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

[Mark Schreiber]

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:
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>  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        }
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>
>  - --
>  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/
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