Hi Mark,
Thanks for the useful feedback. Please kindly find below the response to your queries:
I do not know if it will conflict with the install anywhere version of 2.8.2 that I previously installed.
The .jnlp version cannot conflict with the install anywhere version that you have previously installed.
The Find command with the Description option checked only searches in the first 10 sequences!
Jalview ‘Find’ operation works based on the current selection group in an alignment. I suspect that you have made a selection on the first 10 sequences. You can use the ‘Deselect All’ option from the ‘Select’ menu in the alignment window to clear the current selection group before carrying out the find operation.
It also does not return the “Finished Searching” dialog box.
The ‘Finished Searching’ dialog box is always returned after every search operation and works perfectly here. Kindly enable the jalview java console from the ’Tools’ menu to see if there are any error logs, and send them to me.
Also, the Find command window should retain the checked options between executions.
This is sensible and I will add it to the bug tracker and implement it as soon as possible.
Also, it is possible to open multiple Find windows. Is this expected?
Yes, this is expected as Jalview permits users to open as much windows as they wish for most of its components.
Also, shouldn’t the Return key be tied to the Find Next button?
The return key is already tied to the ‘Find next’ button and is working perfectly here. What environment did you try it on?
The Find all key does not seem to work.
This also works over here. Please kindly follow these steps and inform me if is still not working for you:
- ensure that the ‘Include description’ option is checked.
- ensure that you have cleared all selection groups. Alternatively, if you intentionally want to search a unique selection group, kindly investigate that the target description exists within the sequences in your current selection group.
I hope you find this helpful. I look forward to hearing from you again.
Kind regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk
···
On 2 Feb 2015, at 06:14 pm, Mark A Saper <saper@umich.edu> wrote:
Hi Charles,
Many thanks for looking at it. I downloaded the .jnlp for the development version and am running it. I do not know if it will conflict with the install anywhere version of 2.8.2 that I previously installed.
The Find command with the Description option checked only searches in the first 10 sequences! It also does not return the “Finished Searching” dialog box.
Also, the Find command window should retain the checked options between executions. Also, it is possible to open multiple Find windows. Is this expected?
Also, shouldn’t the Return key be tied to the Find Next button? It isn’t.
The Find all key does not seem to work.
Mark
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353On Feb 2, 2015, at 6:39 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:
Dear Mark,
The search algorithm have been modified to include the description field of an alignment’s sequences during a search operation. The changes have been committed to the development branch assessable at http://www.jalview.org/development/development-builds. Please kindly try it out let us know if there is any other way we can improve it further.
Kind regards,
CharlesOfoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.ukThe University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096