[Bioc-sig-seq] Rle vs RangedData

[Wolfgang Huber]

Hi Simon

just to be sure - what is n? Number of segments, or length of the 
(expanded) sequence?

And rather than looking at the time needed to access a single value at a 
certain position, shouldn't you be looking at the time needed to access 
the values on a complete equi-spaced grid from begin to end of the sequence?

	bw Wolfgang


Simon Anders ha scritto:
> Hi Michael
> 
> Michael Lawrence wrote:
>> An Rle object, even if it only stores the widths, would be better than 
>> RangedData. Just getting the starts out of a RangedData is an O(n) 
>> operation, and there is in general a lot of overhead for functionality 
>> that is not useful in your case.
> 
> Thanks.
> 
> But wait a second: Isn't there a slot "starts" in a RangedData object?
> So why would it be O(n) if this information is already there?
> 
> My concern was that getting the starts (or even just getting a value at
> a given position) from an Rle object would be O(n) because the Rle
> object does not contain the starts, only the lengths of the intervals.
> 
> So, what information is now stored where?
> 
> Cheers
>   Simon

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber