Well, I have implemented a first version that is running quite well for me and my needs/specifications, although I did not integrate it directly into the biojava class hierarchy yet. Is anyone interested in taking a look at it and giving me some feedback if I shoud invest the time and work to make it includable into biojava?
Hannes On Wed, Nov 9, 2011 at 10:01, Hannes Brandstätter-Müller <[email protected]> wrote: > Thanks. > > I am thinking about implementing a modified MatrixAligner to fit my > needs here. Direct Levenstein Distance is not exactly right for my > application, because there are 0 to n insertions/deletions. > > A direct LevensteinDistance as implemented in would not give me all > the Information I need. > > Thanks for the hints and input. > > Hannes > > PS we seriously need more examples in the Cookbook - I'll submit some > later, but the modified N-W Aligner mentioned below would make a good > example too, don't you think? ;) > > On Mon, Nov 7, 2011 at 16:03, <[email protected]> wrote: >> Hi Hannes, >> >> You could do such a comparison by using the Needleman-Wunsh aligner with gap >> penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. >> The absolute value of the resulting score is exactly the number of errors. >> >> But it will not stop when a maximal number of errors is reached ... >> >> JS >> >> Le 7 nov. 2011 à 15:42, Andreas Prlic a écrit : >> >>> Hi Hannes, >>> >>> you are right, this does not exist yet. Somebody else asked the same >>> question a few weeks ago. As such it would be great if you could >>> provide a patch, there might be other people interested in that, too. >>> >>> Andreas >>> >>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandstätter-Müller >>> <[email protected]> wrote: >>>> Following up: >>>> >>>> If there is no such thing, should I make it available if I write it? >>>> >>>> Hannes >>>> >>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandstätter-Müller >>>> <[email protected]> wrote: >>>>> Hi! >>>>> >>>>> Is there a Class/Method in Biojava that calculates the Levenshtein >>>>> distance between two sequences? I could not find anything in the docs >>>>> at first search. >>>>> >>>>> I need to compare 2 DNASequences (or Strings) and get the number of >>>>> insertions, deletions, and substitutions. Ideally, there would be an >>>>> option to abort the comparison if the number of mismatches exceeds a >>>>> certain number. >>>>> >>>>> Hannes >>>>> >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list - [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
