nanlandetian / forester Goto Github PK

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

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

note missing 'e' in calculat~

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.

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!

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

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

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

If so, I could volunteer to help :)

Thanks!
Bruno

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?

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!

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).

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