Ignore:
Timestamp:
Aug 31, 2006, 10:52:02 AM (15 years ago)
Author:
Jari Häkkinen
Message:

Removed gslapi namespace and put the code into utility namespace.
Move #ifndef _header_ idiom to top of touched header files.
Removed unneccesary #includes, and added needed #includes.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/c++_tools/utility/Alignment.cc

    r301 r616  
    22
    33#include <c++_tools/utility/Alignment.h>
    4 #include <c++_tools/gslapi/matrix.h>
     4#include <c++_tools/utility/matrix.h>
    55
    66#include <utility>
     
    1111namespace alignment {
    1212
    13   double NeedlemanWunsch(const gslapi::matrix& s,
     13  double NeedlemanWunsch(const utility::matrix& s,
    1414                         std::vector<std::pair<size_t, size_t> >& path,
    1515                         const double gap)
    1616  {
    17     gslapi::matrix m(s.rows()+1,s.columns()+1);
     17    utility::matrix m(s.rows()+1,s.columns()+1);
    1818    // Init upper and left border of matrix
    1919    for (size_t i=1; i<m.rows(); i++)
     
    2323    // choice(i,j) tells us how we came to s(i,j). 1 is diagonal, 2
    2424    // vertical, and 3 horizontal,
    25     gslapi::matrix choice(m.rows(),m.columns());
     25    utility::matrix choice(m.rows(),m.columns());
    2626
    2727    // Calculating NeedlemanWunsch matrix
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