Ignore:
Timestamp:
Feb 22, 2008, 4:29:56 PM (14 years ago)
Author:
Peter
Message:

fixes #308

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/yat/utility/Alignment.cc

    r1120 r1121  
    2525
    2626#include "Alignment.h"
    27 #include "matrix.h"
     27#include "Matrix.h"
    2828#include "stl_utility.h"
    2929
     
    3636namespace utility {
    3737
    38   double NeedlemanWunsch(const utility::matrix& s,
     38  double NeedlemanWunsch(const utility::Matrix& s,
    3939                         std::vector<std::pair<size_t, size_t> >& path,
    4040                         const double gap)
    4141  {
    42     utility::matrix m(s.rows()+1,s.columns()+1);
     42    utility::Matrix m(s.rows()+1,s.columns()+1);
    4343    // Init upper and left border of matrix
    4444    for (size_t i=1; i<m.rows(); i++)
     
    4848    // choice(i,j) tells us how we came to s(i,j). 1 is diagonal, 2
    4949    // vertical, and 3 horizontal,
    50     utility::matrix choice(m.rows(),m.columns());
     50    utility::Matrix choice(m.rows(),m.columns());
    5151
    5252    // Calculating NeedlemanWunsch matrix
     
    9090                 double open_gap)
    9191  {
    92     matrix m(first.size(), second.size());
     92    Matrix m(first.size(), second.size());
    9393    for (size_t i=0; i<first.size(); ++i)
    9494      for (size_t j=0; j<second.size(); ++j)
     
    9898
    9999
    100   double SmithWaterman(const utility::matrix& s,
     100  double SmithWaterman(const utility::Matrix& s,
    101101                       double gap, double open_gap)
    102102  {
     
    104104
    105105    // Calculating S-W 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);
    108108    for (size_t i=1; i<m.rows(); ++i)
    109109      for (size_t j=1; j<m.columns(); ++j){
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