BitMagic-C++
svsample09.cpp

Use of sparse vector for compressed DNA strings (2 bits per bp) Construction of comparison functions on bit-transposed compressed containers, benchmarking.

See also
bm::sparse_vector
bm::sparse_vector_find_first_mismatch
bm::bvector<>::find_first_mismatch()
/*
Copyright(c) 2002-2019 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
For more information please visit: http://bitmagic.io
*/
/** \example svsample09.cpp
Use of sparse vector for compressed DNA strings (2 bits per bp)
Construction of comparison functions on bit-transposed compressed
containers, benchmarking.
\sa bm::sparse_vector
\sa bm::sparse_vector_find_first_mismatch
\sa bm::bvector<>::find_first_mismatch()
*/
/*! \file svsample09.cpp
\brief Example: Use of sparse vector mismatch search
*/
#include <assert.h>
#include <stdlib.h>
#include <iostream>
#include <vector>
#include <utility>
#include "bm.h"
#include "bmsparsevec.h"
#include "bmundef.h" /* clear the pre-proc defines from BM */
using namespace std;
int main(void)
{
try
{
cout << "sparse vectors without NULL:" << endl;
{
svector_u32 sv1, sv2;
sv1.push_back(1);
sv1.push_back(2);
sv1.push_back(2);
sv1.push_back(3);
sv2 = sv1;
bool found = bm::sparse_vector_find_first_mismatch(sv1, sv2, pos);
if (found)
std::cout << "Mismatch found." << endl; // this would be an error
else
std::cout << "Mismatch not found" << endl; // identical vectors
// modify sv2 to introduce a mismatch
sv2[2] = 0;
found = bm::sparse_vector_find_first_mismatch(sv1, sv2, pos);
if (found)
{
std::cout << "Mismatch found at: " << pos << endl; // at 2
}
}
// bm::sparse_vector_find_first_mismatch works with NULL-able vectors
// first NULL (unsassigned) between vectors is a mimatch
//
cout << endl << "sparse vectors with NULL:" << endl;
{
sv1[1] = 1;
sv1[2] = 2;
sv1.set_null(3); // set element 3 to NULL
sv1[4] = 0;
sv2 = sv1;
bool found = bm::sparse_vector_find_first_mismatch(sv1, sv2, pos);
if (found)
std::cout << "Mismatch found." << endl; // this would be an error
else
std::cout << "Mismatch not found" << endl; // identical vectors
sv2[4] = 10;
found = bm::sparse_vector_find_first_mismatch(sv1, sv2, pos);
if (found)
{
std::cout << "Mismatch found at: " << pos << endl; // at 4
}
// set element 3 to 0, now we have a situation when element 3 in both
// vectors has value 0, except it is NULL value in vector 1
// mismatch search should detect it
//
sv2[3] = 0;
found = bm::sparse_vector_find_first_mismatch(sv1, sv2, pos);
if (found)
{
std::cout << "Mismatch found at: " << pos << endl; // at 3
}
}
}
catch(std::exception& ex)
{
std::cerr << ex.what() << std::endl;
return 1;
}
return 0;
}