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#include "muscle.h"
#include "msa.h"
#include "seqvect.h"
#include "textfile.h"
#define MEMDEBUG 0
#if MEMDEBUG
#include <crtdbg.h>
#endif
void MUSCLE(SeqVect &v, MSA &msaOut);
// Append msa2 at the end of msa1
void AppendMSA(MSA &msa1, const MSA &msa2)
{
const unsigned uSeqCount = msa1.GetSeqCount();
const unsigned uColCount1 = msa1.GetColCount();
const unsigned uColCount2 = msa2.GetColCount();
const unsigned uColCountCat = uColCount1 + uColCount2;
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
unsigned uId = msa1.GetSeqId(uSeqIndex);
unsigned uSeqIndex2;
bool bFound = msa2.GetSeqIndex(uId, &uSeqIndex2);
if (bFound)
{
for (unsigned uColIndex = 0; uColIndex < uColCount2; ++uColIndex)
{
const char c = msa2.GetChar(uSeqIndex2, uColIndex);
msa1.SetChar(uSeqIndex, uColCount1 + uColIndex, c);
}
}
else
{
for (unsigned uColIndex = 0; uColIndex < uColCount2; ++uColIndex)
msa1.SetChar(uSeqIndex, uColCount1 + uColIndex, '-');
}
}
}
static void SeqFromMSACols(const MSA &msa, unsigned uSeqIndex, unsigned uColFrom,
unsigned uColTo, Seq &s)
{
s.Clear();
s.SetName(msa.GetSeqName(uSeqIndex));
s.SetId(msa.GetSeqId(uSeqIndex));
for (unsigned uColIndex = uColFrom; uColIndex <= uColTo; ++uColIndex)
{
char c = msa.GetChar(uSeqIndex, uColIndex);
if (!IsGapChar(c))
s.AppendChar(c);
}
}
static void SeqVectFromMSACols(const MSA &msa, unsigned uColFrom, unsigned uColTo,
SeqVect &v)
{
v.Clear();
const unsigned uSeqCount = msa.GetSeqCount();
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
Seq s;
SeqFromMSACols(msa, uSeqIndex, uColFrom, uColTo, s);
v.AppendSeq(s);
}
}
void RefineW(const MSA &msaIn, MSA &msaOut)
{
const unsigned uSeqCount = msaIn.GetSeqCount();
const unsigned uColCount = msaIn.GetColCount();
// Reserve same nr seqs, 20% more cols
const unsigned uReserveColCount = (uColCount*120)/100;
msaOut.SetSize(uSeqCount, uReserveColCount);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
msaOut.SetSeqName(uSeqIndex, msaIn.GetSeqName(uSeqIndex));
msaOut.SetSeqId(uSeqIndex, msaIn.GetSeqId(uSeqIndex));
}
const unsigned uWindowCount = (uColCount + g_uRefineWindow - 1)/g_uRefineWindow;
if (0 == g_uWindowTo)
g_uWindowTo = uWindowCount - 1;
#if MEMDEBUG
_CrtSetBreakAlloc(1560);
#endif
if (g_uWindowOffset > 0)
{
MSA msaTmp;
MSAFromColRange(msaIn, 0, g_uWindowOffset, msaOut);
}
fprintf(stderr, "\n");
for (unsigned uWindowIndex = g_uWindowFrom; uWindowIndex <= g_uWindowTo; ++uWindowIndex)
{
fprintf(stderr, "Window %d of %d \r", uWindowIndex, uWindowCount);
const unsigned uColFrom = g_uWindowOffset + uWindowIndex*g_uRefineWindow;
unsigned uColTo = uColFrom + g_uRefineWindow - 1;
if (uColTo >= uColCount)
uColTo = uColCount - 1;
assert(uColTo >= uColFrom);
SeqVect v;
SeqVectFromMSACols(msaIn, uColFrom, uColTo, v);
#if MEMDEBUG
_CrtMemState s1;
_CrtMemCheckpoint(&s1);
#endif
MSA msaTmp;
MUSCLE(v, msaTmp);
AppendMSA(msaOut, msaTmp);
if (uWindowIndex == g_uSaveWindow)
{
MSA msaInTmp;
unsigned uOutCols = msaOut.GetColCount();
unsigned un = uColTo - uColFrom + 1;
MSAFromColRange(msaIn, uColFrom, un, msaInTmp);
char fn[256];
sprintf(fn, "win%d_inaln.tmp", uWindowIndex);
TextFile fIn(fn, true);
msaInTmp.ToFile(fIn);
sprintf(fn, "win%d_inseqs.tmp", uWindowIndex);
TextFile fv(fn, true);
v.ToFile(fv);
sprintf(fn, "win%d_outaln.tmp", uWindowIndex);
TextFile fOut(fn, true);
msaTmp.ToFile(fOut);
}
#if MEMDEBUG
void FreeDPMemSPN();
FreeDPMemSPN();
_CrtMemState s2;
_CrtMemCheckpoint(&s2);
_CrtMemState s;
_CrtMemDifference(&s, &s1, &s2);
_CrtMemDumpStatistics(&s);
_CrtMemDumpAllObjectsSince(&s1);
exit(1);
#endif
//#if DEBUG
// AssertMSAEqIgnoreCaseAndGaps(msaInTmp, msaTmp);
//#endif
}
fprintf(stderr, "\n");
// AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);//@@uncomment!
}
void DoRefineW()
{
SetOutputFileName(g_pstrOutFileName);
SetInputFileName(g_pstrInFileName);
SetStartTime();
SetMaxIters(g_uMaxIters);
SetSeqWeightMethod(g_SeqWeight1);
TextFile fileIn(g_pstrInFileName);
MSA msa;
msa.FromFile(fileIn);
const unsigned uSeqCount = msa.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file");
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = msa.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
msa.FixAlpha();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
MSA msaOut;
RefineW(msa, msaOut);
// ValidateMuscleIds(msa);
// TextFile fileOut(g_pstrOutFileName, true);
// msaOut.ToFile(fileOut);
MuscleOutput(msaOut);
}
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