struct color input_ambient(int argc, char *in[]){
int i = 0;
while(strcmp(in[i],"-ambient")!= 0){
if(i>=argc-1)
return create_color(1,1,1);
i++;
}
double x = 1;
double y = 1;
double z = 1;
if(i+1<argc && !equalToFlag(argc,in,i+1))
x = convert_double(in[i+1],1);
else
return create_color(x,y,z);
if(i+2<argc&& !equalToFlag(argc,in,i+2))
y = convert_double(in[i+2],1);
else
return create_color(x,y,z);
if(i+3<argc&& !equalToFlag(argc,in,i+3))
z = convert_double(in[i+3],1);
else
return create_color(x,y,z);
return create_color(x,y,z);
}
struct point input_eye(int argc, char *in[]){
int i = 0;
while(strcmp(in[i],"-eye")!= 0){
if(i>=argc-1)
return create_point(0,0,-14);
i++;
}
double x = 0;
double y = 0;
double z = -14;
if(i+1<argc && !equalToFlag(argc,in,i+1))
x = convert_double(in[i+1],0);
else
return create_point(x,y,z);
if(i+2<argc && !equalToFlag(argc,in,i+2))
y = convert_double(in[i+2],0);
else
return create_point(x,y,z);
if(i+3<argc && !equalToFlag(argc,in,i+3))
z = convert_double(in[i+3],-14);
else
return create_point(x,y,z);
return create_point(x,y,z);
}
void test_convert_double()
{
char s1[]={"3.4\0"};
double a = convert_double(s1,4.2);
checkit_double(a,3.4);
char s2[]={"asdfcxzv\0"};
double b = convert_double(s2,3.2);
checkit_double(b,3.2);
char s3[]={"asdfdfs3.4asdfasdf\0"};
double c = convert_double(s3,32.1);
checkit_double(c,32.1);
char s4[]={"-3.2\0"};
double d = convert_double(s4,4.2);
checkit_double(d,-3.2);
}
void RateMeyerHaeseler::readRateFile(char *rate_file) {
cout << "Reading site-specific rate file " << rate_file << " ..." << endl;
try {
ifstream in;
in.exceptions(ios::failbit | ios::badbit);
in.open(rate_file);
char line[256];
int site, i;
double rate;
int nsites = phylo_tree->aln->getNSite();
resize(phylo_tree->aln->getNPattern(), -1.0);
int saturated_sites = 0, saturated_ptn = 0;
in.getline(line, sizeof(line));
//if (strncmp(line, "Site", 4) != 0) throw "Wrong header line";
for (i = 0; i < nsites; i++) {
in.getline(line, sizeof(line));
stringstream ss(line);
string tmp;
ss >> tmp;
site = convert_int(tmp.c_str());
if (site <= 0 || site > nsites) throw "Wrong site number (must be between 1 and #sites)";
site--;
ss >> tmp;
rate = convert_double(tmp.c_str());
if (rate < 0.0) throw "Negative rate not allowed";
if (rate <= 0.0) rate = MIN_SITE_RATE;
int ptn = phylo_tree->aln->getPatternID(site);
if (rate >= MAX_SITE_RATE) {
rate = MAX_SITE_RATE;
saturated_sites += phylo_tree->aln->at(ptn).frequency;
saturated_ptn ++;
}
at(ptn) = rate;
}
in.clear();
// set the failbit again
in.exceptions(ios::failbit | ios::badbit);
in.close();
for (i = 0; i < size(); i++)
if (at(i) < 0.0) throw "Some site has no rate information";
if (saturated_sites) {
stringstream str;
str << saturated_sites << " sites (" << saturated_ptn << " patterns) show too high rates (>=" << MAX_SITE_RATE << ")";
outWarning(str.str());
}
} catch (const char *str) {
outError(str);
} catch (string str) {
outError(str);
} catch(ios::failure) {
outError(ERR_READ_INPUT);
}
}
double htrace_conf_get_double(struct htrace_log *log,
const struct htrace_conf *cnf, const char *key)
{
const char *val;
double out = 0;
val = htable_get(cnf->values, key);
if (val) {
if (convert_double(log, key, val, &out)) {
return out;
}
}
val = htable_get(cnf->defaults, key);
if (val) {
if (convert_double(log, key, val, &out)) {
return out;
}
}
return 0;
}
struct view input_view(int argc, char *in[]){
int i = 0;
while(strcmp(in[i],"-view")!= 0){
if(i>=argc-1)
return create_view(-10,10,-7.5,7.5,1024,768);
i++;
}
double minx = -10;
double maxx = 10;
double miny = -7.5;
double maxy = 7.5;
int width = 1024;
int height = 768;
if(i+1<argc && !equalToFlag(argc,in,i+1))
minx = convert_double(in[i+1],-10);
else
return create_view(minx,maxx,miny,maxy,width,height);
if(i+2<argc && !equalToFlag(argc,in,i+2))
maxx = convert_double(in[i+2],10);
else
return create_view(minx,maxx,miny,maxy,width,height);
if(i+3<argc && !equalToFlag(argc,in,i+3))
miny = convert_double(in[i+3],-7.5);
else
return create_view(minx,maxx,miny,maxy,width,height);
if(i+4<argc && !equalToFlag(argc,in,i+4))
maxy = convert_double(in[i+4],7.5);
else
return create_view(minx,maxx,miny,maxy,width,height);
if(i+5<argc && !equalToFlag(argc,in,i+5))
width = convert_double(in[i+5],1024);
else
return create_view(minx,maxx,miny,maxy,width,height);
if(i+6<argc && !equalToFlag(argc,in,i+6))
height = convert_double(in[i+6],768);
else
return create_view(minx,maxx,miny,maxy,width,height);
return create_view(minx,maxx,miny,maxy,width,height);
}
struct light input_light(int argc, char *in[]){
int i = 0;
while(strcmp(in[i],"-light")!= 0){
if(i>=argc-1)
return create_light(create_point(-100,100,-100),create_color(1.5,1.5,1.5));
i++;
}
double x = -100;
double y = 100;
double z = -100;
double r = 1.5;
double g = 1.5;
double b = 1.5;
if(i+1<argc && !equalToFlag(argc,in,i+1))
x = convert_double(in[i+1],-100);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
if(i+2<argc && !equalToFlag(argc,in,i+2))
y = convert_double(in[i+2],100);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
if(i+3<argc && !equalToFlag(argc,in,i+3))
z = convert_double(in[i+3],-100);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
if(i+4<argc && !equalToFlag(argc,in,i+4))
r = convert_double(in[i+4],1.5);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
if(i+5<argc && !equalToFlag(argc,in,i+5))
g = convert_double(in[i+5],1.5);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
if(i+6<argc && !equalToFlag(argc,in,i+6))
b = convert_double(in[i+6],1.5);
else
return create_light(create_point(x,y,z),create_color(r,g,b));
return create_light(create_point(x,y,z),create_color(r,g,b));
}
/* writes data to fcell file for either full or partial rows */
static void put_fp_data(int fd, char *null_buf, const void *rast,
int row, int n, RASTER_MAP_TYPE data_type)
{
struct fileinfo *fcb = &R__.fileinfo[fd];
int compressed = (fcb->open_mode == OPEN_NEW_COMPRESSED);
XDR *xdrs = &fcb->xdrstream;
void *work_buf;
if (row < 0 || row >= fcb->cellhd.rows)
return;
if (n <= 0)
return;
work_buf = G__alloca(fcb->cellhd.cols * fcb->nbytes + 1);
if (compressed)
set_file_pointer(fd, row);
xdrmem_create(xdrs, work_buf,
(unsigned int)fcb->nbytes * fcb->cellhd.cols, XDR_ENCODE);
xdr_setpos(xdrs, 0);
if (data_type == FCELL_TYPE)
convert_float(xdrs, null_buf, rast, row, n);
else
convert_double(xdrs, null_buf, rast, row, n);
xdr_destroy(&fcb->xdrstream);
if (compressed)
write_data_compressed(fd, row, work_buf, n);
else
write_data(fd, row, work_buf, n);
G__freea(work_buf);
}
void NGSAlignment::readFritzFile(const char *filename) {
cout << "Reading Fritz file " << filename << " ..." << endl;
try {
ifstream in;
in.exceptions(ios::failbit | ios::badbit);
in.open(filename);
in.clear();
int i, total_size;
string tmp;
in >> tmp;
ncategory = convert_int(tmp.c_str());
if (ncategory < 1) throw "Wrong number of positions";
in >> tmp;
num_states = convert_int(tmp.c_str());
total_size = ncategory*num_states*num_states;
if (num_states < 1) throw "Wrong number of states";
pair_freq = new double[total_size];
for (i=0; i < total_size; i++) {
in >> tmp;
double count = convert_double(tmp.c_str());
if (count < 0) throw "Wrong count";
pair_freq[i] = count;
}
// set the failbit again
in.exceptions(ios::failbit | ios::badbit);
in.close();
} catch (const char *str) {
outError(str);
} catch (string str) {
outError(str);
} catch (ios::failure) {
outError(ERR_READ_INPUT);
}
cout << ncategory << " matrices of size " << num_states << endl;
}
//
// ------ amount accessor ---
//
double Money::amount(double new_amount)
{
double temp = (*this).amount();
convert_double(new_amount);
return temp;
}
Money::Money(double amount)
{
convert_double(amount);
}
