cmzmasek / forester Goto Github PK

Phyloxml trees with colored nodes or branches are sometimes displayed in black and white. Opening additional trees in archaeopteryx tends to solve this issue, as does restarting the app.

This behaviour occurs both in Windows and linux, but I haven't found a good way to reproduce it.

Parse a tree using parser, from any format - PhyloXML, Newick etc. Calling 
isDuplication() or isSpeciation() will give incorrect values (comparing to what 
is in the file).

Original issue reported on code.google.com by [email protected] on 6 Jan 2015 at 8:33

At BioJava we are using the forester library within the biojava-phylo module. It's all working great with forester, except for the dependency management. We use maven (as many people these days in the java world) but forester does not exist in maven central. In the past we've solved this by publishing a forester artifact under the org.biojava.thirdparty group, but that required some manual work. We now need to update to version 1.038 of forester (see biojava/biojava#350) so we are going to go through the process of publishing to maven again.

To avoid some of that work for the future I'm considering submitting a pull request to mavenise forester. Would that be a welcome solution? It would require some reorganisation of the project so that it follows the maven layout convention (java code under src/main/java, java-related resources under src/main/resources, testing java code under src/test/java).

I have created an Ubuntu snap package for archaeopteryx, to make it easy for ubuntu users to install it. For now, it is based of the .jar from the latest git commit.

I would like to base it off the latest stable release, but to do that the git repository needs to tag stable commits, since the snap build system only accepts tags as targets. Would it be possible to tag stable releases so that users get the latest stable version on ubuntu?

Hi,

using 'infer ancestor taxonomies' and saving the resulting tree results in the following error upon trying to re-open it:

In contrast to archaeopteryx-js this version doesn't read the tag but writes it...
Is this issue already fixed in the current source code? Could the .jar file be updated or should I try to compile the whole thing?

Thanks,
Alex

What steps will reproduce the problem?
1.  Put the attached file (tree_nhx.nhx) in a location where it is accessible 
via HTTP
2.  Execute "java -jar forester_1027.jar"
3.  Select "File > Read Tree from URL/Webservice...", and specify the URL of 
tree_nhx.nhx.

What is the expected output? What do you see instead?

    A tree should be rendered; however, nothing is rendered.

    A tree *is* rendered if the file is downloaded locally and opened via "File > Read Tree from File..."

What version of the product are you using? On what operating system?

    Archaeopteryx 0.9812 A1ST (forester_1027.jar), OS X 10.8.3, Java 1.6.0_43 & 1.7.0_17.

    Archaeopteryx 0.957 beta does render a tree from this NHX file via http using "Read Tree from URL/Webservice..."

Please provide any additional information below.

    Tree file attached.

-- 
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit

Original issue reported on code.google.com by [email protected] on 8 Apr 2013 at 5:11

Attachments:

• tree_nhx.nhx

PhylogenyMethods.calculatBranchLengthStatistics(phylogeny)
PhylogenyMethods.calculatConfidenceStatistics(phylogeny)
PhylogenyMethods.calculatConfidenceStatistics(phylogeny)

note missing 'e' in calculat~

Original issue reported on code.google.com by [email protected] on 6 Jan 2015 at 8:36

What steps will reproduce the problem?
1. get a tree with taxonomic mappings
2. convert to circular type
3. call "Collapse species-specific subtree" command

What is the expected output? What do you see instead?
I expect the species-specific subtrees to collapse, but instead the circular 
tree shrinks and many lines point to nowhere.


What version of the product are you using? On what operating system?
Forester 1.036
Archaeopteryx 0.9898
Java 1.7.0_65
OS Linux amd64 3.2.0-4-amd64

Original issue reported on code.google.com by [email protected] on 16 Sep 2014 at 10:10

Hi, any plans to release forester to the Maven central repository 
(search.maven.org)? 

If so, I could volunteer to help :)

Thanks!
Bruno

Original issue reported on code.google.com by [email protected] on 18 Jun 2014 at 11:46

If there's no sequence, calling getSequence() in NodeData class throws NPE. It 
would be preferable if null was returned instead.

Original issue reported on code.google.com by [email protected] on 6 Jan 2015 at 8:34

Steps to reproduce problem:

1. Open up two identical trees with very different branch lengths
2. Switch each window view mode to "Unrooted"
3. Observe that the scales in the bottom left corners are approximately the 
same size
4. ... and that when you press +x the scale changes size, but the tree does not

I would expect to see that the scale is correct in the unrooted mode.

We're using Forester 1.027 (Acheopteryx .9812).

A fix for this would be awesome and greatly appreciated, as would a disclaimer 
somewhere in the mean time.

Thanks!

Original issue reported on code.google.com by [email protected] on 23 May 2013 at 9:36

If a tree is imported into Archeopteryx which includes nodes that must be 
quoted because they contain special symbols (e.g. brackets), then editing the 
node name to include a quote symbol and saving the tree as a newick file will 
yield a file that cannot be imported again.

'pre_quote_tree.tree' is a two node tree where the node names must be quoted 
due to special symbols.
'fail_quote_tree.tree' is the same tree where I edited the node name in 
Archeopteryx to include a ' and then exported it.

fail_quote_tree.tree can't be imported again.






What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 13 Jun 2013 at 5:40

Attachments:

• pre_quote_tree.tree
• fail_quote_tree.tree

Hi,
I faced some compilation errors in certain cases due to unmappable character 
for encoding ASCII.
This depends on java compiler warning sets


Here is error:
    [javac] /tmp/buildd/biojava3-live-3.0.5/biojava3-forester/src/main/java/org/forester/test/Test.java:1313: unmappable character for encoding ASCII
    [javac]                     .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489???493." ) ) ) {


It is minor but can prevent some builds. Could you please fix this?

Original issue reported on code.google.com by [email protected] on 5 Dec 2012 at 8:47

Hi! The license of this tool is "hidden" under forester/doc. Even github does not find it. Therefore, I suggest to place it in a more standard location, i.e., in the root of the repo. Thanks!

Hi!

thank you for the tool!

{colour-coding is red/blue/green based on reads mapping against specific edges}

Is it possible at all to retain only the coloured and/or wider branches of a tree, rather than scrolling through the tree to tick/untick the desired nodes and then "retain selected node"?

thank you!

Hi @cmzmasek,

currently, @jhcepas, @stamatak and I are working on an update to our article on the incorrect mapping of support values after tree rooting.

Archaeopteryx (and therefore forester) is one of the few tree viewers that correctly supports the distinction between values that belong to inner nodes vs those that belong to edges of the tree. Well done! This is particularly an issue when reading Newick files (as there is no distinction in the format), and can most easily be observed when rerooting the tree - see the article for details.

However, there is one issue that we assume to be a bug: In the section “Display Data” of Archaeopteryx, there is an option "Confidence Values", which however does not display the confidence values, but only shows them when hovering the mouse over a node. Is this behaviour intended?
(This assumes that the option “Internal Node Names are Confidence Values” is checked, as described in the manual.)

If this is not the intention, do you want to fix this? We would be happy to include this as an update to our article.

Edit: We also reported the behaviour of ATV, and found that different versions of it seem to switch between interpreting inner values as belonging to nodes or edges. As far as I could figure it out, ATV is no longer maintained, so we might just drop it from the article. What do you suggest?

Thanks
Lucas

Hi,
the Debian Med team (a group inside Debian with the objective to package free software in life sciences) considers packaging forester for official Debian. It would simplify our work if you would consider release tags to mark what state of code is a release that can be distributed to the users.
Kind regards, Andreas.

I am using forester_1023.jar which I found there is no more this constructor, 
how could I make nodes with my own names?
Thanks!

Original issue reported on code.google.com by [email protected] on 14 Mar 2013 at 9:20

I am seeing an issue with reading phylogenies with your library. I have multiple files to read phylogenies from sequentially.

Issue is that, once I read the first file, the NODE_COUNT in PhylogenyNode does not reset to 0. That is why, the second file's root does not start with 0 but a count after, where the last file ended. This does not appear to be a correct behavior.

I see that method PhylogenyNode.setNodeCount

synchronized final static void setNodeCount( final long i ) {
       PhylogenyNode.NODE_COUNT = i;
   }

is not accessible from outside the class which prevents me to reset it before I run read phylogenies for second file.

Since NODE_COUNT is a static variable it will live till the class remains loaded by a class loader. Is there a reason why the variable is static? Could we expose this setNodeCount() in PhylogenyNode?

This is the code snipped where I am trying to read multiple files, for your reference.

for (String aFile : files) {
            System.out.println(aFile);

            Phylogeny[] phylogeny = ParserUtils.readPhylogenies(aFile);

           for (Phylogeny p : phylogeny) {
                PhylogenyNode root = p.getRoot();
                System.out.println("Root node: " + root.getName() + " , ID: AN" + root.getId());
                //some more code
            }

        }

Alternatively, if this is not a correct usage for the lib please let me know.

I am using forester_1030.jar

According to 
http://www.phyloxml.org/documentation/version_1.10/phyloxml.xsd.html#h-853091232
, I should be able to set Id (i.e. identifier) for Phylogeny, Clade and 
Taxonomy.

I am using class org.forester.phylogeny.PhylogenyNode to create clades.

setIdentifier method is not defined for class 
org.forester.phylogeny.PhylogenyNode 

Original issue reported on code.google.com by [email protected] on 21 Apr 2014 at 11:24