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nj.c
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/* Philip T.L.C. Clausen Jan 2017 [email protected] */
/*
* Copyright (c) 2017, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#define _XOPEN_SOURCE 600
#include <float.h>
#include <limits.h>
#include <pthread.h>
#include <stdlib.h>
#include "dnjheaders/bytescale.h"
#include "dnjheaders/matrix.h"
#include "dnjheaders/nj.h"
#include "dnjheaders/nwck.h"
#include "dnjheaders/qseqs.h"
#include "dnjheaders/pherror.h"
#include "dnjheaders/str.h"
#include "dnjheaders/threader.h"
#include "dnjheaders/vector.h"
void (*limbLengthPtr)(double*, double*, int, int, Vector *, int*, double) = &limbLength;
double (*initQchunkPtr)(Matrix *, double*, int*, double, int*, int*, int, int) = &initQchunk;
double (*minDchunkPtr)(Matrix *, int*, double, int*, int*, int, int) = &minDchunk;
void (*updateDptr)(Matrix *, Vector *, int*, int, int, double, double) = &updateD;
long unsigned (*minDist)(Matrix *, Vector *, int*) = &initQ;
void * (*minDist_thread)(void *) = &initQ_thread;
void limbLength(double *Li, double *Lj, int i, int j, Vector *sD, int *N, double D_ij) {
int Ni, Nj;
double delta_ij;
Ni = N[i] - 2;
Nj = N[j] - 2;
if(0 < Ni && 0 < Nj) {
/* semi-standard */
delta_ij = ((sD->vec[i] - D_ij) / Ni) - ((sD->vec[j] - D_ij) / Nj);
*Li = (D_ij + delta_ij) / 2;
*Lj = (D_ij - delta_ij) / 2;
/* org:
delta_ij = (sD->vec[i] - sD->vec[j]) / N = (sD->vec[i] - D_ij) / N) - ((sD->vec[j] - D_ij) / N;
*/
/* avoid negative branch lengths */
if(*Li < 0) {
*Lj = D_ij;
*Li = 0;
} else if(*Lj < 0) {
*Li = D_ij;
*Lj = 0;
}
} else if(0 < Ni) {
/* j only shares similarity with i */
*Li = 0;
*Lj = D_ij;
} else if(0 < Nj) {
/* i only shares similarity with j */
*Li = D_ij;
*Lj = 0;
} else {
/* i and j only share similarity with eachother */
*Li = (*Lj = D_ij / 2);
}
}
void limbLengthNeg(double *Li, double *Lj, int i, int j, Vector *sD, int *N, double D_ij) {
int Ni, Nj;
double delta_ij;
Ni = N[i] - 2;
Nj = N[j] - 2;
if(0 < Ni && 0 < Nj) {
/* semi-standard */
delta_ij = ((sD->vec[i] - D_ij) / Ni) - ((sD->vec[j] - D_ij) / Nj);
*Li = (D_ij + delta_ij) / 2;
*Lj = (D_ij - delta_ij) / 2;
/* org:
delta_ij = (sD->vec[i] - sD->vec[j]) / N = (sD->vec[i] - D_ij) / N) - ((sD->vec[j] - D_ij) / N;
*/
} else if(0 < Ni) {
/* j only shares similarity with i */
*Li = 0;
*Lj = D_ij;
} else if(0 < Nj) {
/* i only shares similarity with j */
*Li = D_ij;
*Lj = 0;
} else {
/* i and j only share similarity with eachother */
*Li = (*Lj = D_ij / 2);
}
}
int * initSummaD(Vector *sD, Matrix *D, int *N) {
int i, j, *Nptr, *Nvec;
double dist, *sDptr, *sDvec, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/*
sD(i) = summa(d(i,k));
*/
/* alloc */
if(sD->size < (sD->n = D->n)) {
vector_realloc(sD, sD->n);
if(!(N = realloc(N, sD->n * sizeof(int)))) {
ERROR();
}
}
/* init to zero */
i = sD->n + 1;
sDptr = sD->vec - 1;
Nptr = N - 1;
while(--i) {
*++sDptr = 0;
*++Nptr = 1;
}
/* compute sum's */
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
sDptr = sD->vec--;
Nptr = N--;
i = 1;
while(i < D->n) {
++sDptr;
sDvec = sD->vec;
++Nptr;
Nvec = N;
j = ++i;
while(--j) {
dist = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= dist) {
*sDptr += dist;
*++sDvec += dist;
++*Nptr;
++*++Nvec;
} else {
++sDvec;
++Nvec;
}
}
}
++sD->vec;
++N;
return N;
}
long unsigned initQ(Matrix *D, Vector *sD, int *N) {
int i, j, mi, mj, N_i, *Ni, *Nj;
long unsigned pos;
double min, q, sD_i, *sDi, *sDj, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/*
Q(i,j) = (n(i) + n(j) - 4) / 2 * D(i,j) - summa(d(i,k)) - summa(d(k,j));
sD(i) = summa(d(i,k));
org:
Q(i,j) = (n - 2) * D(i,j) - summa(d(i,k)) - summa(d(k,j));
*/
/* init */
mi = 0;
mj = 0;
min = 1;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
sDi = sD->vec;
Ni = N;
i = 0;
while(++i < D->n) {
N_i = *++Ni;
Nj = N - 1;
sD_i = *++sDi;
sDj = sD->vec - 1;
j = -1;
while(++j < i) {
q = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= q) {
q = ((N_i + *++Nj - 4) >> 1) * q - sD_i - *++sDj;
if(q <= min) {
min = q;
mi = i;
mj = j;
}
} else {
++Nj;
++sDj;
}
}
}
/* save pos */
pos = 0;
pos |= mi;
pos <<= sizeof(unsigned) * 8;
pos |= mj;
return pos;
}
double initQchunk(Matrix *D, double *sD, int *N, double min, int *mi, int *mj, int i, int j) {
const int chunk = 65536;
int end, N_i;
double sD_i, Q, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/* init */
end = (j + chunk < i) ? (j + chunk) : i;
N_i = N[i];
N += --j;
sD_i = sD[i];
sD += j;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
/* get chunk */
while(++j < end) {
Q = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= Q) {
Q = ((N_i + *++N - 4) >> 1) * Q - sD_i - *++sD;
if(Q <= min) {
min = Q;
*mi = i;
*mj = j;
}
} else {
++N;
++sD;
}
}
return min;
}
long unsigned initQ_MN(Matrix *D, Vector *sD, int *N) {
int i, j, mi, mj, N_i, *Ni, *Nj;
long unsigned pos;
double max, Q, sD_i, *sDi, *sDj, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/*
Q(i,j) = (n(i) + n(j) - 4) / 2 * D(i,j) - summa(d(i,k)) - summa(d(k,j));
sD(i) = summa(d(i,k));
org:
Q(i,j) = (n - 2) * D(i,j) - summa(d(i,k)) - summa(d(k,j));
*/
/* init */
mi = 0;
mj = 0;
max = -DBL_MAX;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
sDi = sD->vec;
Ni = N;
i = 0;
while(++i < D->n) {
N_i = *++Ni;
Nj = N - 1;
sD_i = *++sDi;
sDj = sD->vec - 1;
j = -1;
while(++j < i) {
Q = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= Q) {
Q = ((N_i + *++Nj - 4) >> 1) * Q - sD_i - *++sDj;
if(max <= Q) {
max = Q;
mi = i;
mj = j;
}
} else {
++Nj;
++sDj;
}
}
}
/* save pos */
pos = 0;
pos |= mi;
pos <<= sizeof(unsigned) * 8;
pos |= mj;
return pos;
}
double initQ_MNchunk(Matrix *D, double *sD, int *N, double max, int *mi, int *mj, int i, int j) {
const int chunk = 65536;
int end, N_i;
double sD_i, Q, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/* init */
end = (j + chunk < i) ? (j + chunk) : i;
N_i = N[i];
N += --j;
sD_i = sD[i];
sD += j;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
/* get chunk */
while(++j < end) {
Q = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= Q) {
Q = ((N_i + *++N - 4) >> 1) * Q - sD_i - *++sD;
if(max <= Q) {
max = Q;
*mi = i;
*mj = j;
}
} else {
++N;
++sD;
}
}
return max;
}
void * initQ_thread(void *arg) {
const int chunk = 65536;
static volatile int thread_begin = 1, thread_wait, Lock = 0;
static int thread_num = 1, next_i, next_j, Mi, Mj;
static double Min;
volatile int *lock = &Lock;
NJthread *thread = arg;
int i, j, mi, mj, *N;
double min, *sDvec;
Matrix *D;
Vector *sD;
/*
Q(i,j) = (n(i) + n(j) - 4) / 2 * D(i,j) - summa(d(i,k)) - summa(d(k,j));
sD(i) = summa(d(i,k));
org:
Q(i,j) = (n - 2) * D(i,j) - summa(d(i,k)) - summa(d(k,j));
*/
/* init */
if(!thread) {
wait_atomic((thread_begin != thread_num));
thread_num = 0;
thread_begin = 0;
return NULL;
}
D = thread->D;
sD = thread->sD;
N = thread->N;
if(thread->min) {
lock(lock);
wait_atomic((thread_begin != thread_num));
/* init start */
Mi = 0;
Mj = 0;
Min = (initQchunkPtr == &initQchunk) ? 1 : -DBL_MAX;
next_i = 1;
next_j = 0;
thread_num = thread->num;
thread_wait = thread_num;
thread_begin = 0;
unlock(lock);
}
do {
wait_atomic(thread_begin);
/* terminate */
if(!thread_num) {
return NULL;
}
/* init */
i = 0;
mi = 0;
mj = 0;
min = (initQchunkPtr == &initQchunk) ? 1 : -DBL_MAX;
sDvec = sD->vec;
/* fill in chunks */
while(i < D->n) {
/* get next chunk */
lockTime(lock, 2);
i = next_i;
j = next_j;
if(i <= (next_j += chunk)) {
++next_i;
next_j = 0;
}
unlock(lock);
/* init chunk */
if(i < D->n) {
min = initQchunkPtr(D, sDvec, N, min, &mi, &mj, i, j);
}
}
/* check min */
lockTime(lock, 2);
if(initQchunkPtr == &initQ_MNchunk) {
if(Min < min) {
Min = min;
Mi = mi;
Mj = mj;
} else if(Min == min && (Mi < mi || (Mi == mi && Mj < mj))) {
/* ensure reproducibility */
Mi = mi;
Mj = mj;
}
} else if(min < Min) {
Min = min;
Mi = mi;
Mj = mj;
} else if(min == Min && (Mi < mi || (Mi == mi && Mj < mj))) {
/* ensure reproducibility */
Mi = mi;
Mj = mj;
}
--thread_wait;
unlock(lock);
wait_atomic(thread_wait);
__sync_add_and_fetch(&thread_begin, 1);
} while(!thread->min);
thread->min = Min;
thread->mi = Mi;
thread->mj = Mj;
return NULL;
}
long unsigned minD(Matrix *D, Vector *sD, int *N) {
int i, j, mi, mj;
long unsigned pos;
double min, dist, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
mi = 0;
mj = 0;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
min = (minDchunkPtr == &minDchunk) ? DBL_MAX : -DBL_MAX;
for(i = 1; i < D->n; ++i) {
for(j = 0; j < i; ++j) {
dist = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= dist && dist <= min) {
min = dist;
mi = i;
mj = j;
}
}
}
/* save pos */
pos = 0;
pos |= mi;
pos <<= sizeof(unsigned) * 8;
pos |= mj;
return pos;
}
double minDchunk(Matrix *D, int *N, double min, int *mi, int *mj, int i, int j) {
const int chunk = 65536;
int end;
double dist, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/* init */
end = (j + chunk < i) ? (j + chunk) : i;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
/* get chunk */
while(++j < end) {
dist = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= dist && dist <= min) {
min = dist;
*mi = i;
*mj = j;
}
}
return min;
}
long unsigned maxD(Matrix *D, Vector *sD, int *N) {
int i, j, mi, mj;
long unsigned pos;
double max, dist, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
mi = 0;
mj = 0;
max = -DBL_MAX;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
for(i = 1; i < D->n; ++i) {
for(j = 0; j < i; ++j) {
dist = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= dist && max <= dist) {
max = dist;
mi = i;
mj = j;
}
}
}
/* save pos */
pos = 0;
pos |= mi;
pos <<= sizeof(unsigned) * 8;
pos |= mj;
return pos;
}
double maxDchunk(Matrix *D, int *N, double max, int *mi, int *mj, int i, int j) {
const int chunk = 65536;
int end;
double dist, *Dptr;
float *Dfptr;
short unsigned *Dsptr;
unsigned char *Dbptr;
/* init */
end = (j + chunk < i) ? (j + chunk) : i;
Dptr = 0;
Dfptr = 0;
Dsptr = 0;
Dbptr = 0;
if(D->mat) {
Dptr = *(D->mat) - 1;
} else if(D->fmat) {
Dfptr = *(D->fmat) - 1;
} else if(D->smat) {
Dsptr = *(D->smat) - 1;
} else {
Dbptr = *(D->bmat) - 1;
}
/* get chunk */
while(++j < end) {
dist = Dptr ? *++Dptr : Dfptr ? *++Dfptr : Dsptr ? uctod(*++Dsptr) : uctod(*++Dbptr);
if(0 <= dist && max <= dist) {
max = dist;
*mi = i;
*mj = j;
}
}
return max;
}
void * minD_thread(void *arg) {
const int chunk = 65536;
static volatile int thread_begin = 1, thread_wait, Lock = 0;
static int thread_num = 1, next_i, next_j, Mi, Mj;
static double Min;
volatile int *lock = &Lock;
NJthread *thread = arg;
int i, j, mi, mj, *N;
double min;
Matrix *D;
/* init */
if(!thread) {
wait_atomic((thread_begin != thread_num));
thread_num = 0;
thread_begin = 0;
return NULL;
}
D = thread->D;
N = thread->N;
if(thread->min) {
lock(lock);
/* init start */
Mi = 0;
Mj = 0;
Min = (minDchunkPtr == &minDchunk) ? DBL_MAX : -2;
next_i = 1;
next_j = 0;
wait_atomic((thread_begin != thread_num));
thread_num = thread->num;
thread_wait = thread_num;
thread_begin = 0;
unlock(lock);
}
do {
wait_atomic(thread_begin);
/* terminate */
if(!thread_num) {
return NULL;
}
/* init */
i = 0;
mi = 0;
mj = 0;
min = (minDchunkPtr == &minDchunk) ? DBL_MAX : -2;
/* fill in chunks */
while(i < D->n) {
/* get next chunk */
lockTime(lock, 2);
i = next_i;
j = next_j;
if(i <= (next_j += chunk)) {
++next_i;
next_j = 0;
}
unlock(lock);
/* init chunk */
if(i < D->n) {
min = minDchunkPtr(D, N, min, &mi, &mj, i, j);
}
}
/* check min */
lockTime(lock, 2);
if(minDchunkPtr == &maxDchunk) {
if(Min < min) {
Min = min;
Mi = mi;
Mj = mj;
} else if(Min == min && (Mi < mi || (Mi == mi && Mj < mj))) {
/* ensure reproducibility */
Mi = mi;
Mj = mj;
}
} else if(min < Min) {
Min = min;
Mi = mi;
Mj = mj;
} else if(min == Min && (Mi < mi || (Mi == mi && Mj < mj))) {
/* ensure reproducibility */
Mi = mi;
Mj = mj;
}
--thread_wait;
unlock(lock);
wait_atomic(thread_wait);
__sync_add_and_fetch(&thread_begin, 1);
} while(!thread->min);
thread->min = Min;
thread->mi = Mi;
thread->mj = Mj;
return NULL;
}
long unsigned minPair(Matrix *Q) {
int i, j, mi, mj;
long unsigned pos;
double min, q, *Qptr;
float *Qfptr;
short unsigned *Qsptr;
unsigned char *Qbptr;
mi = 0;
mj = 0;
min = 1;
Qptr = 0;
Qfptr = 0;
Qsptr = 0;
Qbptr = 0;
if(Q->mat) {
Qptr = *(Q->mat) - 1;
} else if(Q->fmat) {
Qfptr = *(Q->fmat) - 1;
} else if(Q->smat) {
Qsptr = *(Q->smat) - 1;
} else {
Qbptr = *(Q->bmat) - 1;
}
for(i = 1; i < Q->n; ++i) {
for(j = 0; j < i; j++) {
q = Qptr ? *++Qptr : Qfptr ? *++Qfptr : Qsptr ? uctod(*++Qsptr) : uctod(*++Qbptr);
if(q <= min) {
min = q;
mi = i;
mj = j;
}
}
}
/* save pos */
pos = 0;
pos |= mi;
pos <<= sizeof(unsigned) * 8;
pos |= mj;
return pos;
}
void updateD(Matrix *D, Vector *sD, int *N, int i, int j, double Li, double Lj) {
int k, n, Dn, *Nptr;
double dist, sd, D_ik, D_kj, D_ij, *D_i, *D_j, **Dmat, *sDvec;
float *Df_i, *Df_j, **Dfmat;
short unsigned *Ds_i, *Ds_j, **Dsmat;
unsigned char *Db_i, *Db_j, **Dbmat;
/*
D(i,j) = D(j,i) <-> ltd -> j < i
D(k,m) = (D(i,k) + D(k,j) - D(i,j))/2
! D(i,k) -> D(k,m) = D(k,j) - L(j)
! D(k,j) -> D(k,m) = D(i,k) - L(i)
*/
/* init */
Dmat = 0;
D_i = 0;
D_j = 0;
Dfmat = 0;
Df_i = 0;
Df_j = 0;
Dsmat = 0;
Ds_i = 0;
Ds_j = 0;
Dbmat = 0;
Db_i = 0;
Db_j = 0;
if(D->mat) {
Dmat = D->mat;
D_i = Dmat[i] - 1;
D_j = Dmat[j] - 1;
D_ij = Dmat[i][j];
} else if(D->fmat) {
Dfmat = D->fmat;
Df_i = Dfmat[i] - 1;
Df_j = Dfmat[j] - 1;
D_ij = Dfmat[i][j];
} else if(D->smat) {
Dsmat = D->smat;
Ds_i = Dsmat[i] - 1;
Ds_j = Dsmat[j] - 1;
D_ij = uctod(Dsmat[i][j]);
} else {
Dbmat = D->bmat;
Db_i = Dbmat[i] - 1;
Db_j = Dbmat[j] - 1;
D_ij = uctod(Dbmat[i][j]);
}
sDvec = sD->vec - 1;
Nptr = N - 1;
/* prepare upadate on N and sD */
n = 1;
sd = 0;
/* update (first) row */
k = j + 1;
while(--k) {
D_ik = D_i ? *++D_i : Df_i ? *++Df_i : Ds_i ? uctod(*++Ds_i) : uctod(*++Db_i);
D_kj = D_j ? *++D_j : Df_j ? *++Df_j : Ds_j ? uctod(*++Ds_j) : uctod(*++Db_j);
if(0 <= D_ik && 0 <= D_kj) {
dist = (D_ik + D_kj - D_ij) / 2;
dist = dist < 0 ? 0 : dist; /* hnj approx-error */
if(D_j) {
*D_j = dist;
} else if(Df_j) {
*Df_j = dist;
} else if(Ds_j) {
*Ds_j = dtouc(dist, 0.25);
} else {
*Db_j = dtouc(dist, 0.25);
}
/* update N and sD */
*++sDvec -= (D_ik + D_kj - dist);
sd += dist;
--*++Nptr;
++n;
} else if(0 <= D_ik) {
dist = D_ik - Li;
if(D_j) {
*D_j = dist;
} else if(Df_j) {
*Df_j = dist;
} else if(Ds_j) {
*Ds_j = dtouc(dist, 0);
} else {
*Db_j = dtouc(dist, 0);
}
/* update N and sD, sD(k) is new */
*++sDvec -= Li;
++Nptr;
sd += dist;
++n;
} else if(0 <= D_kj) {
if(D_j) {
dist = (*D_j -= Lj);
} else if(Df_j) {
dist = (*Df_j -= Lj);
} else if(Ds_j) {
dist = (*Ds_j -= dtouc(Lj, 0));
dist = uctod(dist);
} else {
dist = (*Db_j -= dtouc(Lj, 0));
dist = uctod(dist);
}
/* update N and sD */
*++sDvec += (dist - D_kj);
--*++Nptr;
sd += dist;
++n;
}
}
/* update jth column */
if(D_j) {
D_j = Dmat[j];
} else if(Df_j) {
Df_j = Dfmat[j];
} else if(Ds_j) {
Ds_j = Dsmat[j];
} else {
Db_j = Dbmat[j];
}
++sDvec;
++Nptr;
Dn = i;
k = j;
while(Dn != D->n) {
if(k == Dn) {
/* skip ith row */
Dn = D->n;
++sDvec;
++Nptr;
}
while(++k < Dn) {
if(Dmat) {
D_ik = k < i ? Dmat[i][k] : Dmat[k][i];
D_kj = Dmat[k][j];
} else if(Dfmat) {
D_ik = k < i ? Dfmat[i][k] : Dfmat[k][i];
D_kj = Dfmat[k][j];
} else if(Dsmat) {
D_ik = k < i ? Dsmat[i][k] : Dsmat[k][i];
D_ik = uctod(D_ik);
D_kj = uctod(Dsmat[k][j]);
} else {
D_ik = k < i ? Dbmat[i][k] : Dbmat[k][i];
D_ik = uctod(D_ik);
D_kj = uctod(Dbmat[k][j]);
}
if(0 <= D_ik && 0 <= D_kj) {
dist = (D_kj + D_ik - D_ij) / 2;
dist = dist < 0 ? 0 : dist; /* hnj approx-error */
if(Dmat) {
Dmat[k][j] = dist;
} else if(Dfmat) {
Dfmat[k][j] = dist;
} else if(Dsmat) {
Dsmat[k][j] = dtouc(dist, 0.25);
} else {
Dbmat[k][j] = dtouc(dist, 0.25);
}
/* update N and sD */
*++sDvec -= (D_ik + D_kj - dist);
--*++Nptr;
sd += dist;
++n;
} else if(0 <= D_ik) {