Rename pll_msa_t fields "count" and "length" to "taxa" and "sites" respectively

[pierrebarbera]

Current definition:

/* multiple sequence alignment */
typedef struct pll_msa_s
{
  int count;
  int length;

  char ** sequence;
  char ** label;
} pll_msa_t;

count and length are completely ambiguous. Renaming them to taxa and sites (or equivalent) would clear up confusion.

Side note: I think their type should be brought into line with the rest of pll also (unsigned int, maybe even long)

[pierrebarbera]

Also lets pluralize sequence and label :)

[amkozlov]

|count| and |length| are completely ambiguous. Renaming them to |taxa| and |sites| (or equivalent) would clear up confusion.

I guess |count| [of sequences] and |length| [of sequences] are still a bit more general, e.g. sequences are not necessarily taxa, strictly speaking - think EPA reads etc.

Side note: I think their type should be brought into line with the rest of pll also (|unsigned int|, maybe even |long|)

Yes, it must be unsigned long, we already agreed upon it with Tomas.

[stamatak]

On 21.09.2016 15:14, Alexey Kozlov wrote:

|count| and |length| are completely ambiguous. Renaming them to |taxa| and |sites| (or equivalent) would clear up confusion.

I guess |count| [of sequences] and |length| [of sequences] are still a bit more general, e.g. sequences are not necessarily taxa, strictly speaking - think EPA reads etc.

up to you guys to decide

Side note: I think their type should be brought into line with the rest of pll also (|unsigned int|, maybe even |long|)

Yes, it must be unsigned long, we already agreed upon it with Tomas.

yes :-)

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University of Arizona at Tucson

www.exelixis-lab.org