void PrintAlignment(
const CSequence& inQuery, uint32 inQueryStart,
const CSequence& inTarget, uint32 inTargetStart)
{
assert(inQuery.length() == inTarget.length());
CMutableSequence q(inQuery.begin(), inQuery.end());
CMutableSequence s(inTarget.begin(), inTarget.end());
while (q.length())
{
uint32 n = q.length();
if (n > 60)
n = 60;
cout << setw(6) << inQueryStart << " ";
for (uint32 i = 0; i < n; ++i)
{
if (q[i] == '-')
cout << '-';
else
{
cout << Decode(q[i]);
++inQueryStart;
}
}
cout << endl;
cout << " ";
for (uint32 i = 0; i < n; ++i)
{
if (s[i] == q[i])
cout << '|';
else
cout << " ";
}
cout << endl;
cout << setw(6) << inTargetStart << " ";
for (uint32 i = 0; i < n; ++i)
{
if (s[i] == '-')
cout << '-';
else
{
cout << Decode(s[i]);
++inTargetStart;
}
}
cout << endl << endl;
q.erase(q.begin(), q.begin() + n);
s.erase(s.begin(), s.begin() + n);
}
cout << endl;
}
void MidLine(const CSequence& inQuery, const CSequence& inTarget,
const CMatrix& inMatrix, uint32& outIdentity, uint32& outPositives,
uint32& outGaps, string& outMidline)
{
outMidline.clear();
outIdentity = 0;
outPositives = 0;
outGaps = 0;
assert(inQuery.length() == inTarget.length());
if (inQuery.length() != inTarget.length())
THROW(("To calculate a midline you need a query and a target of the same length"));
for (CSequence::const_iterator a = inQuery.begin(), b = inTarget.begin();
a != inQuery.end(); ++a, ++b)
{
if (*a == *b)
{
++outIdentity;
++outPositives;
outMidline += Decode(*a);
}
else if (inMatrix(*a, *b) > 0)
{
++outPositives;
outMidline += '+';
}
else
{
if (*a == kSignalGapCode or *b == kSignalGapCode)
++outGaps;
outMidline += ' ';
}
}
}
void CBlastIndex::AddSequence(const CSequence& inSequence)
{
fSequences.push_back(inSequence);
++fSequenceCount;
fTotalSequenceLength += inSequence.length();
}