[Biojava-l] order of circular and compound location

[Schreiber, Mark]

Hi -
 
The problem could be solved if we could come up with a way to retain the coordinates in the order they where used to form the union. I'm guessing that CircularLocation may need it's own block iterator which can guarentee order. Probably need some trickiness in the LocationTools.union() method to deal with this.
 
Another possibility would be for a CircularSequence to have a flag that determined the 5' end...
 
These locations are very tricky and problematic, give me a few days to think about it.
 
- Mark
 

	-----Original Message----- 
	From: Yasumasa Shigemoto [mailto:yshigemo at genes.nig.ac.jp] 
	Sent: Mon 14/04/2003 12:07 p.m. 
	To: Schreiber, Mark 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] order of circular and compound location
	
	

	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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