本文整理汇总了C++中Alignment::setIdentity方法的典型用法代码示例。如果您正苦于以下问题：C++ Alignment::setIdentity方法的具体用法？C++ Alignment::setIdentity怎么用？C++ Alignment::setIdentity使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Alignment的用法示例。
在下文中一共展示了Alignment::setIdentity方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: traceback
//.........这里部分代码省略.........
alignment->setScore(cell->getScore());
int maxlen = s1.length() + s2.length(); // maximum length after the
// aligned sequences
//fprintf(stdout, "maxlen = %d \n", maxlen);
char reversed1[maxlen]; // reversed sequence #1
char reversed2[maxlen]; // reversed sequence #2
char reversed3[maxlen]; // reversed markup
//initialize reversed
for (int i = 0; i < maxlen; i++) {
reversed1[i] = '\0';
reversed2[i] = '\0';
reversed3[i] = '\0';
}
int len1 = 0; // length of sequence #1 after alignment
int len2 = 0; // length of sequence #2 after alignment
int len3 = 0; // length of the markup line
int lenBase1 = 0; //length of sequence1 bases not including gaps
int lenBase2 = 0; //length of sequence 2 bases not including gaps
int identity = 0; // count of identitcal pairs
int similarity = 0; // count of similar pairs
int gaps = 0; // count of gaps
char c1, c2;
int i = cell->getRow(); // traceback start row
int j = cell->getCol(); // traceback start col
int k = i * n;
int stillGoing = 1; // traceback flag: true -> continue & false
// -> stop
//fprintf(stdout, "row = %d, col = %d, k = %d \n", i, j, n);
while (stillGoing) {
switch (pointers[k + j]) {
case UP:
for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) {
reversed1[len1++] = a1.at(--i);
reversed2[len2++] = '-';
reversed3[len3++] = ' ';
k -= n;
gaps++;
lenBase1++;
}
break;
case DIAGONAL:
c1 = a1.at(--i);
c2 = a2.at(--j);
k -= n;
lenBase1++;
lenBase2++;
reversed1[len1++] = c1;
reversed2[len2++] = c2;
if (c1 == c2) {
reversed3[len3++] = '|';
identity++;
similarity++;
} else {
reversed3[len3++] = '.';
}
break;
case LEFT:
for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) {
reversed1[len1++] = '-';
reversed2[len2++] = a2.at(--j);
reversed3[len3++] = ' ';
gaps++;
lenBase2++;
}
break;
case STOP:
stillGoing = 0;
}
}
//fprintf(stdout, "finished stillGoing \n");
//std::cout << "traceback len1 = " << len1 << std::endl;
//std::cout << "traceback rev1 = " << reversed1 << std::endl;
//std::cout << "traceback rev1 len = " << strlen(reversed1) << std::endl;
alignment->setSequence1(reverse(reversed1, len1));
alignment->setStart1(i);
alignment->setLengthOfSequence1(lenBase1);
alignment->setSequence2(reverse(reversed2, len2));
alignment->setStart2(j);
alignment->setLengthOfSequence2(lenBase2);
alignment->setMarkupLine(reverse(reversed3, len3));
alignment->setIdentity(identity);
alignment->setGaps(gaps);
alignment->setSimilarity(similarity);
//delete[] a1;
//delete[] a2;
return alignment;
}