Feature suggestion

The file chooser on the current version of jalview running on OS 10.9.5, latest Oracle Java 7, leaves a lot to be desired. (Apple's is not so great either). No easy way to navigate to recently used folders, etc. Are there better ones out there that could be implemented?

Also when I define a feature and select a color, it appears to be in the foreground rather than the background. Adjusting the contrast helps a bit. Am I missing something? Is it possible to construct a tree based on selected portions of an alignment, or do I have to create a new alignment with the regions of interest.

Many thanks for any comments.

Mark Saper
3040 & 3250 Chemistry Building
Dept of Biological Chemistry
saper@umich.edu
734 764 3353 office 734 276 6505 mobile

Hi Mark,

I see your point about the chooser - we need to look at that.

I'll just answer the last point - others will be better placed to comment on the other issues.

You can certainly make a tree from a selection of columns. Just hide the parts of the alignment you don't want to calculate the tree for.

If you want to keep this view of the alignment and switch from the full alignment to the one with hidden columns then first create a new tabbed view of the alignment and do your hiding there.

The hide columns feature in jalview and the ability to have multiple editable "views" on the same alignment are extremely useful for this sort of thing.

I hope this helps,

Geoff.

···

On 30/01/2015 02:39, Mark Saper wrote:

The file chooser on the current version of jalview running on OS 10.9.5, latest Oracle Java 7, leaves a lot to be desired. (Apple's is not so great either). No easy way to navigate to recently used folders, etc. Are there better ones out there that could be implemented?

Also when I define a feature and select a color, it appears to be in the foreground rather than the background. Adjusting the contrast helps a bit. Am I missing something? Is it possible to construct a tree based on selected portions of an alignment, or do I have to create a new alignment with the regions of interest.

Many thanks for any comments.

Mark Saper
3040 & 3250 Chemistry Building
Dept of Biological Chemistry
saper@umich.edu
734 764 3353 office 734 276 6505 mobile
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--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
College of Life Sciences | University of Dundee, Scotland, UK | g.j.barton@dundee.ac.uk
Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton
  
The University of Dundee is registered Scottish charity: No.SC015096

Hi Mark - thanks for emailing! Here are a few additional comments below..

I see your point about the chooser - we need to look at that.

There are a few ideas in the works, since we're currently in the process of redesigning Jalview, but for the moment you might actually find it easier to drag and drop files into Jalview from the Finder. Once Jalview has accessed a file, clicking on the file in the recent file list will browse to that directory, so you can easily return to a place where you've already imported/saved data.

Also when I define a feature and select a color, it appears to be in the foreground rather than the background. Adjusting the contrast helps a bit. Am I missing something?

Do you mean in the dialog, or in the actual alignment view ? If the latter then you're absolutely right - Jalview renders features *over* the alignment view using an exclusive-or colour blend (with transparency if you adjust the slider), which means the letters can sometimes become difficult to distinguish (this was actually what the earlier most from Haim Askenazy concerned).

Jim.

···

On 30/01/2015 09:42, Geoff Barton wrote:

Jim & Geoff,

Many thanks for your comments! The recent file list available in the Open dialog has been useless on OS X because it is so narrow, and no way of changing it (perhaps I don’t know the Java tricks), even if I widen the entire dialog window. I can send a screenshot off list if you need it. But as you suggested, I most often open files by dragging into the Jalview window.

Also the Save As window has no recent files or directories window. But it will remember where it saved last. But it was nice to see that I can drag a directory into the dialog to change directories (same as OS X functionality).

Hope my comments are helpful. Also, I use Jalview often and appreciate all of your work to share it with the community!

Mark

PastedGraphic-1.png

···

Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
c/o Biophysics, Chem 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

On Jan 30, 2015, at 6:58 AM, Jim Procter <foreveremain@gmail.com> wrote:

Hi Mark - thanks for emailing! Here are a few additional comments below…

On 30/01/2015 09:42, Geoff Barton wrote:

I see your point about the chooser - we need to look at that.

There are a few ideas in the works, since we’re currently in the process of redesigning Jalview, but for the moment you might actually find it easier to drag and drop files into Jalview from the Finder. Once Jalview has accessed a file, clicking on the file in the recent file list will browse to that directory, so you can easily return to a place where you’ve already imported/saved data.

Also when I define a feature and select a color, it appears to be in the foreground rather than the background. Adjusting the contrast helps a bit. Am I missing something?

Do you mean in the dialog, or in the actual alignment view ? If the latter then you’re absolutely right - Jalview renders features over the alignment view using an exclusive-or colour blend (with transparency if you adjust the slider), which means the letters can sometimes become difficult to distinguish (this was actually what the earlier most from Haim Askenazy concerned).

Jim.

Dear Mark,

Thanks for your helpful comments and suggestions. We are now in the fortunate position of having an expanded team working on Jalview, development will progress more quickly, so we are keen to hear suggestions from people who use the program regularly like yourself. Please keep them coming!

All the best,

Geoff.

···

On 30/01/2015 17:09, Mark A Saper wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
College of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096