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nextSpeciesBranchNumber < 0 #4
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I just cloned the |
It looks to me (who still doesn't know anything about what's going on in the package) like the issue might have to do with the construction of Embeddings. When a new Other than that, |
Hm, weird. Now I see the tests succed as well, but it appears the only changes I reverted were some tries related to #5 which were half-baked enough that they prevented compilation anyway… Sorry to fill in this confusing issue. Can you explain |
I'm sorry for the lack of response. A lot of things have been going on, and some related code has been lost. Closing this issue anyway... |
After wondering why I get so many NullPointerExceptions,
I noticed the assertions in
speciesnetwork/src/speciesnetwork/GeneTreeInSpeciesNetwork.java
Line 147 in d26c528
and below and activated assertions in the JVM, which led to
Exception in thread "main" java.lang.AssertionError at speciesnetwork.GeneTreeInSpeciesNetwork.recurseCoalescentEvents(GeneTreeInSpeciesNetwork.java:147)
.I don't know how traversal numbers should behave and what the getDirection function is supposed to do,
but the calls above that look reasonable.
@zhangchicool I sent you my XML files that produce this issue, in case that might help track down the problem because it's a user error.
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