void rna_output_descr(toptions *opts, tsequence *seq)
{
if (seq->descr && seq->descr[0]) {
pcolor(opts->colored_output,COLOR_BOLD);
printf(">%s", seq->descr);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\n");
}
}
void rna_output_optimal(toptions *opts, tsequence *seq, char *algebra, int result_score, int range_begin, int range_end)
{
if (!opts->window_mode) {
printf("\n");
pcolor(opts->colored_output,COLOR_BOLD);
printf("%s: ", algebra);
printf("%.2f kcal/mol", ((float) result_score) / 100);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\n");
}
}
/* print position numbers for sequence;
used in window- and split-output modes */
static void print_subseq_numbers(toptions *opts, int pos, int size){
int i;
if (opts->split_output_mode) size = min(opts->window_pos + opts->window_size, pos + opts->split_output_size) - pos;
pcolor(opts->colored_output, COLOR_BLUE);
printf("%d", pos +1);
pcolor(opts->colored_output,COLOR_DEFAULT);
for (i=1; i<= size - (((int)log10(pos + 1))+1 + ((int)log10(pos + size))+1); i++) printf(" ");
pcolor(opts->colored_output,COLOR_BLUE);
printf("%d", pos + size);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\n");
}
static PyObject *image_pcolor(PyObject *self, PyObject *args, PyObject *kwds)
{
numpy::array_view<const float, 1> x;
numpy::array_view<const float, 1> y;
numpy::array_view<const agg::int8u, 3> d;
unsigned int rows;
unsigned int cols;
float bounds[4];
int interpolation;
Image *result;
if (!PyArg_ParseTuple(args,
"O&O&O&II(ffff)i:pcolor",
&x.converter,
&x,
&y.converter,
&y,
&d.converter_contiguous,
&d,
&rows,
&cols,
&bounds[0],
&bounds[1],
&bounds[2],
&bounds[3],
&interpolation)) {
return NULL;
}
CALL_CPP("pcolor", (result = pcolor(x, y, d, rows, cols, bounds, interpolation)));
return PyImage_cnew(result);
}
Mm ex() {
begin_scope
#line 1 "d:/matcom45/ex.m"
call_stack_begin;
#line 1 "d:/matcom45/ex.m"
// nargin, nargout entry code
double old_nargin=nargin_val; if (!nargin_set) nargin_val=0.0;
nargin_set=0;
double old_nargout=nargout_val; if (!nargout_set) nargout_val=0.0;
nargout_set=0;
// translated code
#line 2 "d:/matcom45/ex.m"
_ subplot(121.0);
#line 3 "d:/matcom45/ex.m"
_ surf((CL(peaks(25.0))));
#line 4 "d:/matcom45/ex.m"
_ subplot(122.0);
#line 5 "d:/matcom45/ex.m"
_ pcolor((CL(peaks(25.0))));
call_stack_end;
// nargin, nargout exit code
nargin_val=old_nargin; nargout_val=old_nargout;
// function exit code
return x_M;
end_scope
}
void SprayBrush::paintParticle(KisRandomAccessor &writeAccessor,const KoColor &color,qreal rx, qreal ry){
// opacity top left, right, bottom left, right
KoColor pcolor(color);
int ipx = int ( rx );
int ipy = int ( ry );
qreal fx = rx - ipx;
qreal fy = ry - ipy;
int btl = qRound( ( 1-fx ) * ( 1-fy ) * OPACITY_OPAQUE );
int btr = qRound( ( fx ) * ( 1-fy ) * OPACITY_OPAQUE );
int bbl = qRound( ( 1-fx ) * ( fy ) * OPACITY_OPAQUE );
int bbr = qRound( ( fx ) * ( fy ) * OPACITY_OPAQUE );
// this version overwrite pixels, e.g. when it sprays two particle next
// to each other, the pixel with lower opacity can override other pixel.
// Maybe some kind of compositing using here would be cool
pcolor.setOpacity ( btl );
writeAccessor.moveTo ( ipx , ipy );
memcpy ( writeAccessor.rawData(), pcolor.data(), m_pixelSize );
pcolor.setOpacity ( btr );
writeAccessor.moveTo ( ipx + 1, ipy );
memcpy ( writeAccessor.rawData(), pcolor.data(), m_pixelSize );
pcolor.setOpacity ( bbl );
writeAccessor.moveTo ( ipx, ipy + 1 );
memcpy ( writeAccessor.rawData(), pcolor.data(), m_pixelSize );
pcolor.setOpacity ( bbr );
writeAccessor.moveTo ( ipx + 1, ipy + 1 );
memcpy ( writeAccessor.rawData(), pcolor.data(), m_pixelSize );
}
void rna_output_subopt_start(toptions *opts, tsequence *seq, char *algebra, int result_score, int range_begin, int range_end)
{
if (!opts->window_mode && (strcmp(algebra, "count"))) {
printf("Suboptimal range: [%.2f kcal/mol - %.2f kcal/mol]\n", ((float) range_begin)/100, ((float) range_end)/100);
printf("\n");
if (seq->descr && seq->descr[0]) {
pcolor(opts->colored_output,COLOR_BOLD);
printf(">%s", seq->descr);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\n");
}
if (!opts->split_output_mode) printf("%s\n", seq->original_seq);
}
// print subsequence for first window iteration
// for later iterations, this is done in function shift_input
if (opts->window_mode && (opts->window_pos==0) && (strcmp(algebra, "count"))) {
print_sequence(opts, seq, opts->window_pos, opts->window_size);
}
}
static void render_pixels(QPainter &p, gint x, gint width, float rgb[TIMELINE_HEIGHT][3], float ratio)
{
int previous = 0, i;
for (i = 1; i <= TIMELINE_HEIGHT; i++) {
if (i != TIMELINE_HEIGHT &&
rgb[previous][0] == rgb[i][0] &&
rgb[previous][1] == rgb[i][1] &&
rgb[previous][2] == rgb[i][2])
continue;
if (rgb[previous][0] != 1.0 || rgb[previous][1] != 1.0 || rgb[previous][2] != 1.0) {
p.fillRect(QRectF(x/ratio, previous, width/ratio, i-previous), pcolor(rgb[previous][0],rgb[previous][1],rgb[previous][2]));
}
previous = i;
}
reset_rgb(rgb);
}
void simple_output_optimal(toptions *opts, tsequence *seq, char *algebra, int result_score, int range_begin, int range_end)
{
printf("\nInput: ");
pcolor(opts->colored_output,COLOR_BOLD);
printf("%s", seq->seq);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf("\nAlgebra: ");
pcolor(opts->colored_output,COLOR_BOLD);
printf("%s", algebra);
pcolor(opts->colored_output,COLOR_DEFAULT);
printf(", score: ");
pcolor(opts->colored_output,COLOR_BOLD);
printf("%d\n", result_score);
pcolor(opts->colored_output,COLOR_DEFAULT);
}
static void render_rectangle(QPainter &p, gint x, gint width, guint height, int dfilter, float r, float g, float b, float ratio)
{
p.fillRect(QRectF(x/ratio, TIMELINE_HEIGHT/2-height, width/ratio, dfilter ? height * 2 : height), pcolor(r,g,b));
}
static void process_args(toptions *opt, char interactive, int argc, char **argv) {
int c;
char manopt, manoptmode;
opterr = 0; optind = 1;
pcolor(opt->colored_output,COLOR_BLUE);
while ((c = getopt (argc, argv, "hH:ve:c:M:w:W:BS:f:z:O")) != -1) {
switch (c) {
// Display this information (-h)
case 'h':
if (interactive) {
printf("Interactive mode:\nEnter sequence directly or use the following commands to change settings:\n");
}
else {
printf("Options:\n");
}
printf(" -h Display this information\n");
printf(" -H <option> Display detailed information on <option>\n");
printf(" -v Show version\n");
printf(" -e <value> Set energy range (kcal/mol)\n");
printf(" -c <value> Set energy range (%%)\n");
printf(" -M <value> Set maximal loop length\n");
printf(" -w <value> Set window size\n");
printf(" -W <value> Set window position increment\n");
printf(" -B Show best results in window mode\n");
printf(" -O Only compute energy, no traceback\n");
printf(" -S <value> Specify output width for structures\n");
printf(" -f <filename> Read input from file\n");
printf(" -z Colored output\n");
if (opt->interactive) {
printf("Additional interactive mode commands:\n");
printf(" :s Show current configuration\n");
printf(" :d Reset configuration\n");
printf(" :e <string> Execute system command\n");
printf(" :q Quit\n");
}
opt->terminate = 1;
break;
// Display detailed information on <option> (-H)
case 'H':
if (optarg[0]=='-') { manoptmode = '-'; manopt = optarg[1]; }
else if (optarg[0]==':') { manoptmode = ':'; manopt = optarg[1]; }
else { manoptmode = '-'; manopt = optarg[0]; }
if (!interactive) printf("\n");
#include "RNAfold-man.c"
if (!interactive) printf("\n");
opt->terminate = 1;
break;
// Show version (-v)
case 'v':
printf("%s (%s)\n",PACKAGE_STRING,RELEASE_DATE);
printf("\n");
opt->terminate = 1;
break;
// Set energy range (kcal/mol) (-e)
case 'e':
sscanf(optarg,"%f",&(opt->traceback_diff));
opt->traceback_diff = max(0, opt->traceback_diff);
if (interactive) printf("Energy range set to %.2f kcal/mol.\n", opt->traceback_diff);
opt->traceback_percent = 0;
break;
// Set energy range (%%) (-c)
case 'c':
sscanf(optarg,"%d",&(opt->traceback_percent));
opt->traceback_percent = max(0, opt->traceback_percent);
if (interactive) printf("Energy range set to %d%% of mfe.\n", opt->traceback_percent);
opt->traceback_diff = 0;
break;
// Set maximal loop length (-M)
case 'M':
sscanf(optarg,"%d",&(opt->maxloop));
opt->maxloop = max(0, opt->maxloop);
if (interactive) printf("Set maximal loop length to %d.\n", opt->maxloop);
break;
// Set window size (-w)
case 'w':
if ((interactive) && (optarg[0] == '-')) {
printf("Window mode disabled.\n");
opt->window_mode = 0;
}
if (optarg[0] != '-') {
opt->window_mode = 1;
sscanf(optarg,"%d",&(opt->window_size));
opt->window_size = max(1, opt->window_size);
if (interactive) printf("Set window size to %d. Type -w - to disable.\n", opt->window_size);
}
break;
// Set window position increment (-W)
case 'W':
sscanf(optarg,"%d",&(opt->window_step));
opt->window_step = max(1, opt->window_step);
if (interactive) printf("Set window position increment to %d.\n", opt->window_step);
break;
// Show best results in window mode (-B)
case 'B':
if (interactive) {
printf("Show best results in window mode");
opt->window_best = 1 - opt->window_best;
if (opt->window_best) printf (" = ON. Type -B again to switch off.\n");
else printf (" = OFF. Type -B again to switch on.\n");
}
else opt->window_best = 1;
break;
// Only compute energy, no traceback (-O)
case 'O':
opt->energy_only = 1;
break;
// Specify output width for structures (-S)
case 'S':
if ((interactive) && (optarg[0] == '-')) {
printf("Output splitting disabled.\n");
opt->split_output_mode = 0;
}
if (optarg[0] != '-') {
opt->split_output_mode = 1;
sscanf(optarg,"%d",&(opt->split_output_size));
opt->split_output_size = max(1, opt->split_output_size);
if (interactive) printf("Set output size to %d. Type -S - to disable.\n", opt->split_output_size);
}
break;
// Read input from file (-f)
case 'f':
if (opt->inputfile) free(opt->inputfile);
opt->inputfile = mkstr(optarg);
break;
// Colored output (-z)
case 'z':
if (interactive) {
printf("Colored output");
opt->colored_output = 1 - opt->colored_output;
if (opt->colored_output) printf (" = ON. Type -z again to switch off.\n");
else printf (" = OFF. Type -z again to switch on.\n");
}
else opt->colored_output = 1;
if (opt->interactive && !opt->colored_output) printf(COLOR_DEFAULT);
break;
case '?':
if (interactive) printf("Unknown option '-%c'. Type -h for more information.\n", optopt);
else {
fprintf (stderr, "%s: unknown option `-%c'.\nTry '%s -h' for more information.\n", argv[0], optopt, argv[0]);
exit(1);
}
break;
default:
abort ();
}
}
pcolor(opt->colored_output,COLOR_DEFAULT);
}
int main (int argc, char **argv) {
toptions *opt;
tsequence *seq;
treadseq *rs = NULL;
ttokenizer *tokenizer = NULL;
char *command;
opt = (toptions *) calloc(1,sizeof(toptions));
init_defaults(opt);
process_args(opt, 0, argc, argv);
if (!opt->terminate) {
if (optind < argc) rs = readseq_open(READSEQ_STRING, argv[optind]);
else if (opt->inputfile) rs = readseq_open(READSEQ_FILE, opt->inputfile);
else if (!isatty(fileno(stdin))) rs = readseq_open(READSEQ_STDIN, NULL);
else {
printf("Interactive mode. Try `./RNAfold -h` for more information.\n", argv[0]);
rl_init();
opt->interactive = 1;
opt->colored_output = 1 - opt->colored_output;
tokenizer = tokenizer_new();
rs = readseq_open(READSEQ_STRING, "");
}
while (1) {
if (opt->interactive) {
if (opt->colored_output)
printf("%s\nInput sequence (upper or lower case); :q to quit, -h for help.\n....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8\n%s",COLOR_RED,COLOR_DEFAULT);
else
printf("\nInput sequence (upper or lower case); :q to quit, -h for help.\n....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8\n");
command = rl_gets();
if (!command || (command[0] == '@') || ((command[0] == ':') && (command[1] == 'q'))) {
pcolor(opt->colored_output,COLOR_BLUE);
printf("Leaving RNAfold.");
pcolor(opt->colored_output,COLOR_DEFAULT);
printf("\n");
exit(0);
}
else if (command[0] == ':') {
pcolor(opt->colored_output,COLOR_BLUE);
if (command[1] == 's') print_settings(opt);
if (command[1] == 'd') {
init_defaults(opt);
opt->colored_output = 1;
opt->interactive = 1;
printf("Activated default configuration.\n");
pcolor(opt->colored_output,COLOR_DEFAULT);
}
if (command[1] == 'e') {
system(command + 2);
}
if (command[1] == 'r') {
system("make update");
system("./RNAfold");
exit(0);
}
}
else if (command[0] == '-') {
tokenizer_exec(tokenizer, argv[0], command);
process_args(opt, 1, tokenizer->count, tokenizer->token);
if (opt->inputfile) {
rs = readseq_free(rs);
rs = readseq_open(READSEQ_FILE, opt->inputfile);
}
free(opt->inputfile);
opt->inputfile = NULL;
}
else {
rs = readseq_free(rs);
rs = readseq_open(READSEQ_STRING, command);
}
}
while (1) {
seq = readseq_next_fasta(rs);
if (!(seq->success)) break;
if (1) {
main_rnafold_mfe(opt, seq);
}
sequence_free(seq);
}
if (!opt->interactive) break;
}
}
exit(0);
}
