double RestraintCache::get_score(kernel::Restraint *r, const Subset &s,
const Assignment &a) const {
IMP_OBJECT_LOG;
set_was_used(true);
Slice slice = get_slice(r, s);
Assignment ra = slice.get_sliced(a);
return get_score(r, ra);
}
/*
* Implement mapping assignment sub-script for the type.
*/
static int sipArray_ass_subscript(PyObject *self, PyObject *key,
PyObject *value)
{
sipArrayObject *array = (sipArrayObject *)self;
SIP_SSIZE_T start, len;
void *value_data;
if (check_writable(array) < 0)
return -1;
if (PyIndex_Check(key))
{
start = PyNumber_AsSsize_t(key, PyExc_IndexError);
if (start == -1 && PyErr_Occurred())
return -1;
if (start < 0)
start += array->len;
if (check_index(array, start) < 0)
return -1;
if ((value_data = get_value(array, value)) == NULL)
return -1;
len = 1;
}
else if (PySlice_Check(key))
{
Py_ssize_t stop, step;
if (sipConvertFromSliceObject(key, array->len, &start, &stop, &step, &len) < 0)
return -1;
if (step != 1)
{
PyErr_SetNone(PyExc_NotImplementedError);
return -1;
}
if ((value_data = get_slice(array, value, len)) == NULL)
return -1;
}
else
{
bad_key(key);
return -1;
}
memmove(element(array, start), value_data, len * array->stride);
return 0;
}
static double iteration(int m0, int m1, int m2, int n0, int n1, int n2,
double Alpha[], double Beta[], MAPTYPE *vol,
double B0[], double B1[], double B2[], double f[], double mx, int nh, double h[], int *psh)
{
int j2, j1, j0, i2, i1, i0;
double *dat, *wt0, *wt1, *Alpha1, *Beta1;
double t2[MAXB*MAXB], t1[MAXB], ll;
dat = (double *)mxCalloc(n1*n0, sizeof(double));
wt0 = (double *)mxCalloc(n1*n0, sizeof(double));
wt1 = (double *)mxCalloc(n1*n0, sizeof(double));
Alpha1 = (double *)mxCalloc(m1*m0*m1*m0, sizeof(double));
Beta1 = (double *)mxCalloc(m1*m0, sizeof(double));
hist(m0,m1,m2, n0,n1,n2, vol, B0,B1,B2,f, nh,(nh-1.0)/mx,h, dat, psh);
ll = 0.0;
for(j2=0;j2<n2; j2++)
{
get_slice(vol,j2,dat);
for(i0=0; i0<m0*m1; i0++)
{
t2[i0] = 0.0;
for(i2=0;i2<m2; i2++)
t2[i0] += B2[j2+n2*i2]*f[i0+m0*m1*i2];
}
for(j1=0; j1<n1; j1++)
{
for(i0=0; i0<m0; i0++)
{
t1[i0] = 0.0;
for(i1=0;i1<m1; i1++)
t1[i0] += B1[j1+n1*i1]*t2[i0+m0*i1];
}
for(j0=0; j0<n0; j0++)
{
double sc = 0.0;
for(i0=0; i0<m0; i0++)
sc += B0[j0+n0*i0]*t1[i0];
weights(dat[j0+n0*j1], exp(sc), nh, (nh-1.0)/mx,h, &wt0[j0+n0*j1], &wt1[j0+n0*j1], &ll);
}
}
kronutil(n0,n1,n2, m0,m1,m2, j2, wt0,wt1, B0,B1,B2, Alpha1,Beta1, Alpha,Beta);
}
mxFree((void *)dat);
mxFree((void *)wt0);
mxFree((void *)wt1);
mxFree((void *)Alpha1);
mxFree((void *)Beta1);
return(ll);
}
/* Create a histogram from data modulated by a linear combination of seperable
* basis functions
* m0 - number of bases in x dimension
* m1 - number of bases in y dimension
* m2 - number of bases in z dimension
* n0 - x dimension of volume
* n1 - y dimension of volume
* n2 - z dimension of volume
* vol - mapped volume
* B0 - seperable bases - x
* B1 - seperable bases - y
* B2 - seperable bases - z
* f - basis function coefficients
* nh - number of histogram bins
* s - scale from image intensity to histogram bin number (1/binwidth)
* h - histogram
* dat - buffer for storing a plane of data
*
* required: m0, m1, m2, n0, n1, n2, vol, B0, B1, B2, f, nh, s
* modified: h, dat
*/
static void hist(int m0, int m1, int m2, int n0, int n1, int n2,
MAPTYPE *vol, double *B0, double *B1, double *B2, double *f,
int nh, double s, double *h, double *dat, int *psh)
{
int i0, i1, i2;
int j0, j1, j2;
double t2[MAXB*MAXB], t1[MAXB];
for(j2=0;j2<n2; j2++)
{
get_slice(vol,j2,dat);
for(i0=0; i0<m0*m1; i0++)
{
t2[i0] = 0.0;
for(i2=0;i2<m2; i2++)
t2[i0] += B2[j2+n2*i2]*f[i0+m0*m1*i2];
}
for(j1=0; j1<n1; j1++)
{
double *pdat = dat+j1*n0;
for(i0=0; i0<m0; i0++)
{
t1[i0] = 0.0;
for(i1=0;i1<m1; i1++)
t1[i0] += B1[j1+n1*i1]*t2[i0+m0*i1];
}
for(j0=0; j0<n0; j0++)
{
double y, y0 = pdat[j0]*s;
#ifdef IGNORE_ZEROS
if (y0>0.0)
#else
if (y0>=0.0)
#endif
{
int iy;
double dy, sc = 0.0;
for(i0=0;i0<m0; i0++)
sc += B0[j0+n0*i0]*t1[i0];
y = y0*exp(sc);
if (y>=0 && y<(nh-1))
{
iy = floor(y);
dy = y-iy;
h[iy] += 1-dy;
h[iy+1] += dy;
}
}
}
}
}
normhist(nh,h,1/s,psh);
}
/**
* Receive messages from the iridium gss send by different iridium terminal
* @param server_fd server socket descriptor
* @param forward_ip the destination ip address
* @return -1 on failure, 0 on client disconnect, n(>0) bytes read
*/
int receive_iridium_msgs(int client_fd)
{
int payload_len = 0;
int finish = 0;
slice *slice = malloc(SLICE_LEN);
payload_len = get_slice(client_fd, slice);
finish = resemble_iridium_msgs(slice, payload_len);
if (finish)
forward_iridium_msg(slice->header.sn);
free(slice);
return 0;
}
void FindBar::replace_text(Gtk::TextIter& start, Gtk::TextIter& end, Glib::ustring& replacement) {
auto buf = window_.current_buffer()->buffer();
if(buf->get_slice(start, end) == replacement) {
return;
}
//Store the offset to the start of the selection set to be replaced
auto offset = start.get_offset();
//Erase the selection
buf->erase(start, end);
//Build a new iterator from the stored offset, and insert the text there
auto new_start = buf->get_iter_at_offset(offset);
buf->insert(new_start, replacement);
}
void Client::
issue_get_for_key(const std::string& column_family,
const std::string& key,
const SlicePredicate& predicate,
std::vector<ColumnOrSuperColumn>& columns,
ConsistencyLevel::type consistency_level)
{
ColumnParent cparent;
cparent.column_family = column_family;
get_slice(columns, key, cparent, predicate, consistency_level);
if (columns.size() == 0)
{
RowNotFoundException row_not_found_ex(column_family, key);
throw row_not_found_ex;
}
}
/*
* Implement sequence assignment slice sub-script for the type.
*/
static int sipArray_ass_slice(PyObject *self, int left, int right,
PyObject *value)
{
sipArrayObject *array = (sipArrayObject *)self;
void *value_data;
if (check_writable(array) < 0)
return -1;
fix_bounds(array->len, &left, &right);
if ((value_data = get_slice(array, value, right - left)) == NULL)
return -1;
memmove(element(array, left), value_data, (right - left) * array->stride);
return 0;
}
/********************************************************************************
* Unused code */
double constr(int m0, int m1, int m2, int n0, int n1, int n2,
double Beta[], MAPTYPE *vol,
double B0[], double B1[], double B2[])
{
int j2, i2, i01;
double *dat, *Beta1, sm;
dat = (double *)mxCalloc(n1*n0, sizeof(double));
Beta1 = (double *)mxCalloc(m1*m0, sizeof(double));
sm = 0.0;
for(j2=0;j2<n2; j2++)
{
get_slice(vol,j2,dat);
kronutil1(n0,n1,m0,m1, dat, B0, B1, Beta1);
for(i2=0; i2<m2; i2++)
for(i01=0; i01<m0*m1; i01++)
Beta[i01 + i2*m0*m1] += Beta1[i01]*B2[j2 + i2*n2];
for(i01=0; i01<n0*n1; i01++)
sm += dat[i01];
}
mxFree((void *)Beta1);
mxFree((void *)dat);
return(sm);
}
void SpOpenRec(void)
{
char fname[MAX_SLICE_LENGTH+1];
int namelen;
int fileorg;
int filemode;
int filetype;
int format;
long mrs;
long fileid;
FILE *fd;
struct FILE_INFO *info;
#ifdef VMS
struct RAB *rab;
RecInfo *rinfo;
unsigned int rfm,rat;
#endif /* VMS */
dbgmsg("SP.OPENREC");
InBuf = &Tbuf[3];
OutBuf = &Tbuf[2];
OutCount = 0;
namelen = get_slice((unsigned char *) fname);
fname[namelen] = '\0';
fileorg = (int) get_8();
filemode = (int) get_8();
filetype = (int) get_8();
format = (int) get_8();
mrs = get_32();
dbgmsg("file=\"%s\" %d:%d:%d:%d %ld", fname, fileorg, filemode,
filetype, format, mrs);
/* Validate request */
if ((strlen(fname) == 0) || (fileorg < 3) || (fileorg > 4) ||
(filetype < 0) || (filetype > 2) ||
(filemode < 1) || (filemode > 6) ||
(format < 0) || (format > 1)) {
SpFail(ER_ERROR);
return;
}
if (filetype == TYPE_DONTCARE)
filetype = TYPE_RECORD;
#ifdef VMS
if (fileorg == ORG_VARIABLE)
rfm = FAB$C_VAR;
rfm = (fileorg == ORG_VARIABLE)?FAB$C_VAR:FAB$C_FIX;
rat = (filetype == TYPE_RECORD)?FAB$M_FTN:0; /* FTN:FAB$M_CR */
/* We ignore format under VMS */
/* decide whether to open or create file */
if ((filemode == 1) || (filemode == 4))
rab = vmsopen(fname, rfm, rat);
else
rab = vmscreate(fname, rfm, rat, rfm);
if (rab == (struct RAB *) NULL) {
SpFail(ER_NOFILE);
return;
}
rinfo = newinfo();
if (rinfo == (RecInfo *) NULL) {
vmsclose(rab);
SpFail(ER_ERROR);
}
else {
rinfo->baserec = 0;
rinfo->prev = (FilePos *) NULL;
rinfo->next = (FilePos *) NULL;
}
fd = stdout; /* Must be something ! */
#else
fd = fopen(fname, OpenModes[fileorg-1][filemode-1]);
if (fd == NULL) {
SpFail(ER_NOFILE);
return;
}
#endif /* VMS */
/* File opened OK */
fileid = RememberFile(fd, fileorg);
if (fileid == NO_SLOT) {
SpFail(ER_NORESOURCE);
return;
}
/* Things are looking good Houston....beep */
info = &FileInfo[fileid];
info->buff = (unsigned char *) malloc((int) mrs+3); /* Room for CR, NL, EOS */
if (info->buff == (unsigned char *) NULL) {
ForgetFile(fileid);
SpFail(ER_NORESOURCE);
return;
}
info->mrs = mrs;
info->recordsize = -1;
info->format = format;
info->type = filetype;
info->recno = 0;
info->lastop = FIOP_NONE;
info->pasteof = false;
#ifdef VMS
info->rab = rab;
info->poslist = rinfo;
#else
if (fileorg == ORG_VARIABLE) {
info->putfn = (format == FMT_FORMATTED)?form_seq_write_rec:unform_seq_write_rec;
info->getfn = (format == FMT_FORMATTED)?form_seq_read_rec:unform_seq_read_rec;
/* Need to allocate a read-ahead buffer for formatted files */
if (format == FMT_FORMATTED) {
info->llbuff = (unsigned char *) malloc(LL_BUF_SIZE);
info->llind = LL_BUF_SIZE;
if (info->llbuff == (unsigned char *) NULL) {
free(info->buff);
ForgetFile(fileid);
SpFail(ER_NORESOURCE);
return;
}
}
else {
info->llbuff = NULL;
info->llind = 0;
}
}
else {
info->putfn = direct_write_rec;
info->getfn = direct_read_rec;
info->llbuff = NULL;
info->llind = 0;
}
#endif /* VMS */
put_8(ER_SUCCESS);
put_32(mrs);
put_32(fileid);
put_32(filetype);
put_count(OutCount);
}
void SpPutRec(void)
{
long fileid;
FILE *fd;
long recordsize;
int chunksize;
long offset;
bool dowrite=false;
struct FILE_INFO *info;
int res;
dbgmsg("SP.PUTREC");
InBuf = &Tbuf[3];
OutBuf = &Tbuf[2];
OutCount = 0;
fileid = get_32();
recordsize = get_32();
chunksize = get_16();
offset = get_32();
if (get_8())
dowrite = true;
dbgmsg("fileid=%ld, recordsize=%ld, chunksize=%d, offset=%ld, write=%d",
fileid, recordsize, chunksize, offset, dowrite);
if ((fileid < 0) || (fileid > MAX_FILES)) {
put_8(ER_BADID);
put_count(OutCount);
return;
}
info = &FileInfo[fileid];
if (info->fd == NULL) {
put_8(ER_BADID);
put_count(OutCount);
return;
}
if (info->lastop == FIOP_READ) {
put_8(ER_NOPOSN);
put_count(OutCount);
return;
}
if (info->recordsize == -1)
info->recordsize = recordsize;
dbgmsg("recordsize=%ld, info->recordsize=%ld", recordsize, info->recordsize);
dbgmsg("info->mrs=%ld", info->mrs);
if ((recordsize > info->recordsize) ||
(recordsize > info->mrs) || (offset+(long)chunksize > info->mrs)) {
dbgmsg("ER_ERROR: recordsize screwup");
put_8(ER_ERROR);
put_count(OutCount);
return;
}
get_slice(&(info->buff[offset]));
info->dirty = true;
if (dowrite == true) {
info->recno++;
#ifdef VMS
res = vmsput(info->rab, info->buff, (int) recordsize);
vmssavepos(info);
#else
res = info->putfn(info->fd, info->buff, recordsize);
#endif /* VMS */
info->dirty = false;
info->recordsize = -1;
}
else
res = ER_SUCCESS;
info->lastop = FIOP_WRITE;
info->pasteof = false;
put_8(res);
put_count(OutCount);
}