BitMagic-C++: svsample09.cpp

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 "bmsparsevec_algo.h"
using namespace std;
typedef bm::sparse_vector<unsigned, bm::bvector<> > svector_u32;
int main(void)
{
try
{
svector_u32::size_type pos;
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;
{
svector_u32 sv1(bm::use_null);
svector_u32 sv2(bm::use_null);
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;
}
bmsparsevec_algo.h
Algorithms for bm::sparse_vector.
bm::sparse_vector
sparse vector with runtime compression using bit transposition method
Definition: bmsparsevec.h:81
bmsparsevec.h
Sparse constainer sparse_vector<> for integer types using bit-transposition transform.
bm::use_null
@ use_null
support "non-assigned" or "NULL" logic
Definition: bmconst.h:215
bm::sparse_vector::set_null
void set_null(size_type idx)
set specified element to unassigned value (NULL)
Definition: bmsparsevec.h:986
bm::sparse_vector_find_first_mismatch
bool sparse_vector_find_first_mismatch(const SV &sv1, const SV &sv2, typename SV::size_type &midx, bm::null_support null_proc=bm::use_null)
Find first mismatch (element which is different) between two sparse vectors (uses linear scan in bit-...
Definition: bmsparsevec_algo.h:170
bm::sparse_vector::push_back
void push_back(value_type v)
push value back into vector
Definition: bmsparsevec.h:1498
main
int main(void)
Definition: svsample09.cpp:53
svector_u32
bm::sparse_vector< unsigned, bm::bvector<> > svector_u32
Definition: svsample09.cpp:50
bm.h
Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.
bm::sparse_vector< unsigned, bm::bvector<> >::size_type
bvector_type::size_type size_type
Definition: bmsparsevec.h:87