Disappearing branches in large tree

[lczech]

Hi,

when loading a large (~10,000 taxa) multifurcating tree and using the vertical zoom (mouse wheel), branches start disappearing at some point.

First:

Then, after a bit more zooming, the horizontal branch in the middle disappears: This happens with all branches after zooming more. The used tree file is the guide tree of SILVA: http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_ssu_123.1.tre

My wild guess is that it is a floating point issue... Dendroscope 3.5.7 on Ubuntu 14.04

Let me know whether you can reproduce or need any more information. Lucas

[husonlab]

Dear Lucas,

this is not a bug, but rather an optimization feature… Dendroscope can happily draw a tree with a couple of million nodes (10,000 is considered a small tree size for Dendroscope). Dendroscope stops drawing the details of a subtree once the number of leaves of the subtree is less than the height (as number of pixels) of the bounding box of the subtree and rather just draws the the bounding box.

If this is a problem for you then I could look into adding an option to turn this optimization off. Could you please send me a screen shot showing a situation where this is a problem. I looked at this on my mac and seems fine to me. However, I recently did some work on this feature and so it may well be the cause that there are some problems with it that I am unaware of

Best wishes daniel

On Jun 4, 2016, at 11:51, Lucas Czech notifications@github.com wrote:

Hi,

when loading a large (~10,000 taxa) multifurcating tree and using the vertical zoom (mouse wheel), branches start disappearing at some point.

First: https://cloud.githubusercontent.com/assets/4741887/15798889/19b1be42-2a4a-11e6-8264-bf28372322d1.png Then, after a bit more zooming, the horizontal branch in the middle disappears: https://cloud.githubusercontent.com/assets/4741887/15798888/19b098e6-2a4a-11e6-8442-c2304e8cecb2.png This happens with all branches after zooming more. The used tree file is the guide tree of SILVA: http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_ssu_123.1.tre http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_ssu_123.1.tre My wild guess is that it is a floating point issue... Dendroscope 3.5.7 on Ubuntu 14.04

Let me know whether you can reproduce or need any more information. Lucas

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[lczech]

Hi Daniel,

thanks for the quick answer. I should have mentioned that this is happening when zooming IN.

The bounding box thing is working correctly when zooming OUT:

However, when zooming in, branches disappear at some point. There should be no bounding box, as there are more than enough pixels per branch in this case (see pictures in my first post again).

I can also produce this behaviour with a very small tree (5 leaves):

((C,D)1,(A,(B,X)3)2,E);

Just by zooming in more and more, at some point, the branches disappear.

Lucas

[husonlab]

Please send me a screen shot because there is no problem for me on my mac or on a linux computer (Ubuntu 14.04)

Can you also try this on a different system?

On Jun 6, 2016, at 13:48, Lucas Czech notifications@github.com wrote:

Hi Daniel,

thanks for the quick answer. I should have mentioned that this is happening when zooming IN.

The bounding box thing is working correctly when zooming OUT: https://cloud.githubusercontent.com/assets/4741887/15820881/96405ff6-2bec-11e6-9b5b-d0264f5b755a.png However, when zooming in, branches disappear at some point. There should be no bounding box, as there are more than enough pixels per branch in this case (see pictures in my first post again).

I can also produce this behaviour with a very small tree (5 leaves):

((C,D)1,(A,(B,X)3)2,E); Just by zooming in more and more, at some point, the branches disappear.

Lucas

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— Daniel Huson, Professor of Algorithms in Bioinformatics, University of Tuebingen, Center for Bioinformatics (ZBIT), Department of Computer Science Sand 14, 72076 Tuebingen, Germany, Tel: +49 7071 2970450 Fax: +49 7071 295148 daniel.huson@uni-tuebingen.de mailto:daniel.huson@uni-tuebingen.de, www-ab.informatik.uni-tuebingen.de http://www-ab.informatik.uni-tuebingen.de/

[lczech]

Hi Daniel,

here is a screenshot-video of the process:

You might need to click on the image to see it in full resolution, as the scaled down version is already missing some branches due to the scaling...

I simply used the mouse wheel to zoom in more and more. You see branches disappearing, first on the left, later all of them. Sometimes, a branch briefly re-appears, which again suggests that this is a floating point issue (some rounding or so).

Lucas