adding new characters to matrix

[László Nagy]

Hi,

this sort of a is a follow-up on a previous conversation on how to add annotations to characters (in nexml, https://groups.google.com/forum/?fromgroups=#!topic/bio-phylo/b2xDbT2dxHo). Thanks to Rutger's example script (http://biophylo.blogspot.com/2012/05/reading-and-writing-complex-character.html), it is now clear how to add annotations, but what if I want to add new characters to the matrix? I have two options at this point. One is to create the matrix (I am generating characters one by one through simulation), write the matrix to a readable format using my own package (e.g. nexus) and try to parse it later in an other script using Bio::Phylo (and add annotations). The other option would be to add characters one by one to a Bio::Phylo matrix as I the simulation goes, write it to file as neXML and parse this neXML file by the next script (I need to write and re-parse the matrix anyway). The latter would be more elegant and maybe more bulletproof. I may miss something here, but I cant figure out how to add new characters to a matrix.

Thanks,
Laszlo Nagy

[Rutger Vos]

Hi László,

the list of characters is automatically updated as the matrix
grows/shrinks. This is done by means of a listener subroutine:
Bio::Phylo::Matrices::Matrix::_update_characters()

As for your second question, I would recommend staying within NeXML if
you want to preserve annotations that cannot be serialized to NEXUS.

Best wishes,

Rutger

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Dr. Rutger A. Vos
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NCB Naturalis
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