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#include "muscle.h"
#include "msa.h"
#include "pwpath.h"
#include "profile.h"
#define TRACE 0
static void AppendDelete(const MSA &msaA, unsigned &uColIndexA,
unsigned uSeqCountA, unsigned uSeqCountB, MSA &msaCombined,
unsigned &uColIndexCombined)
{
#if TRACE
Log("AppendDelete ColIxA=%u ColIxCmb=%u\n",
uColIndexA, uColIndexCombined);
#endif
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
{
char c = msaA.GetChar(uSeqIndexA, uColIndexA);
msaCombined.SetChar(uSeqIndexA, uColIndexCombined, c);
}
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, '-');
++uColIndexCombined;
++uColIndexA;
}
static void AppendInsert(const MSA &msaB, unsigned &uColIndexB,
unsigned uSeqCountA, unsigned uSeqCountB, MSA &msaCombined,
unsigned &uColIndexCombined)
{
#if TRACE
Log("AppendInsert ColIxB=%u ColIxCmb=%u\n",
uColIndexB, uColIndexCombined);
#endif
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
msaCombined.SetChar(uSeqIndexA, uColIndexCombined, '-');
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
{
char c = msaB.GetChar(uSeqIndexB, uColIndexB);
msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, c);
}
++uColIndexCombined;
++uColIndexB;
}
static void AppendUnalignedTerminals(const MSA &msaA, unsigned &uColIndexA, unsigned uColCountA,
const MSA &msaB, unsigned &uColIndexB, unsigned uColCountB, unsigned uSeqCountA,
unsigned uSeqCountB, MSA &msaCombined, unsigned &uColIndexCombined)
{
#if TRACE
Log("AppendUnalignedTerminals ColIxA=%u ColIxB=%u ColIxCmb=%u\n",
uColIndexA, uColIndexB, uColIndexCombined);
#endif
const unsigned uLengthA = msaA.GetColCount();
const unsigned uLengthB = msaB.GetColCount();
unsigned uNewColCount = uColCountA;
if (uColCountB > uNewColCount)
uNewColCount = uColCountB;
for (unsigned n = 0; n < uColCountA; ++n)
{
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
{
char c = msaA.GetChar(uSeqIndexA, uColIndexA + n);
c = UnalignChar(c);
msaCombined.SetChar(uSeqIndexA, uColIndexCombined + n, c);
}
}
for (unsigned n = uColCountA; n < uNewColCount; ++n)
{
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
msaCombined.SetChar(uSeqIndexA, uColIndexCombined + n, '.');
}
for (unsigned n = 0; n < uColCountB; ++n)
{
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
{
char c = msaB.GetChar(uSeqIndexB, uColIndexB + n);
c = UnalignChar(c);
msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined + n, c);
}
}
for (unsigned n = uColCountB; n < uNewColCount; ++n)
{
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined + n, '.');
}
uColIndexCombined += uNewColCount;
uColIndexA += uColCountA;
uColIndexB += uColCountB;
}
static void AppendMatch(const MSA &msaA, unsigned &uColIndexA, const MSA &msaB,
unsigned &uColIndexB, unsigned uSeqCountA, unsigned uSeqCountB,
MSA &msaCombined, unsigned &uColIndexCombined)
{
#if TRACE
Log("AppendMatch ColIxA=%u ColIxB=%u ColIxCmb=%u\n",
uColIndexA, uColIndexB, uColIndexCombined);
#endif
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
{
char c = msaA.GetChar(uSeqIndexA, uColIndexA);
msaCombined.SetChar(uSeqIndexA, uColIndexCombined, c);
}
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
{
char c = msaB.GetChar(uSeqIndexB, uColIndexB);
msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, c);
}
++uColIndexA;
++uColIndexB;
++uColIndexCombined;
}
void AlignTwoMSAsGivenPathSW(const PWPath &Path, const MSA &msaA, const MSA &msaB,
MSA &msaCombined)
{
msaCombined.Clear();
#if TRACE
Log("AlignTwoMSAsGivenPathSW\n");
Log("Template A:\n");
msaA.LogMe();
Log("Template B:\n");
msaB.LogMe();
#endif
const unsigned uColCountA = msaA.GetColCount();
const unsigned uColCountB = msaB.GetColCount();
const unsigned uSeqCountA = msaA.GetSeqCount();
const unsigned uSeqCountB = msaB.GetSeqCount();
msaCombined.SetSeqCount(uSeqCountA + uSeqCountB);
// Copy sequence names into combined MSA
for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)
{
msaCombined.SetSeqName(uSeqIndexA, msaA.GetSeqName(uSeqIndexA));
msaCombined.SetSeqId(uSeqIndexA, msaA.GetSeqId(uSeqIndexA));
}
for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)
{
msaCombined.SetSeqName(uSeqCountA + uSeqIndexB, msaB.GetSeqName(uSeqIndexB));
msaCombined.SetSeqId(uSeqCountA + uSeqIndexB, msaB.GetSeqId(uSeqIndexB));
}
unsigned uColIndexA = 0;
unsigned uColIndexB = 0;
unsigned uColIndexCombined = 0;
const unsigned uEdgeCount = Path.GetEdgeCount();
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &Edge = Path.GetEdge(uEdgeIndex);
#if TRACE
Log("\nEdge %u %c%u.%u\n",
uEdgeIndex,
Edge.cType,
Edge.uPrefixLengthA,
Edge.uPrefixLengthB);
#endif
const char cType = Edge.cType;
const unsigned uPrefixLengthA = Edge.uPrefixLengthA;
unsigned uColCountA = 0;
if (uPrefixLengthA > 0)
{
const unsigned uNodeIndexA = uPrefixLengthA - 1;
const unsigned uTplColIndexA = uNodeIndexA;
if (uTplColIndexA > uColIndexA)
uColCountA = uTplColIndexA - uColIndexA;
}
const unsigned uPrefixLengthB = Edge.uPrefixLengthB;
unsigned uColCountB = 0;
if (uPrefixLengthB > 0)
{
const unsigned uNodeIndexB = uPrefixLengthB - 1;
const unsigned uTplColIndexB = uNodeIndexB;
if (uTplColIndexB > uColIndexB)
uColCountB = uTplColIndexB - uColIndexB;
}
AppendUnalignedTerminals(msaA, uColIndexA, uColCountA, msaB, uColIndexB, uColCountB,
uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);
switch (cType)
{
case 'M':
{
assert(uPrefixLengthA > 0);
assert(uPrefixLengthB > 0);
const unsigned uColA = uPrefixLengthA - 1;
const unsigned uColB = uPrefixLengthB - 1;
assert(uColIndexA == uColA);
assert(uColIndexB == uColB);
AppendMatch(msaA, uColIndexA, msaB, uColIndexB, uSeqCountA, uSeqCountB,
msaCombined, uColIndexCombined);
break;
}
case 'D':
{
assert(uPrefixLengthA > 0);
const unsigned uColA = uPrefixLengthA - 1;
assert(uColIndexA == uColA);
AppendDelete(msaA, uColIndexA, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);
break;
}
case 'I':
{
assert(uPrefixLengthB > 0);
const unsigned uColB = uPrefixLengthB - 1;
assert(uColIndexB == uColB);
AppendInsert(msaB, uColIndexB, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);
break;
}
default:
assert(false);
}
}
unsigned uInsertColCountA = uColCountA - uColIndexA;
unsigned uInsertColCountB = uColCountB - uColIndexB;
AppendUnalignedTerminals(msaA, uColIndexA, uInsertColCountA, msaB, uColIndexB,
uInsertColCountB, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);
}
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