Hi Gershon. Thanks for taking the time to think about this.
You mentioned that there is a need for a few minor patches for this Node (ancestral) sequence - feature. i already started to look on Jalviewlite source and seems very organized
and well documented. Now we are short in time and our best interest to make it happen the sooner the better because we need it for our new FastML server.
i am familiar with Java and with your assist i am positive i could write these patches.
OK - that’s really good to hear !
The first steps are to register on http://issues.jalview.org, and then see if you can checkout the jalview source via
git clone http://source.jalview.org/git/jalview.git
Since you’re interested in making a quick patch, I’d suggest working off the v2.7 branch, rather than the v2.8 branch which is still under development. I’m assuming you’re not familiar with git, and have provided below all the necessary commands to create a new branch of the 2_7 source that will allow you to easily patch it. If you’d prefer to work another way, feel free!
git checkout Release_2_7_Branch
git branch -b JAL-1055_ancestral_nodes
This will create a new local branch that you can work in. I use the git-flow formalism for working with the jalview source, so when your happy with your new features, do the following:
(do commits to branch with git commit)
git checkout Release_2_7_Branch
git merge JAL-1055_ancestral_nodes --squash --no-ff
I’ll then give your issues.jalview.org username write access to the repository so you can push the changes, alternately, you can send me a patch and I’ll commit it to the repository myself.
As for developing, you should be able to use the cloned directory as a project in your favourite java dev. I use eclipse - and you should be able to import the project from the file system. Eclipse should use the ant build.xml to build jalview. There’s also a netbeans project, but that might not work straight out of the box. For testing, use the applet launcher with arguments as you would normally use for the applet tag in the web page, and if you like, you could also add in another example to the ‘examples’ directory demonstrating the ancestral node/alignment connection.
Ok - now the patch. There are two parts to this:
- Patch the node/sequence association routine in the tree viewer so that you can associate internal nodes with alignment sequences.
The association happens in the constructor : jalview.analysis.NJTree(SequenceI seqs, NewickFile treefile)
All you need to do is make Jalview loop over the internal nodes, too, and find a match for those nodes in the sequence set.
- Patch the mousePressed handler method in the TreeCanvas so it includes the internal nodes when :
- a node is clicked - this should select the associated ancestral sequence
- the tree area is clicked so the tree is partitioned and partitions include the ancestral sequences for the subtrees.
Finally, you might want to consider the following:
3. Add an option in the ‘View’ menu of the tree allowing the user to disable the ancestral sequence associations when interacting with the tree and so recover the original jalview v2.7 behaviour. Sometimes, only the ‘real’ sequences may be desired - although I think a bit of experimentation will be needed to work out when this is really the case - there might also be a need to mark these sequences in the alignment view too, enabling the user to select them or exclude them from some analyses.
Oh - I’ve also added you to the jalview-dev email list, which I’ve also cc’ed this message to.
Let me know how you get on !
Jim.