Hi Jim,
Great! I will start working on the Tree Puzzle web service in a
couple of weeks. I would be happy to share my work and would
definitely welcome assistance from yourself and Peter. I need to wrap
some other tasks up before I can turn to the web service development.
Thanks,
Joni
···
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1. Re: jabaws question about tree web service (Jim Procter)
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Message: 1
Date: Fri, 09 Sep 2011 12:28:35 +0100
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Subject: Re: [Jalview-discuss] jabaws question about tree web service
To: jalview-discuss@jalview.org, jabaws-discuss@compbio.dundee.ac.uk
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Hello Joni.
On 09/09/2011 11:57, Peter Troshin wrote:
Last but not least - we are very much interested in having a Tree-Puzzle
service in JABAWS. I wonder if you would consider sharing your work with
us. In that case I may be able to help you with the implementation.
I'd also like to second what Peter said. It is high time that Jalview
included services for phylogeny, and I would be very happy to help out
if you are willing to contribute your work to Jalview's codebase.
Hope to hear from you soon...
Jim.
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Excellent news!
I'll shortly add you to the jalview development mailing list, and once you've registered at issues.jalview.org, I'll set you up with commit rights to the git repository.
Adding in a phylogeny service interface should be reasonably straight-forward from Jalview's side, providing the JABAWS interface returns a standard newick tree file. (If you need anything more complex... e.g. parsing of NHX format files or working with phyloXML, then the phylogeny parser in jalview may need an upgrade).
Jim.
···
On 12/09/2011 18:13, Joni Fazo wrote:
Hi Jim,
Great! I will start working on the Tree Puzzle web service in a
couple of weeks. I would be happy to share my work and would
definitely welcome assistance from yourself and Peter. I need to wrap
some other tasks up before I can turn to the web service development.
It would be nice to have NHX capabilities, so we can annotate the various nodes and work with arbitrary length names.
-David
David M. Goodstein, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
Center for Integrative Genomics / UCBerkeley
http://www.phytozome.net
···
On 12 Sep 2011, at 10:51, Jim Procter wrote:
On 12/09/2011 18:13, Joni Fazo wrote:
Hi Jim,
Great! I will start working on the Tree Puzzle web service in a
couple of weeks. I would be happy to share my work and would
definitely welcome assistance from yourself and Peter. I need to wrap
some other tasks up before I can turn to the web service development.
Excellent news!
I’ll shortly add you to the jalview development mailing list, and once
you’ve registered at issues.jalview.org, I’ll set you up with commit
rights to the git repository.
Adding in a phylogeny service interface should be reasonably
straight-forward from Jalview’s side, providing the JABAWS interface
returns a standard newick tree file. (If you need anything more
complex… e.g. parsing of NHX format files or working with phyloXML,
then the phylogeny parser in jalview may need an upgrade).
Jim.
Jalview-discuss mailing list
Jalview-discuss@jalview.org
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Hi David.
It would be nice to have NHX capabilities, so we can annotate the various nodes and work with arbitrary length names.
Jalview's tree viewer doesn't support any NHX annotations, but the parser does support quoted node names and preserves all node comments within the tree datamodel, so they are there if you want to parse them out.
Unfortunately, when I was working on it, I didn't have a comprehensive set of NHX files to test the parser with, and instead left in checks that will raise a warning dialog if the tree file contains NHX annotations to warn the user that there may be problems. If you know (and trust) the source of the file, however, then it should be possible to safely squash that error within the JABAWS phylogeny service web service client.
What NHX annotations are you interested in using ? It's of course possible to extend Jalview to cope with anything, but we should seriously consider if it will be more efficient to incorporate Archeopteryx, if you need full NHX capabilities.
Jim.
ps. Everyone on this thread is now subscribed to the jalview-dev list, so we should move further discussion there.
pps. arbitrary length node names are only important if you are importing trees from outside of Jalview. Normally, any sequences sent to a service have an autogenerated ID string, and jalview replaces the ID with the displayed sequence name when the results are retrieved.
···
On 12/09/2011 19:05, David M. Goodstein wrote:
Hi David.
It would be nice to have NHX capabilities, so we can annotate the various nodes and work with arbitrary length names.
Jalview’s tree viewer doesn’t support any NHX annotations, but the parser does support quoted node names and preserves all node comments within the tree datamodel, so they are there if you want to parse them out.
Unfortunately, when I was working on it, I didn’t have a comprehensive set of NHX files to test the parser with, and instead left in checks that will raise a warning dialog if the tree file contains NHX annotations to warn the user that there may be problems. If you know (and trust) the source of the file, however, then it should be possible to safely squash that error within the JABAWS phylogeny service web service client.
What NHX annotations are you interested in using ? It’s of course possible to extend Jalview to cope with anything, but we should seriously consider if it will be more efficient to incorporate Archeopteryx, if you need full NHX capabilities.
If we can support long names, bootstraps, and the ability to provide URLs to crown nodes with the current Jalview version of newick, there probably isn’t any need to go to NHX.
-David
Jim.
ps. Everyone on this thread is now subscribed to the jalview-dev list, so we should move further discussion there.
pps. arbitrary length node names are only important if you are importing trees from outside of Jalview. Normally, any sequences sent to a service have an autogenerated ID string, and jalview replaces the ID with the displayed sequence name when the results are retrieved.
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley
···
On Sep 13, 2011, at 1:30 AM, Jim Procter wrote:
On 12/09/2011 19:05, David M. Goodstein wrote: