void concludeContactCoulomb(const PxcSolverConstraintDesc& desc, PxcSolverContext& /*cache*/)
{
PxU8* PX_RESTRICT cPtr = desc.constraint;
const FloatV zero = FZero();
const PxcSolverContactCoulombHeader* PX_RESTRICT firstHeader = (const PxcSolverContactCoulombHeader*)cPtr;
PxU8* PX_RESTRICT last = desc.constraint + firstHeader->frictionOffset;//getConstraintLength(desc);
while(cPtr < last)
{
const PxcSolverContactCoulombHeader* PX_RESTRICT hdr = (const PxcSolverContactCoulombHeader*)cPtr;
cPtr += sizeof(PxcSolverContactCoulombHeader);
const PxU32 numNormalConstr = hdr->numNormalConstr;
//if(cPtr < last)
//Ps::prefetchLine(cPtr, 512);
Ps::prefetchLine(cPtr,128);
Ps::prefetchLine(cPtr,256);
Ps::prefetchLine(cPtr,384);
const PxU32 pointStride = hdr->type == PXS_SC_TYPE_EXT_CONTACT ? sizeof(PxcSolverContactExt)
: sizeof(PxcSolverContact);
for(PxU32 i=0;i<numNormalConstr;i++)
{
PxcSolverContact *c = reinterpret_cast<PxcSolverContact*>(cPtr);
cPtr += pointStride;
c->setScaledBias(FMax(c->getScaledBias(), zero));
}
}
PX_ASSERT(cPtr == last);
}
float GetSpeed(FVector projdirection, FVector PawnVelocity)
{
FVector projvelocity = Scale(Normal(projdirection), 3920.0);
projvelocity.Z += 0;
float ForwardPct = FMin(Dot(Normal(PawnVelocity), Normal(projdirection)), 0.5);
float InheritPct = FMax(0.5, ForwardPct);
projvelocity.X += InheritPct * PawnVelocity.X;
projvelocity.Y += InheritPct * PawnVelocity.Y;
projvelocity.Z += 0.5 * PawnVelocity.Z;
return VSize(projvelocity);
}
bool setupFinalizeExtSolverConstraintsCoulomb(PxcNpWorkUnit& n,
const ContactBuffer& buffer,
const PxcCorrelationBufferCoulomb& c,
const PxTransform& bodyFrame0,
const PxTransform& bodyFrame1,
bool /*perPointFriction*/,
PxU8* workspace,
PxReal invDt,
PxReal bounceThreshold,
PxsSolverExtBody& b0,
PxsSolverExtBody& b1,
PxU32 frictionCountPerPoint,
PxReal invMassScale0, PxReal invInertiaScale0,
PxReal invMassScale1, PxReal invInertiaScale1)
{
// NOTE II: the friction patches are sparse (some of them have no contact patches, and
// therefore did not get written back to the cache) but the patch addresses are dense,
// corresponding to valid patches
PxU8* PX_RESTRICT ptr = workspace;
const FloatV zero=FZero();
//KS - TODO - this should all be done in SIMD to avoid LHS
const PxF32 maxPenBias0 = b0.mLinkIndex == PxcSolverConstraintDesc::NO_LINK ? b0.mBodyData->penBiasClamp : getMaxPenBias(*b0.mFsData)[b0.mLinkIndex];
const PxF32 maxPenBias1 = b1.mLinkIndex == PxcSolverConstraintDesc::NO_LINK ? b1.mBodyData->penBiasClamp : getMaxPenBias(*b1.mFsData)[b0.mLinkIndex];
const FloatV maxPen = FLoad(PxMax(maxPenBias0, maxPenBias1)/invDt);
const FloatV restDistance = FLoad(n.restDistance);
Ps::prefetchLine(c.contactID);
Ps::prefetchLine(c.contactID, 128);
bool useExtContacts = (n.flags & (PxcNpWorkUnitFlag::eARTICULATION_BODY0|PxcNpWorkUnitFlag::eARTICULATION_BODY1))!=0;
const PxU32 frictionPatchCount = c.frictionPatchCount;
const bool staticBody = ((n.flags & PxcNpWorkUnitFlag::eDYNAMIC_BODY1) == 0);
const PxU32 pointStride = useExtContacts ? sizeof(PxcSolverContactExt) : sizeof(PxcSolverContact);
const PxU32 frictionStride = useExtContacts ? sizeof(PxcSolverFrictionExt) : sizeof(PxcSolverFriction);
const PxU8 pointHeaderType = Ps::to8(useExtContacts ? PXS_SC_TYPE_EXT_CONTACT : (staticBody ? PXS_SC_TYPE_STATIC_CONTACT : PXS_SC_TYPE_RB_CONTACT));
const PxU8 frictionHeaderType = Ps::to8(useExtContacts ? PXS_SC_TYPE_EXT_FRICTION : (staticBody ? PXS_SC_TYPE_STATIC_FRICTION : PXS_SC_TYPE_FRICTION));
PxReal d0 = n.dominance0 * invMassScale0;
PxReal d1 = n.dominance1 * invMassScale1;
PxReal angD0 = n.dominance0 * invInertiaScale0;
PxReal angD1 = n.dominance1 * invInertiaScale1;
for(PxU32 i=0;i< frictionPatchCount;i++)
{
const PxU32 contactCount = c.frictionPatchContactCounts[i];
if(contactCount == 0)
continue;
const Gu::ContactPoint* contactBase0 = buffer.contacts + c.contactPatches[c.correlationListHeads[i]].start;
const PxcFrictionPatchCoulomb& frictionPatch = c.frictionPatches[i];
const Vec3V normalV = Ps::aos::V3LoadU(frictionPatch.normal);
const PxVec3 normal = frictionPatch.normal;
const PxReal combinedRestitution = contactBase0->restitution;
PxcSolverContactCoulombHeader* PX_RESTRICT header = reinterpret_cast<PxcSolverContactCoulombHeader*>(ptr);
ptr += sizeof(PxcSolverContactCoulombHeader);
Ps::prefetchLine(ptr, 128);
Ps::prefetchLine(ptr, 256);
Ps::prefetchLine(ptr, 384);
header->numNormalConstr = (PxU8)contactCount;
header->type = pointHeaderType;
header->setRestitution(combinedRestitution);
header->setDominance0(d0);
header->setDominance1(d1);
header->angDom0 = angD0;
header->angDom1 = angD1;
header->setNormal(normalV);
for(PxU32 patch=c.correlationListHeads[i];
patch!=PxcCorrelationBuffer::LIST_END;
patch = c.contactPatches[patch].next)
{
const PxU32 count = c.contactPatches[patch].count;
const Gu::ContactPoint* contactBase = buffer.contacts + c.contactPatches[patch].start;
PxU8* p = ptr;
for(PxU32 j=0;j<count;j++)
{
const Gu::ContactPoint& contact = contactBase[j];
PxcSolverContactExt* PX_RESTRICT solverContact = reinterpret_cast<PxcSolverContactExt*>(p);
p += pointStride;
const FloatV separation = FLoad(contact.separation);
PxVec3 ra = contact.point - bodyFrame0.p;
PxVec3 rb = contact.point - bodyFrame1.p;
Vec3V targetVel = V3LoadU(contact.targetVel);
const FloatV maxImpulse = FLoad(contact.maxImpulse);
solverContact->scaledBiasX_targetVelocityY_maxImpulseZ = V3Merge(FMax(maxPen, FSub(separation, restDistance)), V3Dot(normalV,targetVel), maxImpulse);
//TODO - should we do cross only in vector land and then store. Could cause a LHS but probably no worse than
//what we already have (probably has a LHS from converting from vector to scalar above)
const PxVec3 raXn = ra.cross(normal);
const PxVec3 rbXn = rb.cross(normal);
Cm::SpatialVector deltaV0, deltaV1;
PxReal unitResponse = getImpulseResponse(b0, Cm::SpatialVector(normal, raXn), deltaV0, d0, angD0,
b1, Cm::SpatialVector(-normal, -rbXn), deltaV1, d1, angD1);
const PxReal vrel = b0.projectVelocity(normal, raXn)
- b1.projectVelocity(normal, rbXn);
solverContact->raXnXYZ_appliedForceW = V4SetW(Vec4V_From_Vec3V(V3LoadU(raXn)), zero);
solverContact->rbXnXYZ_velMultiplierW = V4SetW(Vec4V_From_Vec3V(V3LoadU(rbXn)), zero);
completeContactPoint(*solverContact, unitResponse, vrel, invDt, header->restitution, bounceThreshold);
solverContact->setDeltaVA(deltaV0.linear, deltaV0.angular);
solverContact->setDeltaVB(deltaV1.linear, deltaV1.angular);
}
ptr = p;
}
}
//construct all the frictions
PxU8* PX_RESTRICT ptr2 = workspace;
const PxF32 orthoThreshold = 0.70710678f;
const PxF32 eps = 0.00001f;
bool hasFriction = false;
for(PxU32 i=0;i< frictionPatchCount;i++)
{
const PxU32 contactCount = c.frictionPatchContactCounts[i];
if(contactCount == 0)
continue;
PxcSolverContactCoulombHeader* header = reinterpret_cast<PxcSolverContactCoulombHeader*>(ptr2);
header->frictionOffset = PxU16(ptr - ptr2);
ptr2 += sizeof(PxcSolverContactCoulombHeader) + header->numNormalConstr * pointStride;
PxVec3 normal = c.frictionPatches[i].normal;
const Gu::ContactPoint* contactBase0 = buffer.contacts + c.contactPatches[c.correlationListHeads[i]].start;
const PxReal staticFriction = contactBase0->staticFriction;
const PxU32 disableStrongFriction = contactBase0->internalFaceIndex1 & PxMaterialFlag::eDISABLE_FRICTION;
const bool haveFriction = (disableStrongFriction == 0);
PxcSolverFrictionHeader* frictionHeader = (PxcSolverFrictionHeader*)ptr;
frictionHeader->numNormalConstr = Ps::to8(c.frictionPatchContactCounts[i]);
frictionHeader->numFrictionConstr = Ps::to8(haveFriction ? c.frictionPatches[i].numConstraints : 0);
ptr += sizeof(PxcSolverFrictionHeader);
ptr += frictionHeader->getAppliedForcePaddingSize(c.frictionPatchContactCounts[i]);
Ps::prefetchLine(ptr, 128);
Ps::prefetchLine(ptr, 256);
Ps::prefetchLine(ptr, 384);
const PxVec3 t0Fallback1(0.f, -normal.z, normal.y);
const PxVec3 t0Fallback2(-normal.y, normal.x, 0.f) ;
const PxVec3 tFallback1 = orthoThreshold > PxAbs(normal.x) ? t0Fallback1 : t0Fallback2;
const PxVec3 vrel = b0.getLinVel() - b1.getLinVel();
const PxVec3 t0_ = vrel - normal * (normal.dot(vrel));
const PxReal sqDist = t0_.dot(t0_);
const PxVec3 tDir0 = (sqDist > eps ? t0_: tFallback1).getNormalized();
const PxVec3 tDir1 = tDir0.cross(normal);
PxVec3 tFallback[2] = {tDir0, tDir1};
PxU32 ind = 0;
if(haveFriction)
{
hasFriction = true;
frictionHeader->setStaticFriction(staticFriction);
frictionHeader->setDominance0(n.dominance0);
frictionHeader->setDominance1(n.dominance1);
frictionHeader->angDom0 = angD0;
frictionHeader->angDom1 = angD1;
frictionHeader->type = frictionHeaderType;
PxU32 totalPatchContactCount = 0;
for(PxU32 patch=c.correlationListHeads[i];
patch!=PxcCorrelationBuffer::LIST_END;
patch = c.contactPatches[patch].next)
{
const PxU32 count = c.contactPatches[patch].count;
const PxU32 start = c.contactPatches[patch].start;
const Gu::ContactPoint* contactBase = buffer.contacts + start;
PxU8* p = ptr;
for(PxU32 j =0; j < count; j++)
{
const PxU32 contactId = totalPatchContactCount + j;
const Gu::ContactPoint& contact = contactBase[j];
const PxVec3 ra = contact.point - bodyFrame0.p;
const PxVec3 rb = contact.point - bodyFrame1.p;
for(PxU32 k = 0; k < frictionCountPerPoint; ++k)
{
PxcSolverFrictionExt* PX_RESTRICT f0 = reinterpret_cast<PxcSolverFrictionExt*>(p);
p += frictionStride;
f0->contactIndex = contactId;
PxVec3 t0 = tFallback[ind];
ind = 1 - ind;
PxVec3 raXn = ra.cross(t0);
PxVec3 rbXn = rb.cross(t0);
Cm::SpatialVector deltaV0, deltaV1;
PxReal unitResponse = getImpulseResponse(b0, Cm::SpatialVector(t0, raXn), deltaV0, d0, angD0,
b1, Cm::SpatialVector(-t0, -rbXn), deltaV1, d1, angD1);
f0->setVelMultiplier(FLoad(unitResponse>0.0f ? 1.f/unitResponse : 0.0f));
f0->setRaXn(raXn);
f0->setRbXn(rbXn);
f0->setNormal(t0);
f0->setAppliedForce(0.0f);
f0->setDeltaVA(deltaV0.linear, deltaV0.angular);
f0->setDeltaVB(deltaV1.linear, deltaV1.angular);
}
}
totalPatchContactCount += c.contactPatches[patch].count;
ptr = p;
}
}
}
//PX_ASSERT(ptr - workspace == n.solverConstraintSize);
return hasFriction;
}
Vector SDKGradientClass::Output(BaseShader *sh, ChannelData *sd)
{
Vector p=sd->p;
Real r=0.0,angle,xx,yy;
if (gdata.turbulence>0.0)
{
Vector res;
Real scl=5.0*gdata.scale,tt=sd->t*gdata.freq*0.3;
res = Vector(Turbulence(p*scl,tt,gdata.octaves,TRUE),Turbulence((p+Vector(0.34,13.0,2.43))*scl,tt,gdata.octaves,TRUE),0.0);
if (gdata.absolute)
{
p.x = Mix(p.x,res.x,gdata.turbulence);
p.y = Mix(p.y,res.y,gdata.turbulence);
}
else
{
p.x += (res.x-0.5)*gdata.turbulence;
p.y += (res.y-0.5)*gdata.turbulence;
}
}
// rotation
p.x -= 0.5;
p.y -= 0.5;
xx = gdata.ca*p.x-gdata.sa*p.y + 0.5;
yy = gdata.sa*p.x+gdata.ca*p.y + 0.5;
p.x = xx;
p.y = yy;
if (gdata.mode<=SDKGRADIENTSHADER_MODE_CORNER && gdata.cycle && (sd->texflag&TEX_TILE))
{
if (sd->texflag & TEX_MIRROR)
{
p.x = Modulo(p.x,RCO 2.0);
if (p.x>=1.0) p.x=2.0-p.x;
p.y = Modulo(p.y,RCO 2.0);
if (p.y>= 1.0) p.y=2.0-p.y;
}
else
{
p.x = Modulo(p.x, RCO 1.0);
p.y = Modulo(p.y, RCO 1.0);
}
}
switch (gdata.mode)
{
case SDKGRADIENTSHADER_MODE_U:
r = p.x;
break;
case SDKGRADIENTSHADER_MODE_V:
r = 1.0-p.y;
break;
case SDKGRADIENTSHADER_MODE_DIAGONAL:
r = (p.x+p.y)*0.5;
break;
case SDKGRADIENTSHADER_MODE_RADIAL:
p.x-=0.5;
p.y-=0.5;
if (p.x==0.0) p.x=0.00001;
angle = ATan(p.y/p.x);
if (p.x<0.0) angle+=pi;
if (angle<0.0) angle+=pi2;
r = angle/pi2;
break;
case SDKGRADIENTSHADER_MODE_CIRCULAR:
p.x-=0.5;
p.y-=0.5;
r = Sqrt(p.x*p.x+p.y*p.y)*2.0;
break;
case SDKGRADIENTSHADER_MODE_BOX:
p.x = Abs(p.x - 0.5);
p.y = Abs(p.y - 0.5);
r = FMax(p.x,p.y)*2.0;
break;
case SDKGRADIENTSHADER_MODE_STAR:
p.x = Abs(p.x - 0.5)-0.5;
p.y = Abs(p.y - 0.5)-0.5;
r = Sqrt(p.x*p.x+p.y*p.y) * 1.4142;
break;
case SDKGRADIENTSHADER_MODE_CORNER:
{
Real cx;
Vector ca,cb;
cx = FCut01(p.x);
ca = Mix(gdata.c[0],gdata.c[1],cx);
cb = Mix(gdata.c[2],gdata.c[3],cx);
return Mix(ca,cb,FCut01(p.y));
break;
}
}
return gdata.gradient->CalcGradientPixel(FCut01(r));
}
void solveContactCoulomb_BStatic(const PxcSolverConstraintDesc& desc, PxcSolverContext& /*cache*/)
{
PxcSolverBody& b0 = *desc.bodyA;
Vec3V linVel0 = V3LoadA(b0.linearVelocity);
Vec3V angVel0 = V3LoadA(b0.angularVelocity);
PxcSolverContactCoulombHeader* firstHeader = (PxcSolverContactCoulombHeader*)desc.constraint;
const PxU8* PX_RESTRICT last = desc.constraint + firstHeader->frictionOffset;//getConstraintLength(desc);
//hopefully pointer aliasing doesn't bite.
const PxU8* PX_RESTRICT currPtr = desc.constraint;
const FloatV zero = FZero();
while(currPtr < last)
{
PxcSolverContactCoulombHeader* PX_RESTRICT hdr = (PxcSolverContactCoulombHeader*)currPtr;
currPtr += sizeof(PxcSolverContactCoulombHeader);
const PxU32 numNormalConstr = hdr->numNormalConstr;
PxcSolverContact* PX_RESTRICT contacts = (PxcSolverContact*)currPtr;
Ps::prefetchLine(contacts);
currPtr += numNormalConstr * sizeof(PxcSolverContact);
PxF32* appliedImpulse = (PxF32*) (((PxU8*)hdr) + hdr->frictionOffset + sizeof(PxcSolverFrictionHeader));
Ps::prefetchLine(appliedImpulse);
const Vec3V normal = hdr->getNormal();
const FloatV invMassDom0 = FLoad(hdr->dominance0);
FloatV normalVel1 = V3Dot(normal, linVel0);
const Vec3V delLinVel0 = V3Scale(normal, invMassDom0);
FloatV accumDeltaF = zero;
//FloatV accumImpulse = zero;
for(PxU32 i=0;i<numNormalConstr;i++)
{
PxcSolverContact& c = contacts[i];
Ps::prefetchLine(&contacts[i+1]);
//const Vec4V normalXYZ_velMultiplierW = c.normalXYZ_velMultiplierW;
const Vec4V raXnXYZ_appliedForceW = c.raXnXYZ_appliedForceW;
const Vec4V rbXnXYZ_velMultiplierW = c.rbXnXYZ_velMultiplierW;
//const Vec3V normal = c.normal;
//const Vec3V normal = Vec3V_From_Vec4V(normalXYZ_velMultiplierW);
const Vec3V raXn = Vec3V_From_Vec4V(raXnXYZ_appliedForceW);
const FloatV appliedForce = V4GetW(raXnXYZ_appliedForceW);
const FloatV velMultiplier = V4GetW(rbXnXYZ_velMultiplierW);
//const FloatV velMultiplier = V4GetW(normalXYZ_velMultiplierW);
const Vec3V delAngVel0 = Vec3V_From_Vec4V(c.delAngVel0_InvMassADom);
const FloatV targetVel = c.getTargetVelocity();
const FloatV nScaledBias = FNeg(c.getScaledBias());
const FloatV maxImpulse = c.getMaxImpulse();
//Compute the normal velocity of the constraint.
//const FloatV normalVel1 = V3Dot(normal, linVel0);
const FloatV normalVel2 = V3Dot(raXn, angVel0);
const FloatV normalVel = FAdd(normalVel1, normalVel2);
//const FloatV unbiasedErr = FMul(targetVel, velMultiplier);
const FloatV biasedErr = FMulAdd(targetVel, velMultiplier, nScaledBias);
// still lots to do here: using loop pipelining we can interweave this code with the
// above - the code here has a lot of stalls that we would thereby eliminate
const FloatV _deltaF = FMax(FNegMulSub(normalVel, velMultiplier, biasedErr), FNeg(appliedForce));
const FloatV _newForce = FAdd(appliedForce, _deltaF);
const FloatV newForce = FMin(_newForce, maxImpulse);
const FloatV deltaF = FSub(newForce, appliedForce);
//linVel0 = V3MulAdd(delLinVel0, deltaF, linVel0);
normalVel1 = FScaleAdd(invMassDom0, deltaF, normalVel1);
angVel0 = V3ScaleAdd(delAngVel0, deltaF, angVel0);
accumDeltaF = FAdd(accumDeltaF, deltaF);
c.setAppliedForce(newForce);
Ps::aos::FStore(newForce, &appliedImpulse[i]);
Ps::prefetchLine(&appliedImpulse[i], 128);
//accumImpulse = FAdd(accumImpulse, newAppliedForce);
}
linVel0 = V3ScaleAdd(delLinVel0, accumDeltaF, linVel0);
//hdr->setAccumlatedForce(accumImpulse);
}
// Write back
V3StoreU(linVel0, b0.linearVelocity);
V3StoreU(angVel0, b0.angularVelocity);
PX_ASSERT(currPtr == last);
}
/* Function: EmitConsensusSequence()
* Date: SRE, Wed Nov 11 11:08:59 1998 [St. Louis]
*
* Purpose: Generate a "consensus sequence". For the purposes
* of a profile HMM, this is defined as:
* - for each node:
* - if StateOccupancy() says that M is used
* with probability >= 0.5, this M is "consensus".
* Then, choose maximally likely residue.
* if P>0.5 (protein) or P>0.9 (DNA), make
* it upper case; else make it lower case.
* - if StateOccupancy() says that I
* is used with P >= 0.5, this I is "consensus";
* use it 1/(1-TII) times (its expectation value).
* Generate an "x" from each I.
*
* The function expects that the model is config'ed
* by Plan7NakedConfig(): that is, for a single global pass
* with no N,C,J involvement.
*
*
* Args: hmm - the model
* ret_seq - RETURN: consensus sequence (pass NULL if unwanted)
* ret_dsq - RETURN: digitized consensus sequence (pass NULL if unwanted)
* ret_L - RETURN: length of generated sequence
* ret_tr - RETURN: generated trace (pass NULL if unwanted)
*
* Returns: void
*/
void
EmitConsensusSequence(struct plan7_s *hmm, char **ret_seq, char **ret_dsq, int *ret_L, struct p7trace_s **ret_tr)
{
struct p7trace_s *tr; /* RETURN: traceback */
char *dsq, *seq; /* sequence in digitized and undigitized form */
float *mp, *ip, *dp; /* state occupancies from StateOccupancy() */
int nmat, ndel, nins; /* number of matches, deletes, inserts used */
int k; /* counter for nodes */
int tpos; /* position in trace */
int i; /* position in seq (equiv pos in dsq is i+1 */
int x; /* symbol choice (M) or # symbols (I) */
float mthresh; /* >= this, show symbol as upper case */
if (Alphabet_type == hmmAMINO) mthresh = 0.5;
else mthresh = 0.9;
StateOccupancy(hmm, &mp, &ip, &dp);
/* First pass: how many states do we need in the trace?
* how long will the sequence be?
*/
nmat = ndel = nins = 0;
for (k = 1; k <= hmm->M; k++)
{
if (mp[k] >= 0.5) nmat++; else ndel++;
if (k < hmm->M && ip[k] >= 0.5)
nins += (int) (1.f / (1.f - hmm->t[k][TII]));
}
/* Allocations
*/
P7AllocTrace(6 + nmat + ndel + nins, &tr);
dsq = MallocOrDie(sizeof(char) * (nmat+nins+3));
seq = MallocOrDie(sizeof(char) * (nmat+nins+1));
/* Main pass.
* Construct consensus trace, seq, and dsq.
*/
TraceSet(tr, 0, STS, 0, 0);
TraceSet(tr, 1, STN, 0, 0);
TraceSet(tr, 2, STB, 0, 0);
dsq[0] = Alphabet_iupac; /* guard byte */
tpos = 3;
i = 0;
for (k = 1; k <= hmm->M; k++)
{
if (mp[k] >= 0.5)
{
x = FMax(hmm->mat[k], Alphabet_size);
TraceSet(tr, tpos, STM, k, i+1);
seq[i] = Alphabet[x];
dsq[i+1] = x;
if (hmm->mat[k][x] < mthresh)
seq[i] = tolower((int) seq[i]);
i++;
tpos++;
}
else
{
TraceSet(tr, tpos, STD, k, 0);
tpos++;
}
if (k < hmm->M && ip[k] >= 0.5)
{
x = (int) (1.f / (1.f - hmm->t[k][TII]));
while (x--)
{
TraceSet(tr, tpos, STI, k, i+1);
seq[i] = 'x';
dsq[i+1] = Alphabet_iupac - 1;
i++;
tpos++;
}
}
}
TraceSet(tr, tpos, STE, 0, 0); tpos++;
TraceSet(tr, tpos, STC, 0, 0); tpos++;
TraceSet(tr, tpos, STT, 0, 0); tpos++;
dsq[i+1] = Alphabet_iupac;
free(mp);
free(ip);
free(dp);
if (ret_seq != NULL) *ret_seq = seq; else free(seq);
if (ret_dsq != NULL) *ret_dsq = dsq; else free(dsq);
if (ret_L != NULL) *ret_L = i;
if (ret_tr != NULL) *ret_tr = tr; else P7FreeTrace(tr);
}
/* Function: EmitBestSequence()
* Date: SRE, Tue Nov 10 16:21:59 1998 [St. Louis]
*
* Purpose: Given a model, emit the maximum probability sequence
* from it: argmax_{seq} P(seq | model).
* This is a sensible HMM equivalent to a "consensus"
* sequence.
* The model should be Plan7NakedConfig()'ed;
* in particular, if we allowed B->M and M->E,
* the highest probability sequence would be
* artifactually short. (We could do the highest
* scoring sequence instead, to get around this problem,
* but the highest scoring sequence is prone to
* other artifacts -- any looping state N,C,J, or I
* with a positively scoring residue leads to
* an infinitely long "best scoring" sequence.)
*
* Args: hmm - the model
* ret_seq - RETURN: best sequence
* ret_L - RETURN: length of sequence
* ret_tr - RETURN: traceback of the model/seq alignment; or NULL.
*
* Returns: void
*/
void
EmitBestSequence(struct plan7_s *hmm, char **ret_dsq, int *ret_L, struct p7trace_s **ret_tr)
{
char *seq; /* RETURN: best seq */
struct p7trace_s *tr; /* RETURN: traceback */
float *mmx, *imx, *dmx; /* log P forward scores for M,D,I */
char *mtb, *itb, *dtb; /* traceback ptrs for M,D,I */
int x; /* counter for symbols */
int k; /* counter for nodes */
float sc; /* tmp var for a log P */
int bestsym;
int rpos; /* position in a sequence */
int tpos; /* position in a trace */
int tlen; /* length of the traceback */
/* Initial allocations. We only need a 1D matrix and its shadow;
* it's overkill to use the Plan7Matrix structures, so don't.
*/
mmx = MallocOrDie(sizeof(float) * (hmm->M+1));
imx = MallocOrDie(sizeof(float) * (hmm->M));
dmx = MallocOrDie(sizeof(float) * (hmm->M));
mtb = MallocOrDie(sizeof(char) * (hmm->M+1));
itb = MallocOrDie(sizeof(char) * (hmm->M));
dtb = MallocOrDie(sizeof(char) * (hmm->M));
/* Initialization.
* We can safely assume a max probability path of S->N->B->(M1 or D1),
* so just init M1 and D1.
*/
mmx[1] = log(hmm->xt[XTN][MOVE]) + log(1.F - hmm->tbd1);
dmx[1] =
/* Main recursion, done as a push.
* The model is used in probability form; no wing folding needed.
*/
for (k = 1; k < hmm->M; k++)
{
/* Transits out of match state (init with these)
*/
mmx[k+1] = mmx[k] + log(hmm->t[k][TMM]); mtb[k+1] = STM;
dmx[k+1] = mmx[k] + log(hmm->t[k][TMD]); dtb[k+1] = STM;
if (k < hmm->M-1)
imx[k] = mmx[k] + log(hmm->t[k][TMI]); itb[k] = STM;
/* Transits out of delete state
*/
if ((sc = dmx[k] + log(hmm->t[k][TDM])) > mmx[k+1])
{ mmx[k+1] = sc; mtb[k+1] = STD; }
if ((sc = dmx[k] + log(hmm->t[k][TDD])) > dmx[k+1])
{ dmx[k+1] = sc; dtb[k+1] = STD; }
/* Transits out of insert state (self-loops are never good)
*/
if ((sc = imx[k] + log(hmm->t[k][TIM])) > mmx[k+1])
{ mmx[k+1] = sc; mtb[k+1] = STI; }
/* Best emissions
*/
x = FMax(hmm->mat[k+1], Alphabet_size);
mmx[k+1] += log(hmm->mat[k+1][x]);
if (k < hmm->M-1) {
x = FMax(hmm->ins[k+1], Alphabet_size);
imx[k+1] += log(hmm->ins[k+1][x]);
}
}
}