Make tree hovers and highlights easier to see when viewing very large trees

[Robert Leach]

USE CASE: WHAT DO YOU WANT TO DO?

I want to look at a very large tree and see where selections and highlights are.

STEPS TO REPRODUCE AN ISSUE (OR TRIGGER A NEW FEATURE)

1. Open 11.cdt
2. Select a node of the gene tree that is close to the root
3. Hover around the tree

CURRENT BEHAVIOR

Yellow selections and red highlights are randomly broken by black branches that are drawn over them:

EXPECTED BEHAVIOR

The overall shape & breadth of selections and hovered subtrees should be clearly visible.

DEVELOPERS ONLY SECTION

SUGGESTED CHANGE (Pseudocode optional)

One idea is to paint the different colors in different orders, instead of painting all colors as we encounter each branch. For example, drawing things in this order could help:

1. All yellow branch highlights
2. All black branches
3. All red branches
4. All yellow subtree dots
5. The red subtree dot

One problem with this is that in the example data, you'd never see the yellow branch highlights. A better solution might be to draw black and then yellow highlights.

FILES AFFECTED (where the changes will be implemented) - developers only

ArrayDrawer.java

LEVEL OF EFFORT - developers only

medium

COMMENTS

Note, the gene tree file (.gtr) for John's data 11.cdt might be messed up. I think that the problem is very much mitigated by having a properly formatted tree file.

[Robert Leach]

I discovered that TV2 displays this tree the same way - as a mess of branches going in all sorts of bad directions (some even "up"). When viewing another properly generated version of the tree, both TV2 and TV3 display it the same way and branch highlights are not bad. There are still some overdrawn branches, but it's not nearly as bad as the depiction in this issue's attached image. Thus, I am marking the priority of this issue as trivial.

[Robert Leach]

Tree highlights are actually not that bad. The file used in generating the screen captures in this issue had corrupted tree data, which makes the issue look worse than it actually is. There should actually be an issue to catch tree data corruption like this.

[Robert Leach]

Removing milestone: Trees (automated comment)