END_TEST
START_TEST (test_resi)
{
const char *commands[] = {"c1, resi 1+2-4",
"c2, resi 2-4",
"c3, resi 1",
"c4, resi 1 AND resi 2-4",
"c5, resi 1 OR resi 2-4",
"c6, resi 1-2+2-4",
"c7, resi 1+2-4+3",
"c8, resi 1-2+7+9+3-5+100",
"c9, resi 1-4 AND NOT resi 2-4"};
freesasa_set_verbosity(FREESASA_V_SILENT);
test_select(commands,9);
freesasa_set_verbosity(FREESASA_V_NORMAL);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(resi_1,result) + addup(resi_2r4,result), 1e-10));
ck_assert(float_eq(value[1], addup(resi_2r4,result), 1e-10));
ck_assert(float_eq(value[2], addup(resi_1,result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5], value[0], 1e-10));
ck_assert(float_eq(value[6], value[0], 1e-10));
ck_assert(float_eq(value[7], value[0], 1e-10));
ck_assert(float_eq(value[8], value[2], 1e-10));
}
END_TEST
START_TEST (test_symbol)
{
const char *commands[] = {"c1, symbol o+c",
"c2, symbol O",
"c3, symbol C",
"c4, symbol O AND symbol C",
"c5, symbol O OR symbol C",
"c6, symbol O+C+SE",
"c7, symbol SE",
"c8, symbol O+C+SE and not symbol se"};
test_select(commands,8);
ck_assert_str_eq(selection_name[0], "c1");
ck_assert_str_eq(selection_name[1], "c2");
ck_assert_str_eq(selection_name[2], "c3");
ck_assert(value[0] > 5); //just to check that it's non-zero
ck_assert(float_eq(value[0], addup(symb_O,result) + addup(symb_C,result), 1e-10));
ck_assert(float_eq(value[1], addup(symb_O,result), 1e-10));
ck_assert(float_eq(value[2], addup(symb_C,result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5],
addup(symb_O,result) + addup(symb_C,result) + addup(symb_SE,result),
1e-10));
ck_assert(float_eq(value[6], addup(symb_SE,result), 1e-10));
ck_assert(float_eq(value[7], value[0], 1e-10));
}
END_TEST
START_TEST (test_resn)
{
const char *commands[] = {"c1, resn ala+arg",
"c2, resn ala",
"c3, resn arg",
"c4, resn ala AND resn arg",
"c5, resn ala OR resn arg",
"c6, resn ala+arg AND NOT resn arg"};
test_select(commands,6);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(resn_A,result) + addup(resn_R,result), 1e-10));
ck_assert(float_eq(value[1], addup(resn_A,result), 1e-10));
ck_assert(float_eq(value[2], addup(resn_R,result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[4], value[0], 1e-10));
ck_assert(float_eq(value[5], value[1], 1e-10));
}
END_TEST
START_TEST (test_chain)
{
const char *commands[] = {"c1, chain A+B",
"c2, chain A",
"c3, chain B",
"c4, chain A AND chain B",
"c5, chain A OR chain B",
"c6, chain A-B",
"c7, chain A-B AND NOT chain A"};
test_select(commands,7);
ck_assert(value[0] > 5);
ck_assert(float_eq(value[0], addup(chain_A,result) + addup(chain_B,result), 1e-10));
ck_assert(float_eq(value[0], value[4], 1e-10));
ck_assert(float_eq(value[0], value[5], 1e-10));
ck_assert(float_eq(value[1], addup(chain_A,result), 1e-10));
ck_assert(float_eq(value[2], addup(chain_B,result), 1e-10));
ck_assert(float_eq(value[3], 0, 1e-10));
ck_assert(float_eq(value[6], addup(chain_B,result), 1e-10));
}
void agsurv3(int *sn, int *snvar, int *sncurve,
int *snpt, int *sse, double *score,
double *sy, double *r, double *coef,
double *var, double *cmean, int *scn,
double *cy, double *cx, double *ssurv,
double *varh, double *sused, int *smethod)
{
register int i,j,k,l;
double *start, *stop, *event;
int cn;
int npt,
nvar2,
method;
int kk=0, psave;
int itime;
int person;
int deaths, nrisk;
int need;
double *a=0, *a2=0;
double weight=0,
e_denom,
denom;
double inc,
sumt,
km=0;
double temp,
downwt,
d2;
double haz,
varhaz;
double **oldx=0;
n = *sn; nvar = *snvar;
cn = *scn; npt = *snpt;
se = *sse;
mean = cmean;
ncurve = *sncurve;
method = *smethod;
death = method/10;
method = method - death*10;
y = sy;
start = cy;
stop = cy+ cn;
event = cy+ cn+ cn;
strata = r;
/*
** scratch space
*/
need = 2*n + se*nvar*(2+ n*(n+1)/2);
nscore = (double *) ALLOC(need, sizeof(double));
isurv = nscore + n;
for (i=0; i<n; i++) isurv[i]=1;
if (se==1) {
a = isurv + n;
a2= a + nvar;
tvar = (double **) ALLOC(n, sizeof(double *));
/* be tricky here, as only the bottom half is used */
tvar[0] = a2 + nvar;
for (i=1; i<n; i++)
tvar[i] = tvar[i-1] +i;
}
/*
** Set up the ragged arrays
*/
if (se==1) oldx = dmatrix(cx, cn, nvar);
newx = dmatrix(r+n, n, nvar);
imat = dmatrix(var, nvar, nvar);
surv = dmatrix(ssurv, npt, ncurve);
vsurv = dmatrix(varh, npt, ncurve);
used = dmatrix(sused, npt, ncurve);
for (i=0; i<ncurve; i++)
for (j=0; j<npt; j++) surv[i][j] =1;
/*
** compute the risk scores, and center the data for stability
*/
if (se==1) {
for (i=0; i<cn; i++) {
for (j=0; j<nvar; j++)
oldx[j][i] -= mean[j];
}
}
for (i=0; i<n; i++) {
nscore[i] =0;
for (j=0; j<nvar; j++) {
newx[j][i] -= mean[j];
nscore[i] += coef[j]* newx[j][i];
}
nscore[i] = exp(nscore[i]);
}
/*
** outer loop keeps a running track of the baseline hazard
** the addup function adds things up
*/
itime =0;
nvar2 = nvar * se; /*simpler than a lot of " if (se==1)" statements */
for (person=0; person<cn;) {
if (event[person]==0) person++;
else {
/*
** compute the mean and denominator over the risk set
*/
denom =0;
e_denom=0;
for(i=0; i<nvar2; i++){
a[i] =0;
a2[i]=0;
}
time = stop[person];
nrisk =0;
deaths=0;
for (k=person; k<cn; k++) {
if (start[k] < time) {
nrisk++;
weight = score[k];
denom += weight;
for (i=0; i<nvar2; i++) {
a[i] += weight*(oldx[i][k]);
}
}
if (stop[k]==time && event[k]==1) {
kk=k;
deaths++;
e_denom += weight;
for (i=0; i<nvar2; i++) {
a2[i] += weight*(oldx[i][k]);
}
}
}
/*
** Now compute the increment in the hazard and variance at "time"
*/
if (method <3) for (i=0; i<nvar2; i++) mean[i] = a[i]/denom;
if (method==1) {
for (psave=person; psave<cn && stop[psave]==time; psave++)
/*
** kalbfleisch estimator requires iteration;
*/
if (deaths == nrisk) km=0;
else if (deaths ==1) {
km = pow(1- score[kk]/denom, 1/score[kk]);
}
else { /*find the zero of an equation */
km = .5;
inc = .25;
for (l=0; l<35; l++) { /* bisect it to death */
sumt =0;
for (k=person; k<psave; k++) {
if (event[k] ==1)
sumt += score[k]/(1-pow(km, score[k]));
}
if (sumt < denom) km += inc;
else km -= inc;
inc = inc/2;
}
}
if (km==0)
addup(itime, 0.0, 0.0);
else {
haz = log(km);
varhaz = deaths/(denom *(denom-e_denom)); /* Greenwood */
addup(itime, haz, varhaz);
}
person = psave;
}
else if (method==2) {
addup(itime, deaths/denom, deaths/(denom*denom));
for (; person<cn && stop[person]==time; person++);
}
else {
temp =0; haz=0; varhaz=0;
for (k=person; k<cn && stop[k]==time; k++) {
if (event[k]==1) {
downwt = temp++/deaths;
d2 = (denom - downwt*e_denom);
haz = 1/d2;
varhaz = 1/(d2*d2);
for (i=0; i<nvar2; i++)
mean[i] = (a[i] - downwt*a2[i])/ d2;
addup(itime, haz, varhaz);
}
person++;
}
}
start[itime] = time;
stop[itime] = nrisk;
event[itime]= deaths;
itime++;
}
}
}
