[Seqan-dev] LCP computation fail

[Robert Bakaric <bakaric@evolbio.mpg.de>]

Hi,


Some more questions. First of all is this the right place to post a questions of the type i am asking below or is there some seqan-user mailing list, where i can ask questions about using seqan? 


Ok, the first question is why is this not working:

1)

#include <seqan/index.h>

seqan::String<Dna> concatSet= concat(seqs); // seqs -  is my string set
seqan::String<unsigned> sa;
seqan::String<unsigned> lcp;


resize(sa, i);
 
    // create SA - works like a charm
    createSuffixArray(sa, concatSet, seqan::BwtWalk<seqan::BwtWalkFast>());


resize(lcp, i); 
   
    // create lcp table --- NOT working
    createLcpTable(lcp, concatSet, sa);


ERROR:

error: no matching function for call to ‘createLcpTable(seqan::String<unsigned int, seqan::Alloc<void> >&, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<void> >&, seqan::String<unsigned int, seqan::Alloc<void> >&)’


but this function is there, right ??

"

Creates a lcp table from a given text and suffix array.

createLcpTable(lcp, text, suffixArray[, algo_tag])

Include Headers

seqan/index.h

Parameters

lcp	The resulting lcp table.
text	A given text.
suffixArray	The suffix array of text.
algo_tag	A tag that identifies the algorithm which is used for creation.

Remarks

This function should not be called directly. Please use indexCreate or indexRequire. The size of lcp must be at least length(text) before calling this function.

2)

"...This function should not be called directly... "

Why is that so ??? How do you call it then?


3)

"algo_tag"

What kind of tag should be there ??? Does it refer to : Kasai, Manzini ... ??


thank you

r