//--------------------------------------------------------------
void testApp::draw(){
ofEnableNormalizedTexCoords();
switch(switchInt)
{
case 1:
posterize();
break;
case 2:
rgbPosterize();
break;
case 3:
wobble();
break;
case 4:
abberation();
break;
case 5:
perlinLab();
break;
case 6:
wobbleAbberation();
break;
case 7:
liquifyRender();
break;
case 8:
perlinXyz();
break;
default:
liquifyRenderS();
break;
}
/*
cout << "\nMFCCS: ";
ofSetColor(255, 0, 0,100);
float xinc = 900.0 / 13;
for(int i=0; i < 13; i++) {
float height = mfccs[i] * 250.0;
ofRect(100 + (i*xinc),600 - height,40, height);
cout << mfccs[i] << ",";
}
*/
}
void
Sim4::slide_intron(int in_w, Exon *first, Exon *last, int spl_model, sim4_stats_t *st)
{
Exon *t0, *t1, *head = first;
splice_t *g, *c, *cell;
char type;
int w1, w2;
int numG=0, numC=0, numE=0, numN=0, model;
t0 = head;
while (t0 && (t0!=last) && (t1=t0->next_exon) && t1->toGEN) {
g = c = NULL;
if (t1->frEST-t0->toEST-1==0) {
if (!strncmp((char *)(_genSeq+t0->toGEN),"GT",2) &&
!strncmp((char *)(_genSeq+t1->frGEN-3),"AG",2)) {
t0->ori = 'G';
numG++;
#ifdef SPLSCORE
t0->splScore = 999999;
#endif
}
else if (!strncmp((char *)(_genSeq+t0->toGEN),"CT",2) &&
!strncmp((char *)(_genSeq+t1->frGEN-3),"AC",2)) {
t0->ori = 'C';
numC++;
#ifdef SPLSCORE
t0->splScore = 888888;
#endif
}
else {
int gtag=0, ctac=0;
char *s;
w1 = MIN(in_w, (int)(0.5*MIN(t0->length-2, t0->toGEN-t0->frGEN-1)));
w2 = MIN(in_w, (int)(0.5*MIN(t1->length-2, t1->toGEN-t1->frGEN-1)));
model = ((t0->toGEN-w1<=MAX_SPAN) || (t1->frGEN+w2+MAX_SPAN+2>_genLen)) ?
SPLICE_ORIGINAL : spl_model;
splice(_genSeq, t0->toGEN-w1, t0->toGEN+w1, t1->frGEN-w2, t1->frGEN+w2,
_estSeq, t0->toEST-w1, t1->frEST+w2, &g, &c, BOTH, model);
if (g->score>c->score) { cell = g; type = 'G'; }
else if (c->score>g->score) { cell = c; type = 'C'; }
else { cell = g; type = 'G'; }
#ifdef SPLSCORE
t0->splScore = (model==spl_model) ? cell->score : 777777;
#endif
t0->toGEN = cell->xs; t0->toEST = cell->ys;
t1->frGEN = cell->xe; t1->frEST = cell->ye;
t0->length = t0->toEST-t0->frEST+1;
t1->length = t1->toEST-t1->frEST+1;
wobble(t0,t1,(type=='G')? "GT":"CT",(type=='G')? "AG":"AC",_genSeq);
ckfree(g);
ckfree(c);
/* determine the type, based on the # matches w/ GT-AG (CT-AC) */
s = _genSeq+t0->toGEN;
if (*s=='G') gtag++; else if (*s=='C') ctac++;
++s;
if (*s=='T') { gtag++; ctac++;}
s = _genSeq+t1->frGEN-3;
if (*s=='A') { gtag++; ctac++; }
++s;
if (*s=='G') gtag++; else if (*s=='C') ctac++;
if (gtag>ctac) {
type = 'G';
numG++;
}
else if (ctac>gtag) {
type = 'C';
numC++;
}
else {
type = 'N';
numN++;
}
t0->ori = type;
}
} else {
t0->ori = 'E';
numE++;
}
t0 = t1;
}
st->orientation = BOTH;
if ((numG > 0) && ((numC + numE + numN) == 0)) {
st->orientation = FWD;
} else if ((numC > 0) && ((numG + numE + numN) == 0)) {
st->orientation = BWD;
}
/* code not actually used - sim4cc (-interspecies) currently uses only
sync_slide_intron(), but provided here in case that changes */
if ((globalParams->_interspecies) && (st->orientation == BOTH)) {
if (numG > numC)
st->orientation = FWD;
if (numG < numC)
st->orientation = BWD;
}
if ((globalParams->_forceStrandPrediction) && (st->orientation == BOTH)) {
if (numG > numC)
st->orientation = FWD;
if (numG < numC)
st->orientation = BWD;
// otherwise, st->orientation = match orientation, but we
// don't know that here. It's set in sim4string.C:run()
}
}
void
Sim4::sync_slide_intron(int in_w, Exon *first, Exon *last, int spl_model, sim4_stats_t *st) {
Exon *t0=NULL, *t1=NULL, *head = first;
splice_t *g=NULL, *c=NULL, *cell=NULL;
splice_t **Glist, **Clist;
int Gscore=0, Cscore=0;
char *oris;
int w1, w2, ni, i, numC, numG, model;
ni = 0;
numG = numC = 0;
// Count the exons to allocate space for Glist, Clist and oris
//
t0 = head;
while (t0 && (t0!=last) && (t1=t0->next_exon) && t1->toGEN) {
ni++;
t0 = t1;
}
Glist = (splice_t **)ckalloc((ni + 1) * sizeof(splice_t *));
Clist = (splice_t **)ckalloc((ni + 1) * sizeof(splice_t *));
oris = (char *) ckalloc((ni + 1) * sizeof(char));
memset(Glist, 0, (ni + 1) * sizeof(splice_t *));
memset(Clist, 0, (ni + 1) * sizeof(splice_t *));
memset(oris, 0, (ni + 1) * sizeof(char));
if ((Glist == 0L) || (Clist == 0L) || (oris == 0L)) {
fprintf(stderr, "Can't allocate memory for sync_slide_intron() with %d exons.\n", ni);
exit(1);
}
ni = 0;
/* assume forward orientation */
t0 = head;
while (t0 && (t0!=last) && (t1=t0->next_exon) && t1->toGEN) {
g = c = NULL;
if (t1->frEST-t0->toEST-1==0) {
if (!strncmp((char *)(_genSeq+t0->toGEN),"GT",2) &&
!strncmp((char *)(_genSeq+t1->frGEN-3),"AG",2)) {
g = new_splice('G',t0->toGEN,t1->frGEN,t0->toEST,t1->frEST,-1,NULL);
t0->ori = 'G';
oris[ni] = 'G';
numG++;
#ifdef SPLSCORE
t0->splScore = 999999;
#endif
} else if (!strncmp((char *)(_genSeq+t0->toGEN),"CT",2) &&
!strncmp((char *)(_genSeq+t1->frGEN-3),"AC",2)) {
c = new_splice('C',t0->toGEN,t1->frGEN,t0->toEST,t1->frEST,-1,NULL);
t0->ori = 'C';
oris[ni] = 'C';
numC++;
#ifdef SPLSCORE
t0->splScore = 888888;
#endif
} else {
w1 = MIN(in_w, (int)(0.5*MIN(t0->length-1, t0->toGEN-t0->frGEN)));
w2 = MIN(in_w, (int)(0.5*MIN(t1->length-1, t1->toGEN-t1->frGEN)));
model = ((t0->toGEN-w1<=MAX_SPAN) || (t1->frGEN+w2+MAX_SPAN+2>_genLen)) ?
SPLICE_ORIGINAL : spl_model;
splice(_genSeq, t0->toGEN-w1, t0->toGEN+w1, t1->frGEN-w2, t1->frGEN+w2,
_estSeq, t0->toEST-w1, t1->frEST+w2, &g, &c, BOTH, model);
Gscore += g->score; Cscore += c->score;
cell = NULL; oris[ni] = '*';
if (g->score>c->score) {
numG++; cell = g; oris[ni] = 'G';
} else if (c->score>g->score) {
numC++; cell = c; oris[ni] = 'C';
} else if (c->score==g->score) {
numG++; numC++; cell = g; oris[ni] = 'G';
}
#ifdef SPLSCORE
t0->splScore = (model==spl_model) ? cell->score : 777777;
#endif
t0->ori = oris[ni];
t0->toGEN = cell->xs; t0->toEST = cell->ys;
t1->frGEN = cell->xe; t1->frEST = cell->ye;
t0->length = t0->toEST-t0->frEST+1;
t1->length = t1->toEST-t1->frEST+1;
}
Clist[ni] = c; Glist[ni] = g;
} else {
t0->ori = 'E'; oris[ni] = 'E';
}
ni++;
t0 = t1;
}
st->orientation = BOTH;
if ((numG==1) && (numC==1) &&
(!Glist[0] || !Clist[0] || !Glist[1] || !Clist[1])) goto free_all;
if (numG && numG>=numC) {
/* revisit all previous assignments that are inconsistent */
for (i=0, t0=head; i<ni; i++, t0=t1) {
t1 = t0->next_exon;
switch (oris[i]) {
case 'G': break;
case 'C': if (Glist[i]==NULL) {
/* compute the values for C */
w1 = MIN(in_w, (int)(0.5*MIN(t0->length-1, t0->toGEN-t0->frGEN)));
w2 = MIN(in_w, (int)(0.5*MIN(t1->length-1, t1->toGEN-t1->frGEN)));
model = ((t0->toGEN-w1<=MAX_SPAN) || (t1->frGEN+w2+MAX_SPAN+2>_genLen)) ?
SPLICE_ORIGINAL : spl_model;
splice(_genSeq, t0->toGEN-w1, t0->toGEN+w1,
t1->frGEN-w2, t1->frGEN+w2, _estSeq,
t0->toEST-w1, t1->frEST+w2, &g, &c, FWD, model);
} else g = Glist[i];
#ifdef SPLSCORE
t0->splScore = (model==spl_model) ? g->score : 777777;
#endif
t0->ori = 'G';
t0->toGEN = g->xs; t0->toEST = g->ys;
t1->frGEN = g->xe; t1->frEST = g->ye;
t0->length = t0->toEST-t0->frEST+1;
t1->length = t1->toEST-t1->frEST+1;
break;
case 'E': break;
default : fatal("sim4b1.c: intron orientation not initialized.");
}
if (oris[i]!='E') wobble(t0,t1,"GT","AG",_genSeq);
}
st->orientation = FWD;
} else if (numC) {
/* analyze all assignments for consistency */
for (i=0, t0=head; i<ni; i++, t0=t1) {
t1 = t0->next_exon;
switch (oris[i]) {
case 'C': break;
case 'G': if (Clist[i]==NULL) {
/* compute the values for C */
w1 = MIN(in_w, (int)(0.5*MIN(t0->length-1, t0->toGEN-t0->frGEN)));
w2 = MIN(in_w, (int)(0.5*MIN(t1->length-1, t1->toGEN-t1->frGEN)));
model = ((t0->toGEN-w1<=MAX_SPAN) || (t1->frGEN+w2+MAX_SPAN+2>_genLen)) ?
SPLICE_ORIGINAL : spl_model;
splice(_genSeq, t0->toGEN-w1, t0->toGEN+w1,
t1->frGEN-w2, t1->frGEN+w2,
_estSeq, t0->toEST-w1, t1->frEST+w2, &g, &c, BWD, model);
} else c = Clist[i];
#ifdef SPLSCORE
t0->splScore = (spl_model==model) ? c->score : 777777;
#endif
t0->ori = 'C';
t0->toGEN = c->xs; t0->toEST = c->ys;
t1->frGEN = c->xe; t1->frEST = c->ye;
t0->length = t0->toEST-t0->frEST+1;
t1->length = t1->toEST-t1->frEST+1;
break;
case 'E': break;
default : fatal("sim4b1.c: intron orientation not initialized.");
}
if (oris[i]!='E') wobble(t0,t1,"CT","AC",_genSeq);
}
st->orientation = BWD;
}
/* now free all memory allocated */
free_all:
for (i=0; i<ni; i++) {
ckfree(Glist[i]);
ckfree(Clist[i]);
}
ckfree(Glist);
ckfree(Clist);
ckfree(oris);
return;
}
void main(void) {
uint32_t limit;
gpio_init();
pwm_init();
systick_init();
pwm_set(0);
while(1) {
wait:
limit = 10;
while(!get_switch())
;
fade_to(PWM_MAX, 5);
delay_ticks(RELEASE_TIME);
start:
if(limit > 120)
limit = 120;
for(uint32_t i = 0; i < limit * 60 * 100; i++) {
uint32_t cnt = 0;
while(get_switch()) {
cnt++;
if(cnt > 300) {
limit = 60;
strobe();
delay_ticks(2*RELEASE_TIME);
goto start;
}
delay_ticks(10);
}
if(cnt) {
fade_to(0, 5);
goto wait;
}
delay_ticks(10);
}
wobble();
for(uint32_t i = 0; i < 30 * 100; i++) {
uint32_t cnt = 0;
while(get_switch()) {
cnt++;
if(cnt > 300) {
limit = 60;
strobe();
delay_ticks(2*RELEASE_TIME);
goto start;
}
delay_ticks(10);
}
if(cnt) {
limit += limit;
delay_ticks(1000);
goto start;
}
delay_ticks(10);
}
fade_to(0, 30);
}
}
