int main(int argc, char **argv)
{
AjPSeq seq = NULL;
AjPStr strand = NULL;
AjPStr substr = NULL;
AjPStr squares = NULL;
AjPStr diamonds = NULL;
AjPStr octags = NULL;
AjBool amphipathic;
AjPStr txt = NULL;
AjPGraph graph = NULL;
ajint begin;
ajint end;
ajint lc;
ajint i;
ajint j;
ajint r;
ajint count;
ajint pstart;
ajint pstop;
float xmin = 0.0;
float xmax = 150.0;
float ymin = 0.0;
float ymax = 112.5;
float xstart;
float ystart;
float ch = (float)1.8;
float xinc;
float yinc;
AjPStr fstr = NULL;
float x;
float y;
embInit("pepnet", argc, argv);
seq = ajAcdGetSeq("sequence");
graph = ajAcdGetGraph("graph");
octags = ajAcdGetString("octags");
squares = ajAcdGetString("squares");
diamonds = ajAcdGetString("diamonds");
amphipathic = ajAcdGetToggle("amphipathic");
ajStrFmtUpper(&octags);
ajStrFmtUpper(&squares);
ajStrFmtUpper(&diamonds);
if(amphipathic)
{
ajStrAssignC(&squares,"ACFGILMVWY");
ajStrAssignC(&diamonds,"");
ajStrAssignC(&octags,"");
}
substr = ajStrNew();
txt = ajStrNew();
fstr = ajStrNew();
begin = ajSeqGetBegin(seq);
end = ajSeqGetEnd(seq);
strand = ajSeqGetSeqCopyS(seq);
ajStrFmtUpper(&strand);
ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1);
ajGraphAppendTitleS(graph, ajSeqGetUsaS(seq));
ajGraphOpenWin(graph, xmin,xmax,ymin,ymax);
for(count=begin-1,r=0;count<end;count+=231)
{
if (count > begin)
ajGraphNewpage(graph, ajFalse);
pstart=count;
pstop = AJMIN(end-1, count+230);
ajGraphicsSetCharscale(0.75);
xstart = 145.0;
ystart = 80.0;
yinc = ch * (float)2.5;
xinc = yinc / (float)2.5;
x = xstart;
for(i=pstart;i<=pstop;i+=7)
{
lc = i;
if(x < 10.0*xinc)
{
x = xstart;
ystart -= (float)7.5*yinc;
}
y=ystart;
ajFmtPrintS(&txt,"%d",i+1);
ajGraphicsSetFgcolour(RED);
ajGraphicsDrawposTextJustify(x-xinc,y-yinc-1,ajStrGetPtr(txt),0.5);
for(j=0;j<4;++j)
{
x -= xinc;
y += yinc;
if(lc <= pstop)
pepnet_plotresidue(*(ajStrGetPtr(substr)+r),x,y,
ajStrGetPtr(squares),ajStrGetPtr(octags),
ajStrGetPtr(diamonds));
++r;
++lc;
}
y=ystart+yinc/(float)2.0;
for(j=4;j<7;++j)
{
x -= xinc;
y += yinc;
if(lc <= pstop)
pepnet_plotresidue(*(ajStrGetPtr(substr)+r),x,y,
ajStrGetPtr(squares),ajStrGetPtr(octags),
ajStrGetPtr(diamonds));
++r;
++lc;
}
}
}
ajGraphicsClose();
ajGraphxyDel(&graph);
ajStrDel(&strand);
ajStrDel(&fstr);
ajSeqDel(&seq);
ajStrDel(&substr);
ajStrDel(&squares);
ajStrDel(&diamonds);
ajStrDel(&octags);
ajStrDel(&txt);
embExit();
return 0;
}
static PSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
const PRinfo rlp, ajint begin, ajint radj,
AjBool rev, ajint end)
{
PSilent ret;
const char *p = NULL;
const char *q = NULL;
const char *s = NULL;
char *t;
const char *u;
ajint matchpos;
ajint framep;
ajint count;
AjPTrn table = NULL;
AjPStr s1 = NULL;
AjPStr s2 = NULL;
char c;
char rc;
ajint min = INT_MAX; /* Reverse sense intentional! */
ajint max = -INT_MAX;
ajint fpos;
ajint rpos;
ajint x;
AjPStr tstr = NULL;
matchpos = match->start;
fpos = matchpos;
rpos=radj-fpos-match->len;
tstr = ajStrNewS(seq);
t = ajStrGetuniquePtr(&tstr);
p = t+fpos-(begin+1);
u = q = ajStrGetPtr(rlp->site);
/* Test here for whether cut site is within sequence substring */
if(rlp->ncuts==4)
{
min = AJMIN(rlp->cut1,rlp->cut2);
max = AJMAX(rlp->cut3,rlp->cut4);
}
else if(rlp->ncuts==2)
{
min = AJMIN(rlp->cut1,rlp->cut2);
max = AJMAX(rlp->cut1,rlp->cut2);
}
else
{
ajWarn("Possibly corrupt RE file");
ajStrDel(&tstr);
return NULL;
}
if(!rev) /* forward strand */
{
if(matchpos+min<0||matchpos+max>end+1)
{
/*Cut site not in sequence range*/
ajStrDel(&tstr);
return NULL;
}
}
else /* reverse strand */
{
if(radj-matchpos-1-min>end+1||radj-matchpos-1-max<begin)
{
/*Cut site not in sequence range*/
ajStrDel(&tstr);
return NULL;
}
}
count=0;
while(ajBaseAlphaToBin(*q++) & ajBaseAlphaToBin(*p++))
++count;
/* Changed base postion */
x = fpos+count-(begin+1);
/* Where the frame starts on the reverse strand */
framep = (end-begin+1)%3;
c = t[x];
rc = u[count];
if(!rev) /* forward strand */
s = t+x-x%3;
else /* reverse strand */
s = t+x-(x-framep)%3;
table = ajTrnNewI(0);
/* translates codon pointed to by s (original seq) */
s1 = ajStrNewK(ajTrnCodonC(table,s));
t[x] = rc;
/* translates codon pointed to by s (mutated base from RS pattern */
s2 = ajStrNewK(ajTrnCodonC(table,s));
t[x] = c; /* changes mutated base in seq back to original base */
AJNEW(ret);
ret->obase = c;
ret->nbase = rc;
ret->code = ajStrNewC(ajStrGetPtr(rlp->code));
ret->site = ajStrNewC(ajStrGetPtr(rlp->site));
ret->seqaa = ajStrNewC(ajStrGetPtr(s1));
ret->reaa = ajStrNewC(ajStrGetPtr(s2));
if(ajStrMatchS(s1,s2))
ret->issilent = ajTrue;
else
ret->issilent = ajFalse;
if(!rev)
{
ret->match = matchpos;
ret->base = matchpos+count;
}
else
{
ret->match = rpos;
ret->base = rpos+match->len-1-count;
}
ajStrDel(&tstr);
ajStrDel(&s1);
ajStrDel(&s2);
ajTrnDel(&table);
return ret;
}
int main(int argc, char **argv)
{
AjPSeq seq = NULL;
AjPStr strand = NULL;
AjPStr substr = NULL;
AjPStr squares = NULL;
AjPStr diamonds = NULL;
AjPStr octags = NULL;
AjBool wheel;
AjBool amphipathic;
AjPGraph graph=0;
AjBool first;
AjBool startloop;
ajint begin;
ajint end;
ajint len;
ajint steps;
ajint turns;
ajint lc;
ajint i;
ajint j;
ajint k;
float xmin = (float) -1.0;
float xmax = (float) 1.0;
float ymin = (float) -0.75;
float ymax = (float) 0.75;
float minresplot = (float) 36.0;
float resgap = (float) 0.0533;
float wheelgap = (float) 0.00;
float nresgap = (float) 0.08;
float angle;
float oldangle;
float ang;
float radius;
float wradius;
float xx1;
float xx2;
float yy1;
float yy2;
embInit("pepwheel", argc, argv);
seq = ajAcdGetSeq("sequence");
steps = ajAcdGetInt("steps");
turns = ajAcdGetInt("turns");
graph = ajAcdGetGraph("graph");
octags = ajAcdGetString("octags");
squares = ajAcdGetString("squares");
diamonds = ajAcdGetString("diamonds");
wheel = ajAcdGetBoolean("wheel");
amphipathic = ajAcdGetToggle("amphipathic");
ajStrFmtUpper(&octags);
ajStrFmtUpper(&squares);
ajStrFmtUpper(&diamonds);
if(amphipathic)
{
ajStrAssignC(&squares,"ACFGILMVWY");
ajStrAssignC(&diamonds,"");
ajStrAssignC(&octags,"");
}
substr = ajStrNew();
begin = ajSeqGetBegin(seq);
end = ajSeqGetEnd(seq);
ajDebug("begin: %d end: %d\n", begin, end);
strand = ajSeqGetSeqCopyS(seq);
ajStrFmtUpper(&strand);
ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1);
len = ajStrGetLen(substr);
ajGraphAppendTitleS(graph, ajSeqGetUsaS(seq));
ajGraphOpenWin(graph,xmin,xmax,ymin,ymax);
ajGraphicsSetFgcolour(AJB_BLACK);
ang = ((float)360.0 / (float)steps) * (float)turns;
first = ajTrue;
angle = (float) 90.0 + ang;
if(end-begin > (ajint)minresplot)
wradius = (float) 0.2;
else
wradius = (float) 0.40;
for(i=0,lc=0,radius=wradius+wheelgap;i<len;i+=steps)
{
wradius += wheelgap;
startloop = ajTrue;
k = AJMIN(i+steps, end);
for(j=i;j<k;++j)
{
oldangle = angle;
angle = oldangle-ang;
if(first)
startloop = first = ajFalse;
else
{
if(startloop)
{
if(wheel)
{
ajCvtPolToRec(wradius-wheelgap,oldangle,&xx1,&yy1);
ajCvtPolToRec(wradius,angle,&xx2,&yy2);
ajGraphicsDrawposLine(xx1,yy1,xx2,yy2);
}
startloop=ajFalse;
}
else
if(wheel)
{
ajCvtPolToRec(wradius,oldangle,&xx1,&yy1);
ajCvtPolToRec(wradius,angle,&xx2,&yy2);
ajGraphicsDrawposLine(xx1,yy1,xx2,yy2);
}
}
pepwheel_plotresidue(*(ajStrGetPtr(substr)+lc),radius+resgap,angle,
ajStrGetPtr(squares),ajStrGetPtr(octags),
ajStrGetPtr(diamonds),
xmin,xmax,ymin,ymax);
++lc;
if(lc==len)
break;
}
radius += nresgap;
}
ajGraphicsClose();
ajGraphxyDel(&graph);
ajStrDel(&strand);
ajStrDel(&substr);
ajSeqDel(&seq);
ajStrDel(&squares);
ajStrDel(&diamonds);
ajStrDel(&octags);
embExit();
return 0;
}
