Changeset 1121 for trunk/yat/utility/Alignment.cc
 Timestamp:
 Feb 22, 2008, 4:29:56 PM (15 years ago)
 File:

 1 edited
Legend:
 Unmodified
 Added
 Removed

trunk/yat/utility/Alignment.cc
r1120 r1121 25 25 26 26 #include "Alignment.h" 27 #include " matrix.h"27 #include "Matrix.h" 28 28 #include "stl_utility.h" 29 29 … … 36 36 namespace utility { 37 37 38 double NeedlemanWunsch(const utility:: matrix& s,38 double NeedlemanWunsch(const utility::Matrix& s, 39 39 std::vector<std::pair<size_t, size_t> >& path, 40 40 const double gap) 41 41 { 42 utility:: matrix m(s.rows()+1,s.columns()+1);42 utility::Matrix m(s.rows()+1,s.columns()+1); 43 43 // Init upper and left border of matrix 44 44 for (size_t i=1; i<m.rows(); i++) … … 48 48 // choice(i,j) tells us how we came to s(i,j). 1 is diagonal, 2 49 49 // vertical, and 3 horizontal, 50 utility:: matrix choice(m.rows(),m.columns());50 utility::Matrix choice(m.rows(),m.columns()); 51 51 52 52 // Calculating NeedlemanWunsch matrix … … 90 90 double open_gap) 91 91 { 92 matrix m(first.size(), second.size());92 Matrix m(first.size(), second.size()); 93 93 for (size_t i=0; i<first.size(); ++i) 94 94 for (size_t j=0; j<second.size(); ++j) … … 98 98 99 99 100 double SmithWaterman(const utility:: matrix& s,100 double SmithWaterman(const utility::Matrix& s, 101 101 double gap, double open_gap) 102 102 { … … 104 104 105 105 // Calculating SW matrix 106 matrix m(s.rows()+1,s.columns()+1);107 matrix array(m);106 Matrix m(s.rows()+1,s.columns()+1); 107 Matrix array(m); 108 108 for (size_t i=1; i<m.rows(); ++i) 109 109 for (size_t j=1; j<m.columns(); ++j){
Note: See TracChangeset
for help on using the changeset viewer.