[Biojava-l] order of circular and compound location

[Yasumasa Shigemoto]

Hi,

In the following case, the location should be 'join(13..14,18..20,1..4)'.
So I would like to get each contiguous locations in order
13..14, 18..20 and 1..4.

If the location has a CDS Feature, 5'end and 3'end of the location
is very important for me.

Thanks,
Yasumasa Shigemoto

"Schreiber, Mark" wrote:

> Hi -
>
> I'm not sure I follow why you want to have any particular location first. The locations are by nature circular so the location you want is simply a circular permutation of the one reported so unless I'm mistaken they are the same thing aren't they?
>
> - Mark
>
>
>         -----Original Message-----
>         From: Yasumasa Shigemoto [mailto:yshigemo at genes.nig.ac.jp]
>         Sent: Fri 11/04/2003 1:23 p.m.
>         To: biojava-l at biojava.org
>         Cc:
>         Subject: [Biojava-l] order of circular and compound location
>
>
>
>         Hi,
>
>         I am using CircularLocation and LocationTools.union(Location a, Location b).
>         I would like to build a compound location including CircularLocation
>         but the order of sublocation seems to miss in this case.
>
>         The details are as folllows.
>
>         A sample program
>         ---
>         import org.biojava.bio.symbol.*;
>         import java.util.*;
>
>         public class CircularTest2 {
>                 public static void main(String[] args) throws Exception {
>                         CircularLocation[] locs = new CircularLocation[3];
>                         locs[0] = LocationTools.makeCircularLocation(13,14,20);
>                         locs[1] = LocationTools.makeCircularLocation(18,4,20);
>                         locs[2] = (CircularLocation)LocationTools.union(locs[0], locs[1]
>         );
>                         System.out.println(locs[2].toString());
>                         for(Iterator it = locs[2].blockIterator(); it.hasNext();) {
>                                 System.out.println(((Location)it.next()).toString());
>                         }
>                 }
>         }
>         ---
>
>         Result
>         ---
>         1, 20 {([1,4]), ([13,14]), ([18,20])}  (circular)
>         [1,4]
>         [13,14]
>         [18,20]
>         ---
>
>         I would like to get a sublocation [13,14] at first.
>         How do I get a correct order in this case?
>         Does anyone have any suggestion?
>
>         Regards,
>         Yasumasa Shigemoto
>
>         _______________________________________________
>         Biojava-l mailing list  -  Biojava-l at biojava.org
>         http://biojava.org/mailman/listinfo/biojava-l
>
>
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