[Biojava-l] RichLocation.Tools.merge(Collection members) method

[Richard Holland]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Not that I'm aware of.

Mark Schreiber wrote:
> Just to follow up...
> 
> Has there been a fix checked in for this?
> 
> - Mark
> 
> On Mon, Mar 3, 2008 at 4:41 PM, Richard Holland <holland at ebi.ac.uk> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>>  Hash: SHA1
>>
>>  Arnaud - you are correct.
>>
>>  cheers,
>>  Richard
>>
>>
>>
>>  Arnaud Kerhornou wrote:
>>  > Hi everyone,
>>  >
>>  > I don't think the RichLocation.Tools.merge(Collection members) method is
>>  > doing it right.
>>  >
>>  > e.g. Input:
>>  > biojavax:join:[1157624..1158025,1158025..1158420,1158420..1158893]
>>  > Expected output:1157624..1158895
>>  >
>>  > But I get: join:[1157624..1158420,1158420..1158894]
>>  >
>>  > I think the code should have the extra line: parent = union;
>>  > just after c=p; statement line 18 (See source code below),
>>  > otherwise it doesn't take into account the newly generated location.
>>  >
>>  > Is that right ?
>>  >
>>  > Thanks
>>  > Arnaud
>>  >
>>  > Source code:
>>  >
>>  > 1    public static Collection merge(Collection members) {
>>  > 2            // flatten them out first so we don't end up recursing
>>  > 3            List membersList = new ArrayList(flatten(members));
>>  > 4            // all members are now singles so we can use single vs
>>  > single union operations
>>  > 5            if (membersList.size()>1) {
>>  > 6                for (int p = 0; p < (membersList.size()-1); p++) {
>>  > 7                    RichLocation parent =
>>  > (RichLocation)membersList.get(p);
>>  > 8                    for (int c = p+1; c < membersList.size(); c++) {
>>  > 9                        RichLocation child =
>>  > (RichLocation)membersList.get(c);
>>  > 10                       RichLocation union =
>>  > (RichLocation)parent.union(child);
>>  > 11                        // if parent can merge with child
>>  > 12                        if (union.isContiguous()) {
>>  > 13                           // replace parent with union
>>  > 14                            membersList.set(p,union);
>>  > 15                            // remove child
>>  > 16                            membersList.remove(c);
>>  > 17                            // check all children again
>>  > 18                            c=p;
>>  > 19                        }
>>  > 20                    }
>>  > 21                }
>>  > 22            }
>>  > 23            return membersList;
>>  > 24        }
>>  >       _______________________________________________
>>  > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>  >
>>
>>  - --
>>  Richard Holland (BioMart)
>>  EMBL EBI, Wellcome Trust Genome Campus,
>>  Hinxton, Cambridgeshire CB10 1SD, UK
>>  Tel. +44 (0)1223 494416
>>
>>  http://www.biomart.org/
>>  http://www.biojava.org/
>>  -----BEGIN PGP SIGNATURE-----
>>  Version: GnuPG v1.4.2.2 (GNU/Linux)
>>  Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>
>>  iD8DBQFHy7m04C5LeMEKA/QRAj05AJ9SBrv6yz8qvhwbmTrLZVfmwBuHTACgiq57
>>  +J0EpviSyp2Qq00m4A8xLUA=
>>  =re75
>>  -----END PGP SIGNATURE-----
>>
>>
>> _______________________________________________
>>  Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>  http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFHzltM4C5LeMEKA/QRAnk9AKCP7/0jmWk7h7rGd4+jwPkmUK9qUgCfe9Oz
j+UWAU+q9orPHtpWgg48N70=
=lBUD
-----END PGP SIGNATURE-----