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#include "muscle.h"
#include "profile.h"
#include "msa.h"
#include "pwpath.h"
#include "seqvect.h"
#include "clust.h"
#include "tree.h"
#define TRACE 0
struct Range
{
unsigned m_uBestColLeft;
unsigned m_uBestColRight;
};
static void ListVertSavings(unsigned uColCount, unsigned uAnchorColCount,
const Range *Ranges, unsigned uRangeCount)
{
if (!g_bVerbose || !g_bAnchors)
return;
double dTotalArea = uColCount*uColCount;
double dArea = 0.0;
for (unsigned i = 0; i < uRangeCount; ++i)
{
unsigned uLength = Ranges[i].m_uBestColRight - Ranges[i].m_uBestColLeft;
dArea += uLength*uLength;
}
double dPct = (dTotalArea - dArea)*100.0/dTotalArea;
Log("Anchor columns found %u\n", uAnchorColCount);
Log("DP area saved by anchors %-4.1f%%\n", dPct);
}
static void ColsToRanges(const unsigned BestCols[], unsigned uBestColCount,
unsigned uColCount, Range Ranges[])
{
// N best columns produces N+1 vertical blocks.
const unsigned uRangeCount = uBestColCount + 1;
for (unsigned uIndex = 0; uIndex < uRangeCount ; ++uIndex)
{
unsigned uBestColLeft = 0;
if (uIndex > 0)
uBestColLeft = BestCols[uIndex-1];
unsigned uBestColRight = uColCount;
if (uIndex < uBestColCount)
uBestColRight = BestCols[uIndex];
Ranges[uIndex].m_uBestColLeft = uBestColLeft;
Ranges[uIndex].m_uBestColRight = uBestColRight;
}
}
// Return true if any changes made
bool RefineVert(MSA &msaIn, const Tree &tree, unsigned uIters)
{
bool bAnyChanges = false;
const unsigned uColCountIn = msaIn.GetColCount();
const unsigned uSeqCountIn = msaIn.GetSeqCount();
if (uColCountIn < 3 || uSeqCountIn < 3)
return false;
unsigned *AnchorCols = new unsigned[uColCountIn];
unsigned uAnchorColCount;
SetMSAWeightsMuscle(msaIn);
FindAnchorCols(msaIn, AnchorCols, &uAnchorColCount);
const unsigned uRangeCount = uAnchorColCount + 1;
Range *Ranges = new Range[uRangeCount];
#if TRACE
Log("%u ranges\n", uRangeCount);
#endif
ColsToRanges(AnchorCols, uAnchorColCount, uColCountIn, Ranges);
ListVertSavings(uColCountIn, uAnchorColCount, Ranges, uRangeCount);
#if TRACE
{
Log("Anchor cols: ");
for (unsigned i = 0; i < uAnchorColCount; ++i)
Log(" %u", AnchorCols[i]);
Log("\n");
Log("Ranges:\n");
for (unsigned i = 0; i < uRangeCount; ++i)
Log("%4u - %4u\n", Ranges[i].m_uBestColLeft, Ranges[i].m_uBestColRight);
}
#endif
delete[] AnchorCols;
MSA msaOut;
msaOut.SetSize(uSeqCountIn, 0);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCountIn; ++uSeqIndex)
{
const char *ptrName = msaIn.GetSeqName(uSeqIndex);
unsigned uId = msaIn.GetSeqId(uSeqIndex);
msaOut.SetSeqName(uSeqIndex, ptrName);
msaOut.SetSeqId(uSeqIndex, uId);
}
for (unsigned uRangeIndex = 0; uRangeIndex < uRangeCount; ++uRangeIndex)
{
MSA msaRange;
const Range &r = Ranges[uRangeIndex];
const unsigned uFromColIndex = r.m_uBestColLeft;
const unsigned uRangeColCount = r.m_uBestColRight - uFromColIndex;
if (0 == uRangeColCount)
continue;
else if (1 == uRangeColCount)
{
MSAFromColRange(msaIn, uFromColIndex, 1, msaRange);
MSAAppend(msaOut, msaRange);
continue;
}
MSAFromColRange(msaIn, uFromColIndex, uRangeColCount, msaRange);
#if TRACE
Log("\n-------------\n");
Log("Range %u - %u count=%u\n", r.m_uBestColLeft, r.m_uBestColRight, uRangeColCount);
Log("Before:\n");
msaRange.LogMe();
#endif
bool bLockLeft = (0 != uRangeIndex);
bool bLockRight = (uRangeCount - 1 != uRangeIndex);
bool bAnyChangesThisBlock = RefineHoriz(msaRange, tree, uIters, bLockLeft, bLockRight);
bAnyChanges = (bAnyChanges || bAnyChangesThisBlock);
#if TRACE
Log("After:\n");
msaRange.LogMe();
#endif
MSAAppend(msaOut, msaRange);
#if TRACE
Log("msaOut after Cat:\n");
msaOut.LogMe();
#endif
}
#if DEBUG
// Sanity check
AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);
#endif
delete[] Ranges;
if (bAnyChanges)
msaIn.Copy(msaOut);
return bAnyChanges;
}
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