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[Seqan-dev] Merging seeds

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Hi,
I found that the seed merging depends on the order of the merge. For example:
SeedSet< int, SimpleSeed, DefaultNoScore , void > seedset(100, 0);bool yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4),Single()); ::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 

results in:
1 1 1-4
0 1 1-4

the seed containing a preceding location is not added.
On the other hand adding the seeds in reverse order, i.e.:
SeedSet< int, SimpleSeed, DefaultNoScore , void > seedset(100, 0);bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single()); ::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 

gives what one expects:
1 1 0-3
1 1 0-4

Is this a feature or a bug? It should be annotated if it is the former.
It would also be nice to have an example for seed merging in demos (although I found some in tests).
Secondly, If I use the tag Single() while adding the second seed I get a compiler error: 

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4), 0, Single());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl;
Thirdly, two adjacent seeds are currently not concatenated though it would make sense to join them I think: 

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
yep = addSeed(seedset, Seed<int,SimpleSeed>(4, 4, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; gives: 
1 1 0-3
0 1 0-3

rather than:
1 1 0-3
1 1 0-7
And finally, its called SeedSet but if a merge is not successful, like in the last example, no new member in the set is added (by default). Why so? Using appendValue() does also give a compiler error: 

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
yep = addSeed(seedset, Seed<int,SimpleSeed>(4, 4, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 
if (not yep)
   appendValue(seedset, Seed<int,SimpleSeed>(4, 4, 4));
::std::cout << yep << " " << length(seedset) << " " << leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << ::std::endl; 

Cheers,
Fabian

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Fabian Buske
Institute for Molecular Bioscience
The University of Queensland Brisbane, Qld. 4072 Australia 
Phone: (61)-(7)-334-62608
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