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https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> Minor annotation issues https://forum.ugene.net/forum/YaBB.pl?num=1289991652 Message started by Agu on Nov 17^th, 2010 at 6:00pm

Title: Minor annotation issues
Post by Agu on Nov 17^th, 2010 at 6:00pm

1- Ugene's qualifier "protein_len" (for CDS, gene or ORF) is including the stop codon, so it shows one amino acid longer proteins.

2- In annotations created with remote query (blast), the % identity is shown as 0% always (when placing the cursor over the annotation).

3- When exporting a sequence with annotations using the option complementary strand, puts the sequence in the proper (inverted) sense, but leaves the annotations in the original position.

PS: I'm trying to add screenshot, but is not easy...

[smiley=dankk2.gif]

Ugene v1.8, tested in Ubuntu 10.10 and Win XP

Screenshot_protein_len_101117.png (3 KB | )

Screenshot_identities_101117.png (11 KB | )

Title: Re: Minor annotation issues
Post by Konstantin Okonechnikov on Nov 18^th, 2010 at 12:52pm

Agu, thanks for bug report!

All issues are reproduced and will be fixed in 1.8.1 (to be released in the beginning of December).

Title: Re: Minor annotation issues
Post by Agu on Nov 19^th, 2010 at 9:14pm

Excellent.
I have another one, but it doesn't deserve a new post. Is just a weird behavior when touching the arrow of a feature: It "jumps" to the first position. Sometimes it is confusing as you don't know if that is the one you intended to display (see attachments).

gene1.png (22 KB | )

gene2.png (23 KB | )

Title: Re: Minor annotation issues
Post by Mikhail Fursov on Nov 23^rd, 2010 at 6:13pm

This issue was caused by lazy loading of annotations tree and sorting side-effect.

Fixed in v1.8.1

Title: Re: Minor annotation issues
Post by Agu on Feb 25^th, 2011 at 7:27pm

Hi!
This one is still "active" for blast results (jumping to the first position after displaying).

Title: Re: Minor annotation issues
Post by Maxim Syabro on Mar 1^st, 2011 at 7:06pm

Can't reproduce the bug in UGENE 1.9.1. Could you give more detailed scenario to reproduce this issue?

Title: Re: Minor annotation issues
Post by Agu on Mar 1^st, 2011 at 10:12pm

I'm using version 1.9.1 in Ubuntu 10.10. I've been trying to reproduce it in version 1.9.1 and 1.9.2-dev in XP but nothing. So it seems to be a OS related issue. Probably more complicated to fix, so I would forget it...

In case you still want to see it, please find attached a file. Even more strange, you won't see it if you try to drop down the results closer to the bottom, only happens with the upper results. :-?

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=jump.gb (35 KB | )

before_jump.png (152 KB | )

after_jump.png (47 KB | )

Title: Re: Minor annotation issues
Post by Mikhail Fursov on Mar 15^th, 2011 at 1:55pm

Agu, in v1.9.3 we plan to rewrite annotations viewer from the scratch.

The main goal of refactoring is to support very large (more than fits into main memory) data sets. This will affect internals of annotation viewer a lot, especially sorting issue. I would propose wait for 6-7 weeks more before we have v1.9.3 and check the result.