre the canvas on the select species page?

(I'm at an airport hotel in New York. My flight from Atlanta had mechanical issues. So random.)

On Oct 17, 2013, at 9:09 PM, Hans Yu notifications@github.com wrote:

I am cleaning up the chromosome view, so the ePlant page probably won't work for a while.

— Reply to this email directly or view it on GitHub.

[yuzhenmi]

I approximately centered the canvas (changed left offset to -60px).

I imagine after I write the code for loading genes, I can make the icon dock functional (at least for the views that I've currently written).

[yuzhenmi]

I did a temporary fix for the pinning issue to the uncleaned code.

[yuzhenmi]

This should no longer be an issue with the new code.

[jamiewaese]

Sorry to report it's still an issue. Here's a screengrab:

And another:

[yuzhenmi]

Oh yes, I forgot to remove residual popups when the screen becomes inactive, in the new code. Should be fixed now.

[jamiewaese]

Works good!