I see, I've hardcoded the most common attributes stored in nodes into the nodes themselves - branch-lengths and confidence values and so on. I can see this get's mind-bending in cases where nodes have different types and so on. I wonder if a different approach is better - I've just had an idea to do this differently, which might be a lot better. I'll write up some solid code later and post back.
On Tue, Feb 24, 2015 at 8:25 AM, Mauro <mauro...@runbox.com> wrote: > Sorry my first sentence should have read: > > Julia will *not* be able to produce specialised code for any > non-concrete type > > in your PhyNode. > > > > It does not matter whether it's Any or some other > > abstract/parameter-less type. At least that is how I read the docs: > > > http://docs.julialang.org/en/latest/manual/performance-tips/#type-declarations > > > > However, I think a method will only be slow if it actually uses the > > PhyNode.extensions field, otherwise it should be fine. > > > > Anyway, can you not construct your type like so: > > type PhyExtension{T} > > value::T > > end > > > > type PhyNode{T} > > name::String > > branchlength::Float64 > > confidence::Float64 > > extensions::Vector{PhyExtension{T}} > > children::Vector{PhyNode{T}} > > parent::PhyNode{T} > > end > > > > If a user needs to have different types of things in PhyNode.extensions > > she can choose PhyExtension{Any} and loose some performance, otherwise a > > concrete type, like PhyExtension{Float64}, will be fast. > > > > On Tue, 2015-02-24 at 02:30, Ben Ward <axolotlfan9...@gmail.com> wrote: > >> Hi, > >> > >> In Julia, if you are not sure of an arguments type beforehand, you can > use > >> 'Any', or if you know it comes under an abstract type, you can use that. > >> > >> I've been working on a type for BioJulia which allows for > representation of > >> a node of a phylogenetic tree that will allow annotation with biological > >> data in the form of other types from the packages from BioJulia: > >> > >> @doc """ > >> PhyExtension allows defining arbitrary metadata to annotate nodes. > >> > >> > >> this allows the PhyNode type to support any phylogenetic tree format > >> that includes annotations (e.g. PhyloXML, NeXML), and allows > programmatic > >> extension of nodes with annotations. > >> """ -> > >> type PhyExtension{T} > >> value::T > >> end > >> > >> > >> @doc """ > >> PhyNode represents a node in a phylogenetic tree. > >> > >> > >> A node can have: > >> > >> > >> - `name` > >> - `branchlength` > >> - one or more `extensions` > >> - a reference to its `parent` PhyNode > >> - reference to one or more `children` > >> """ -> > >> type PhyNode > >> name::String > >> branchlength::Float64 > >> confidence::Float64 > >> extensions::Vector{PhyExtension} > >> children::Vector{PhyNode} > >> parent::PhyNode > >> # Inner constructor goes here. > >> > >> As you can see - PhyExtension is parametric so can be constructed to > >> contain any type. > >> > >> I'm wondering, though is this the best that can be done, can I handle > the > >> potential to hold any number of types with unknown variables any better > - > >> if so, how? > >> > >> Is specifying a Vector of PhyExtension, where a PhyExtenision is a type > >> that contains any other type really giving that much information to the > >> Julia system to work on efficiently? > >> > >> My understanding is that PhyExtension is parametric so a version is > >> effectively defined for every possible {T} (including user defined > >> composite types they might come up with). But then I imagine that's not > >> much information when creating the Vector{PhyExtension} as an element > could > >> be any of the many possible PhyExtensions - the compiler has to allow > for > >> an array that can store any PhyExtension? Or is it that the array > contains > >> references to PhyExtensions so actually the array is simple? > >> > >> Thanks, > >> Ben. > >
