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Re: [Seqan-dev] Time complexity of posGlobalize

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<-- date -->
  • From: "Weese, David" <weese@campus.fu-berlin.de>
  • To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Date: Tue, 26 Jul 2011 11:03:24 +0200
  • Acceptlanguage: de-DE
  • Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Subject: Re: [Seqan-dev] Time complexity of posGlobalize

Sorry, not O(m log m) but O(log m) - its a binary search.

--
David Weese				weese@inf.fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
Institut für Informatik			Phone: +49 30 838 75246
Takustraße 9					Algorithmic Bioinformatics
14195 Berlin					Room 021 

Am 26.07.2011 um 08:17 schrieb Weese, David:

> Hi John,
> 
> posGlobalize needs in either case constant time. posLocalize takes constant time only for pairs. Otherwise (for global positions = integers) it takes O(m log m) where m is the number of sequences.
> And yes, global positions help to save memory. But you can configure the type used in the position tables by overloading SAValue for your index. With Packed Pairs you specify the number of bits used for seqno and seqofs.
> 
> HTH
> David
> 
> Sent from my iPod. Sorry for being short.
> 
> Am 25.07.2011 um 11:49 schrieb "John Reid" <j.reid@mail.cryst.bbk.ac.uk>:
> 
>> Suppose I have an iterator over a suffix array. What is the time 
>> complexity of calling posGlobalise() on an occurrence the iterator? I'm 
>> asking because I have the option to store indexes to occurrences as 
>> global positions or as local positions (pairs of sequence ids, position 
>> in sequences). I'm guessing the latter is more time efficient but would 
>> take more storage.
>> 
>> Thanks,
>> John.
>> 
>> _______________________________________________
>> seqan-dev mailing list
>> seqan-dev@lists.fu-berlin.de
>> https://lists.fu-berlin.de/listinfo/seqan-dev
> 
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
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  • References:
    • [Seqan-dev] Time complexity of posGlobalize
      • From: John Reid <j.reid@mail.cryst.bbk.ac.uk>
    • Re: [Seqan-dev] Time complexity of posGlobalize
      • From: "Weese, David" <weese@campus.fu-berlin.de>
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