WIP: new more flexible underlying format to allow unrooted trees and better traversal #16
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due to clashes with `seriescolor` in Plots
Does not work yet
…ist to work efficiently rather than via references through tree.
Simpler tree type aliases also added: RootedTree, ManyRootTree, UnrootedTree
… nodes and branches instead of names.
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Obviously this is intended to address a lot of what's going wrong in #14. |
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This code works on v0.6.4 but segfaults on v1.0.2 on MacOS: julia> using Phylo
julia> nu = Nonultrametric(1000);
julia> treen = rand(nu);
julia> n = getnode(treen, "Node 400");
julia> nh = nodehistory(treen, n);
Segmentation fault: 11
Internal error: encountered unexpected error in runtime:
StackOverflowError()
subtype_ccheck at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:451
var_lt at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:506
exists_subtype at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:1079 [inlined]
forall_exists_subtype at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:1107
subtype_ccheck at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:461
var_lt at /Users/osx/buildbot/slave/package_osx64/build/src/subtype.c:506
... [3MB of repeats] ...
jl_type_infer at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:275
jl_compile_method_internal at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1786
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1830
bracketed_paste at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:1920
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1831
#55 at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:901
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1831
jl_apply at /Users/osx/buildbot/slave/package_osx64/build/src/./julia.h:1537 [inlined]
jl_f__apply at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:556
jl_f__apply_latest at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:594
#invokelatest#1 at ./essentials.jl:697 [inlined]
invokelatest at ./essentials.jl:696 [inlined]
#27 at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:1319
prompt! at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2360
run_interface at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2263
run_frontend at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:1034
run_repl at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:191
#719 at ./logging.jl:309
jfptr_#719_5936.clone_1 at /Users/richardr/Applications/Julia-1.0.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/osx/buildbot/slave/package_osx64/build/src/./julia.h:1537 [inlined]
jl_f__apply at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:556
jl_f__apply_latest at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:594
#invokelatest#1 at ./essentials.jl:697 [inlined]
invokelatest at ./essentials.jl:696 [inlined]
macro expansion at ./logging.jl:306 [inlined]
run_main_repl at ./client.jl:334
exec_options at ./client.jl:246
_start at ./client.jl:425
true_main at /Users/richardr/bin/julia-1.0 (unknown line)
main at /Users/richardr/bin/julia-1.0 (unknown line)now that I check with that. It seems to do it non-deterministically, and I wonder whether it's the garbage collector getting tied up in the recursive data structures, but I have no reason for saying that beyond the fact that it's crashing at different times on different runs... |
plotting of AbstractTrees; close #8
…ist to work efficiently rather than via references through tree.
Simpler tree type aliases also added: RootedTree, ManyRootTree, UnrootedTree
… nodes and branches instead of names.
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Most of the new interface is working now, but not the iterators yet, and there are definitely some problems with finding routes through the tree - Julia v0.6 hangs and v1.0.2 crashes inconsistently. Linked list issues arise from impossibility of forward references - JuliaLang/julia#269 was well aware of this in 2011 - and so branches (edges) can only hold abstract base classes of nodes (vertices), but nodes can hold branches directly. It's a bit of a fudge, but works for now until v1.x when forward references become a thing...
More stuff I'm sure...