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TrimSequence.cpp
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "TrimSequence.h"
#include <assert.h>
#include <iostream>
#include <stdlib.h>
#include <string>
int main(int argc, const char **argv)
{
std::string test;
std::string::iterator result;
//
// from the left:
//
test = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, 'A', true);
assert(result == test.begin());
test = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, '~', true);
assert(result == test.end());
test = "AAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, 'B', true);
assert(result == (test.begin() + 5));
test = "AAAAAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, 'B', true);
assert(result == (test.begin() + 8));
test = "AAAAAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, 'F', true);
assert(result == (test.begin() + 12));
test = "AAAAAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, '@', true);
assert(result == (test.begin() + 0));
test = "AAAAAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, '@', true);
assert(result == (test.begin() + 0));
test = "AAAFAAAABCDEFGHIJKLMNOPQRSTUVWXYZ";
result = trimSequence(test, 'F', true);
assert(result == (test.begin() + 12));
// trim left 12 bases, and untrimmed bases are 'FG' (turn bug into this test cass)
test = "AAAFAAAABCDEFG";
result = trimSequence(test, 'F', true);
assert(result == (test.begin() + 12));
//
// from the right:
//
test = "ZYXWVUTSRQPONMLKJIHGFEDCBA";
result = trimSequence(test, 'A', false);
assert(result == test.end());
test = "ZYXWVUTSRQPONMLKJIHGFEDCBA";
result = trimSequence(test, '~', false);
assert(result == test.begin());
test = "ZYXWVUTSRQPONMLKJIHGFEDCBAAAAA";
result = trimSequence(test, 'B', false);
assert(result == (test.end() - 5));
test = "ZYXWVUTSRQPONMLKJIHGFEDCBAAAAAAA";
result = trimSequence(test, 'B', false);
assert(result == (test.end() - 7));
test = "ZYXWVUTSRQPONMLKJIHGFEDCBAAAAAAAA";
result = trimSequence(test, 'F', false);
assert(result == (test.end() - 12));
test = "ZYXWVUTSRQPONMLKJIHGFEDCBAAAAAAAA";
result = trimSequence(test, '@', false);
assert(result == (test.end() + 0));
test = "ZYXWVUTSRQPONMLKJIHGFEDCBAAAAFAAA";
result = trimSequence(test, 'F', false);
assert(result == (test.end() - 12));
test = "#################################";
result = trimSequence(test, 'F', false);
assert(result == (test.begin()));
#if 0
// TODO: add explanation why this test case should trim 5 right most bases?
test = ">BC@>28B==>=><?@=?>@8(>0309261/;6=@";
result = trimSequence(test, '0', false);
assert(result == (test.end())-5);
#endif
exit(0);
}