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#include "multaln.h"
PWPath::PWPath()
{
m_uArraySize = 0;
m_uEdgeCount = 0;
m_Edges = 0;
}
PWPath::~PWPath()
{
Clear();
}
void PWPath::Clear()
{
delete[] m_Edges;
m_Edges = 0;
m_uArraySize = 0;
m_uEdgeCount = 0;
}
void PWPath::ExpandPath(unsigned uAdditionalEdgeCount)
{
PWEdge *OldPath = m_Edges;
unsigned uEdgeCount = m_uArraySize + uAdditionalEdgeCount;
m_Edges = new PWEdge[uEdgeCount];
m_uArraySize = uEdgeCount;
if (m_uEdgeCount > 0)
memcpy(m_Edges, OldPath, m_uEdgeCount*sizeof(PWEdge));
delete[] OldPath;
}
void PWPath::AppendEdge(const PWEdge &Edge)
{
if (0 == m_uArraySize || m_uEdgeCount + 1 == m_uArraySize)
ExpandPath(200);
m_Edges[m_uEdgeCount] = Edge;
++m_uEdgeCount;
}
void PWPath::AppendEdge(char cType, unsigned uPrefixLengthA, unsigned uPrefixLengthB)
{
PWEdge e;
e.uPrefixLengthA = uPrefixLengthA;
e.uPrefixLengthB = uPrefixLengthB;
e.cType = cType;
AppendEdge(e);
}
void PWPath::PrependEdge(const PWEdge &Edge)
{
if (0 == m_uArraySize || m_uEdgeCount + 1 == m_uArraySize)
ExpandPath(1000);
if (m_uEdgeCount > 0)
memmove(m_Edges + 1, m_Edges, sizeof(PWEdge)*m_uEdgeCount);
m_Edges[0] = Edge;
++m_uEdgeCount;
}
const PWEdge &PWPath::GetEdge(unsigned uEdgeIndex) const
{
assert(uEdgeIndex < m_uEdgeCount);
return m_Edges[uEdgeIndex];
}
void PWPath::Validate() const
{
const unsigned uEdgeCount = GetEdgeCount();
if (0 == uEdgeCount)
return;
const PWEdge &FirstEdge = GetEdge(0);
const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
unsigned uStartA = FirstEdge.uPrefixLengthA;
unsigned uStartB = FirstEdge.uPrefixLengthB;
if (FirstEdge.cType != 'I')
--uStartA;
if (FirstEdge.cType != 'D')
--uStartB;
unsigned uPrefixLengthA = FirstEdge.uPrefixLengthA;
unsigned uPrefixLengthB = FirstEdge.uPrefixLengthB;
for (unsigned uEdgeIndex = 1; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &Edge = GetEdge(uEdgeIndex);
switch (Edge.cType)
{
case 'M':
if (uPrefixLengthA + 1 != Edge.uPrefixLengthA)
Quit("PWPath::Validate MA %u", uPrefixLengthA);
if (uPrefixLengthB + 1 != Edge.uPrefixLengthB)
Quit("PWPath::Validate MB %u", uPrefixLengthB);
++uPrefixLengthA;
++uPrefixLengthB;
break;
case 'D':
if (uPrefixLengthA + 1 != Edge.uPrefixLengthA)
Quit("PWPath::Validate DA %u", uPrefixLengthA);
if (uPrefixLengthB != Edge.uPrefixLengthB)
Quit("PWPath::Validate DB %u", uPrefixLengthB);
++uPrefixLengthA;
break;
case 'I':
if (uPrefixLengthA != Edge.uPrefixLengthA)
Quit("PWPath::Validate IA %u", uPrefixLengthA);
if (uPrefixLengthB + 1 != Edge.uPrefixLengthB)
Quit("PWPath::Validate IB %u", uPrefixLengthB);
++uPrefixLengthB;
break;
}
}
}
void PWPath::LogMe() const
{
for (unsigned uEdgeIndex = 0; uEdgeIndex < GetEdgeCount(); ++uEdgeIndex)
{
const PWEdge &Edge = GetEdge(uEdgeIndex);
if (uEdgeIndex > 0)
Log(" ");
Log("%c%d.%d",
Edge.cType,
Edge.uPrefixLengthA,
Edge.uPrefixLengthB);
if ((uEdgeIndex > 0 && uEdgeIndex%10 == 0) ||
uEdgeIndex == GetEdgeCount() - 1)
Log("\n");
}
}
void PWPath::Copy(const PWPath &Path)
{
Clear();
const unsigned uEdgeCount = Path.GetEdgeCount();
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &Edge = Path.GetEdge(uEdgeIndex);
AppendEdge(Edge);
}
}
void PWPath::FromMSAPair(const MSA &msaA, const MSA &msaB)
{
const unsigned uColCount = msaA.GetColCount();
if (uColCount != msaB.GetColCount())
Quit("PWPath::FromMSAPair, lengths differ");
Clear();
unsigned uPrefixLengthA = 0;
unsigned uPrefixLengthB = 0;
for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
{
bool bIsGapA = msaA.IsGapColumn(uColIndex);
bool bIsGapB = msaB.IsGapColumn(uColIndex);
PWEdge Edge;
char cType;
if (!bIsGapA && !bIsGapB)
{
cType = 'M';
++uPrefixLengthA;
++uPrefixLengthB;
}
else if (bIsGapA && !bIsGapB)
{
cType = 'I';
++uPrefixLengthB;
}
else if (!bIsGapA && bIsGapB)
{
cType = 'D';
++uPrefixLengthA;
}
else
{
assert(bIsGapB && bIsGapA);
continue;
}
Edge.cType = cType;
Edge.uPrefixLengthA = uPrefixLengthA;
Edge.uPrefixLengthB = uPrefixLengthB;
AppendEdge(Edge);
}
}
void PWPath::AssertEqual(const PWPath &Path) const
{
const unsigned uEdgeCount = GetEdgeCount();
if (uEdgeCount != Path.GetEdgeCount())
{
Log("PWPath::AssertEqual, this=\n");
LogMe();
Log("\nOther path=\n");
Path.LogMe();
Log("\n");
Quit("PWPath::AssertEqual, Edge count different %u %u\n",
uEdgeCount, Path.GetEdgeCount());
}
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &e1 = GetEdge(uEdgeIndex);
const PWEdge &e2 = Path.GetEdge(uEdgeIndex);
if (e1.cType != e2.cType || e1.uPrefixLengthA != e2.uPrefixLengthA ||
e1.uPrefixLengthB != e2.uPrefixLengthB)
{
Log("PWPath::AssertEqual, this=\n");
LogMe();
Log("\nOther path=\n");
Path.LogMe();
Log("\n");
Log("This edge %c%u.%u, other edge %c%u.%u\n",
e1.cType, e1.uPrefixLengthA, e1.uPrefixLengthB,
e2.cType, e2.uPrefixLengthA, e2.uPrefixLengthB);
Quit("PWPath::AssertEqual, edge %u different\n", uEdgeIndex);
}
}
}
bool PWPath::Equal(const PWPath &Path) const
{
const unsigned uEdgeCount = GetEdgeCount();
if (uEdgeCount != Path.GetEdgeCount())
return false;
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &e1 = GetEdge(uEdgeIndex);
const PWEdge &e2 = Path.GetEdge(uEdgeIndex);
if (e1.cType != e2.cType || e1.uPrefixLengthA != e2.uPrefixLengthA ||
e1.uPrefixLengthB != e2.uPrefixLengthB)
return false;
}
return true;
}
unsigned PWPath::GetMatchCount() const
{
unsigned uMatchCount = 0;
const unsigned uEdgeCount = GetEdgeCount();
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &e = GetEdge(uEdgeIndex);
if ('M' == e.cType)
++uMatchCount;
}
return uMatchCount;
}
unsigned PWPath::GetInsertCount() const
{
unsigned uInsertCount = 0;
const unsigned uEdgeCount = GetEdgeCount();
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &e = GetEdge(uEdgeIndex);
if ('I' == e.cType)
++uInsertCount;
}
return uInsertCount;
}
unsigned PWPath::GetDeleteCount() const
{
unsigned uDeleteCount = 0;
const unsigned uEdgeCount = GetEdgeCount();
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &e = GetEdge(uEdgeIndex);
if ('D' == e.cType)
++uDeleteCount;
}
return uDeleteCount;
}
void PWPath::FromStr(const char Str[])
{
Clear();
unsigned uPrefixLengthA = 0;
unsigned uPrefixLengthB = 0;
while (char c = *Str++)
{
switch (c)
{
case 'M':
++uPrefixLengthA;
++uPrefixLengthB;
break;
case 'D':
++uPrefixLengthA;
break;
case 'I':
++uPrefixLengthB;
break;
default:
Quit("PWPath::FromStr, invalid state %c", c);
}
AppendEdge(c, uPrefixLengthA, uPrefixLengthB);
}
}
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