SLIDESORT is also available as C++ library.

Availability

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How to call libSlideSort

  • Similar pairs are obtained from call-back function which is defined by user.
  • Return value and arguments of the call-back function are as follows.
     int UserDefFuncName(const char* fasta_head1, const char* fasta_head2, TYPE_INDEX seqid1, TYPE_INDEX seqid2, char* aln1, char* aln2, double dist, int aln_size);
  • TYPE_INDEX is "unsigned int" for 4G package, "long long" for LL package.
  • fasta_head1: fasta header of a seqyence of the similar pair.
  • fasta_head2: fasta header of the other sequence.
  • seqid1: internal id of a seqyence of the similar pair.
  • seqid2; internal id of the other sequence.
  • Sequence name is obtained by object_name.sq.seqName[ internal_id ].
  • aln1: alignment of seq1.
  • aln2: alignment of seq2.
  • dist: edit/hamming distance of the similar pair.
  • aln_size: length of the alignment
  • Important point 1... If your program is executed without option "-a", aln1, aln2 and aln_size become NULL. So, use "-a" to obtain alignment information.
  • Important point 2... To avoid disk access overhead caused by output of large number of similar pairs, I recommend to use "-l" option.
  • An examble of source code
    • int UserDefFuncName?(const char* head1, const char* head2, int seqid1, int seqid2, char* aln1, char* aln2, double dist, int aln_size){
    • cerr<<seqid1<<" - "<<seqid2<<" : "<<dist<<"\n";
    • return(0);
    • }
  • void main(int argc, char** argv){
  • GETRESFUNC infptr = &UserDefFuncName;
  • multisort ml;
  • ml.setResGetFuncPtr?(infptr);
  • ml.getParam(argc, argv);
  • ml.exec();
  • }

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Last-modified: 2011-02-24 (Thu) 04:57:59 (3456d). Site admin: Kana Shimizu