int main(int argc, char *argv[])
{
embInitPV("gbaseinformationcontent", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr position = 0;
ajint PatLen = 0;
ajint upstream = 0;
ajint downstream = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
position = ajAcdGetSelectSingle("position");
PatLen = ajAcdGetInt("patlen");
upstream = ajAcdGetInt("upstream");
downstream = ajAcdGetInt("downstream");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(!ajStrGetLen(seqid))
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(seqid))
{
ajFmtError("No valid header information\n");
embExitBad();
}
ajStrAssignS(&restid, seqid);
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/base_information_content/position=%S/"
"PatLen=%d/upstream=%d/downstream=%d/output=f/tag=gene",
base, restid, position, PatLen, upstream, downstream);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("position");
gpp.ylab = ajStrNewC("information content");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
ajStrDel(&position);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPFile infile = NULL;
AjPFile outfile = NULL;
AjPStr line;
AjPGraph graphLB = NULL;
AjPGraphdata xygraph = NULL;
AjPGraphdata xygraph2 = NULL;
AjBool doplot;
ajint N=0;
float *xdata = NULL;
float *ydata = NULL;
float *V = NULL;
float *S = NULL;
float a;
float b;
float upperXlimit;
float upperYlimit;
float A;
float B;
float C;
float D;
float xmin;
float xmax;
float ymin;
float ymax;
float xmin2;
float xmax2;
float ymin2;
float ymax2;
float Vmax;
float Km;
float cutx;
float cuty;
float amin = 0.;
float amax = 0.;
float bmin = 0.;
float bmax = 0.;
embInit("findkm", argc, argv);
infile = ajAcdGetInfile("infile");
outfile = ajAcdGetOutfile ("outfile");
doplot = ajAcdGetBoolean("plot");
graphLB = ajAcdGetGraphxy("graphLB");
line = ajStrNew();
/* Determine N by reading infile */
while(ajReadlineTrim(infile, &line))
if(ajStrGetLen(line) >0)
N++;
/* only allocate memory to the arrays */
AJCNEW(xdata, N);
AJCNEW(ydata, N);
AJCNEW(S, N);
AJCNEW(V, N);
ajFileSeek(infile, 0L, 0);
N=0;
while(ajReadlineTrim(infile, &line))
{
if(ajStrGetLen(line) > 0)
{
sscanf(ajStrGetPtr(line),"%f %f",&S[N],&V[N]);
if(S[N] > 0.0 && V[N] > 0.0)
{
xdata[N] = S[N];
ydata[N] = S[N]/V[N];
N++;
}
}
}
/* find the max and min values for the graph parameters*/
xmin = (float)0.5*findkm_findmin(xdata, N);
xmax = (float)1.5*findkm_findmax(xdata, N);
ymin = (float)0.5*findkm_findmin(ydata, N);
ymax = (float)1.5*findkm_findmax(ydata, N);
xmin2 = (float)0.5*findkm_findmin(S, N);
xmax2 = (float)1.5*findkm_findmax(S, N);
ymin2 = (float)0.5*findkm_findmin(V, N);
ymax2 = (float)1.5*findkm_findmax(V, N);
/*
** In case the casted ints turn out to be same number on the axis,
** make the max number larger than the min so graph can be seen.
*/
if((ajint)xmax == (ajint)xmin)
++xmax;
if((ajint)ymax == (ajint)ymin)
++ymax;
if((ajint)xmax2 == (ajint)xmin2)
++xmax2;
if((ajint)ymax2 == (ajint)ymin2)
++ymax2;
/*
** Gaussian Elimination for Best-fit curve plotting and
** calculating Km and Vmax
*/
A = findkm_summation(xdata, N);
B = findkm_summation(ydata, N);
C = findkm_multisum(xdata, ydata, N);
D = findkm_multisum(xdata, xdata, N);
/*
** To find the best fit line, Least Squares Fit: y =ax +b;
** Two Simultaneous equations, REARRANGE FOR b
**
** findkm_summation(ydata, N) - findkm_summation(xdata,N)*a - N*b =0;
** b = (findkm_summation(ydata,N) - findkm_summation(xdata,N)*a) / N;
** b = (B - A*a)/ N;
**
** C - D*a - A*((B - A*a)/ N) =0;
** C - D*a - A*B/N + A*A*a/N =0;
** C - A*B/N = D*a - A*A*a/N;
*/
/* REARRANGE FOR a */
a = (N*C - A*B)/ (N*D - A*A);
b = (B - A*a)/ N;
/*
** Equation of Line - Lineweaver burk eqn
** 1/V = (Km/Vmax)*(1/S) + 1/Vmax;
*/
Vmax = 1/a;
Km = b/a;
cutx = -1/Km;
cuty = Km/Vmax;
/* set limits for last point on graph */
upperXlimit = findkm_findmax(xdata,N)+3;
upperYlimit = (upperXlimit)*a + b;
ajFmtPrintF(outfile, "---Hanes Woolf Plot Calculations---\n");
ajFmtPrintF(outfile, "Slope of best fit line is a = %.2f\n", a);
ajFmtPrintF(outfile,"Coefficient in Eqn of line y = ma +b is b "
"= %.2f\n", b);
ajFmtPrintF(outfile, "Where line cuts x axis = (%.2f, 0)\n", cutx);
ajFmtPrintF(outfile, "Where line cuts y axis = (0, %.2f)\n", cuty);
ajFmtPrintF(outfile, "Limit-point of graph for plot = (%.2f, %.2f)\n\n",
upperXlimit, upperYlimit);
ajFmtPrintF(outfile, "Vmax = %.2f, Km = %f\n",Vmax, Km);
/* draw graphs */
if(doplot)
{
xygraph = ajGraphdataNewI(N);
ajGraphdataAddXY(xygraph, S, V);
ajGraphDataAdd(graphLB, xygraph);
ajGraphdataSetTitleC(xygraph, "Michaelis Menten Plot");
ajGraphdataSetXlabelC(xygraph, "[S]");
ajGraphdataSetYlabelC(xygraph, "V");
ajGraphxySetXstartF(graphLB, 0.0);
ajGraphxySetXendF(graphLB, xmax2);
ajGraphxySetYstartF(graphLB, 0.0);
ajGraphxySetYendF(graphLB, ymax2);
ajGraphxySetXrangeII(graphLB, (ajint)0.0, (ajint)xmax2);
ajGraphxySetYrangeII(graphLB, (ajint)0.0, (ajint)ymax2);
ajGraphdataAddposLine(xygraph, 0.0, 0.0, S[0], V[0], (ajint)BLACK);
ajGraphxyShowPointsCircle(graphLB, ajTrue);
ajGraphdataSetMinmax(xygraph,0.0,xmax2,0.0,ymax2);
ajGraphicsCalcRange(S,N,&amin,&amax);
ajGraphicsCalcRange(V,N,&bmin,&bmax);
ajGraphdataSetTruescale(xygraph,amin,amax,bmin,bmax);
ajGraphdataSetTypeC(xygraph,"2D Plot Float");
xygraph2 = ajGraphdataNewI(N);
ajGraphdataAddXY(xygraph2, xdata, ydata);
ajGraphDataAdd(graphLB, xygraph2);
ajGraphdataSetTitleC(xygraph2, "Hanes Woolf Plot");
ajGraphdataSetXlabelC(xygraph2, "[S]");
ajGraphdataSetYlabelC(xygraph2, "[S]/V");
ajGraphxySetXstartF(graphLB, cutx);
ajGraphxySetXendF(graphLB, upperXlimit);
ajGraphxySetYstartF(graphLB, 0.0);
ajGraphxySetYendF(graphLB, upperYlimit);
ajGraphxySetXrangeII(graphLB, (ajint)cutx, (ajint)upperXlimit);
ajGraphxySetYrangeII(graphLB, (ajint)0.0, (ajint)upperYlimit);
ajGraphxyShowPointsCircle(graphLB, ajTrue);
ajGraphdataSetMinmax(xygraph2, cutx,upperXlimit,0.0,upperYlimit);
ajGraphicsCalcRange(xdata,N,&amin,&amax);
ajGraphicsCalcRange(ydata,N,&bmin,&bmax);
ajGraphdataSetTruescale(xygraph2,amin,amax,bmin,bmax);
ajGraphdataSetTypeC(xygraph2,"2D Plot");
ajGraphSetTitleC(graphLB,"FindKm");
ajGraphxySetflagOverlay(graphLB,ajFalse);
ajGraphxyDisplay(graphLB, ajTrue);
}
AJFREE(xdata);
AJFREE(ydata);
AJFREE(S);
AJFREE(V);
ajFileClose(&infile);
ajFileClose(&outfile);
ajGraphxyDel(&graphLB);
ajStrDel(&line);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("ggcskew", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPStr tmpname = NULL;
AjPSeqout tmpout = NULL;
ajint window = 0;
ajint slide = 0;
AjBool cumulative = 0;
AjBool at = 0;
AjBool purine = 0;
AjBool keto = 0;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
window = ajAcdGetInt("window");
slide = ajAcdGetInt("slide");
cumulative = ajAcdGetBoolean("cumulative");
at = ajAcdGetBoolean("at");
purine = ajAcdGetBoolean("purine");
keto = ajAcdGetBoolean("keto");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
ajStrAppendC(&tmpname, ".fasta");
while(ajSeqallNext(seqall, &seq))
{
tmpout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(tmpout, tmpname))
{
embExitBad();
}
ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
ajSeqoutWriteSeq(tmpout, seq);
ajSeqoutClose(tmpout);
ajSeqoutDel(&tmpout);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/"
"at=%d/purine=%d/keto=%d/output=f/", base, restid, window,
slide, cumulative, at, purine, keto);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("location");
gpp.ylab = ajStrNewC("GC skew");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPList list = NULL;
AjPSeq seq;
AjPSeq seq2;
AjPStr aa0str = 0;
AjPStr aa1str = 0;
const char *s1;
const char *s2;
char *strret = NULL;
ajuint i;
ajuint j;
ajuint k;
ajint l;
ajint abovethresh;
ajint total;
ajint starti = 0;
ajint startj = 0;
ajint windowsize;
float thresh;
AjPGraph graph = NULL;
AjPGraph xygraph = NULL;
float flen1;
float flen2;
ajuint len1;
ajuint len2;
AjPTime ajtime = NULL;
time_t tim;
AjBool boxit=AJTRUE;
/* Different ticks as they need to be different for x and y due to
length of string being important on x */
ajuint acceptableticksx[]=
{
1,10,50,100,500,1000,1500,10000,
500000,1000000,5000000
};
ajuint acceptableticks[]=
{
1,10,50,100,200,500,1000,2000,5000,10000,15000,
500000,1000000,5000000
};
ajint numbofticks = 10;
float xmargin;
float ymargin;
float ticklen;
float tickgap;
float onefifth;
float k2;
float max;
char ptr[10];
AjPMatrix matrix = NULL;
ajint** sub;
AjPSeqCvt cvt;
AjPStr subt = NULL;
ajint b1;
ajint b2;
ajint e1;
ajint e2;
AjPStr se1;
AjPStr se2;
ajint ithresh;
AjBool stretch;
PPoint ppt = NULL;
float xa[1];
float ya[1];
AjPGraphdata gdata=NULL;
AjPStr tit = NULL;
AjIList iter = NULL;
float x1 = 0.;
float x2 = 0.;
float y1 = 0.;
float y2 = 0.;
ajuint tui;
se1 = ajStrNew();
se2 = ajStrNew();
embInit("dotmatcher", argc, argv);
seq = ajAcdGetSeq("asequence");
seq2 = ajAcdGetSeq("bsequence");
stretch = ajAcdGetToggle("stretch");
graph = ajAcdGetGraph("graph");
xygraph = ajAcdGetGraphxy("xygraph");
windowsize = ajAcdGetInt("windowsize");
ithresh = ajAcdGetInt("threshold");
matrix = ajAcdGetMatrix("matrixfile");
sub = ajMatrixGetMatrix(matrix);
cvt = ajMatrixGetCvt(matrix);
thresh = (float)ithresh;
ajtime = ajTimeNew();
tim = time(0);
ajTimeSetLocal(ajtime, tim);
b1 = ajSeqGetBegin(seq);
b2 = ajSeqGetBegin(seq2);
e1 = ajSeqGetEnd(seq);
e2 = ajSeqGetEnd(seq2);
len1 = ajSeqGetLen(seq);
len2 = ajSeqGetLen(seq2);
tui = ajSeqGetLen(seq);
flen1 = (float) tui;
tui = ajSeqGetLen(seq2);
flen2 = (float) tui;
ajStrAssignSubC(&se1,ajSeqGetSeqC(seq),b1-1,e1-1);
ajStrAssignSubC(&se2,ajSeqGetSeqC(seq2),b2-1,e2-1);
ajSeqAssignSeqS(seq,se1);
ajSeqAssignSeqS(seq2,se2);
s1 = ajStrGetPtr(ajSeqGetSeqS(seq));
s2 = ajStrGetPtr(ajSeqGetSeqS(seq2));
aa0str = ajStrNewRes(1+len1); /* length plus trailing blank */
aa1str = ajStrNewRes(1+len2);
list = ajListNew();
for(i=0;i<len1;i++)
ajStrAppendK(&aa0str,(char)ajSeqcvtGetCodeK(cvt, *s1++));
for(i=0;i<len2;i++)
ajStrAppendK(&aa1str,(char)ajSeqcvtGetCodeK(cvt, *s2++));
max = (float)len1;
if(len2 > max)
max = (float) len2;
xmargin = ymargin = max *(float)0.15;
ticklen = xmargin*(float)0.1;
onefifth = xmargin*(float)0.2;
subt = ajStrNewC((strret=
ajFmtString("(windowsize = %d, threshold = %3.2f %D)",
windowsize,thresh,ajtime)));
if(!stretch)
{
if( ajStrGetLen(ajGraphGetSubtitleS(graph)) <=1)
ajGraphSetSubtitleS(graph,subt);
ajGraphOpenWin(graph, (float)0.0-ymargin,(max*(float)1.35)+ymargin,
(float)0.0-xmargin,(float)max+xmargin);
ajGraphicsDrawposTextAtmid(flen1*(float)0.5,
(float)0.0-(xmargin/(float)2.0),
ajGraphGetXlabelC(graph));
ajGraphicsDrawposTextAtlineJustify((float)0.0-(xmargin*(float)0.75),
flen2*(float)0.5,
(float)0.0-(xmargin*(float)0.75),flen1,
ajGraphGetYlabelC(graph),0.5);
ajGraphicsSetCharscale(0.5);
}
s1= ajStrGetPtr(aa0str);
s2 = ajStrGetPtr(aa1str);
for(j=0; (ajint)j < (ajint)len2-windowsize;j++)
{
i =0;
total = 0;
abovethresh =0;
k = j;
for(l=0;l<windowsize;l++)
total = total + sub[(ajint)s1[i++]][(ajint)s2[k++]];
if(total >= thresh)
{
abovethresh=1;
starti = i-windowsize;
startj = k-windowsize;
}
while(i < len1 && k < len2)
{
total = total - sub[(ajint)s1[i-windowsize]]
[(ajint)s2[k-windowsize]];
total = total + sub[(ajint)s1[i]][(ajint)s2[k]];
if(abovethresh)
{
if(total < thresh)
{
abovethresh = 0;
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)i-1,(float)k-1,stretch);
}
}
else if(total >= thresh)
{
starti = i-windowsize;
startj = k-windowsize;
abovethresh= 1;
}
i++;
k++;
}
if(abovethresh)
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)i-1,(float)k-1,
stretch);
}
for(i=0; (ajint)i < (ajint)len1-windowsize;i++)
{
j = 0;
total = 0;
abovethresh =0;
k = i;
for(l=0;l<windowsize;l++)
total = total + sub[(ajint)s1[k++]][(ajint)s2[j++]];
if(total >= thresh)
{
abovethresh=1;
starti = k-windowsize;
startj = j-windowsize;
}
while(k < len1 && j < len2)
{
total = total - sub[(ajint)s1[k-windowsize]]
[(ajint)s2[j-windowsize]];
total = total + sub[(ajint)s1[k]][(ajint)s2[j]];
if(abovethresh)
{
if(total < thresh)
{
abovethresh = 0;
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)k-1,(float)j-1,stretch);
}
}
else if(total >= thresh)
{
starti = k-windowsize;
startj = j-windowsize;
abovethresh= 1;
}
j++;
k++;
}
if(abovethresh)
/* draw the line */
dotmatcher_pushpoint(&list,(float)starti,(float)startj,
(float)k-1,(float)j-1,
stretch);
}
if(boxit && !stretch)
{
ajGraphicsDrawposRect(0.0,0.0,flen1, flen2);
i=0;
while(acceptableticksx[i]*numbofticks < len1)
i++;
if(i<=13)
tickgap = (float)acceptableticksx[i];
else
tickgap = (float)acceptableticksx[10];
ticklen = xmargin*(float)0.1;
onefifth = xmargin*(float)0.2;
if(len2/len1 > 10 )
{
/* if a lot smaller then just label start and end */
ajGraphicsDrawposLine((float)0.0,(float)0.0,(float)0.0,(float)0.0-ticklen);
sprintf(ptr,"%d",b1-1);
ajGraphicsDrawposTextAtmid((float)0.0,(float)0.0-(onefifth),ptr);
ajGraphicsDrawposLine(flen1,(float)0.0,
flen1,(float)0.0-ticklen);
sprintf(ptr,"%d",len1+b1-1);
ajGraphicsDrawposTextAtmid(flen1,(float)0.0-(onefifth),ptr);
}
else
for(k2=0.0;k2<len1;k2+=tickgap)
{
ajGraphicsDrawposLine(k2,(float)0.0,k2,(float)0.0-ticklen);
sprintf(ptr,"%d",(ajint)k2+b1-1);
ajGraphicsDrawposTextAtmid(k2,(float)0.0-(onefifth),ptr);
}
i = 0;
while(acceptableticks[i]*numbofticks < len2)
i++;
tickgap = (float)acceptableticks[i];
ticklen = ymargin*(float)0.01;
onefifth = ymargin*(float)0.02;
if(len1/len2 > 10 )
{
/* if a lot smaller then just label start and end */
ajGraphicsDrawposLine((float)0.0,(float)0.0,(float)0.0-ticklen,(float)0.0);
sprintf(ptr,"%d",b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),(float)0.0,ptr);
ajGraphicsDrawposLine((float)0.0,flen2,(float)0.0-ticklen,
flen2);
sprintf(ptr,"%d",len2+b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),flen2,ptr);
}
else
for(k2=0.0;k2<len2;k2+=tickgap)
{
ajGraphicsDrawposLine((float)0.0,k2,(float)0.0-ticklen,k2);
sprintf(ptr,"%d",(ajint)k2+b2-1);
ajGraphicsDrawposTextAtend((float)0.0-(onefifth),k2,ptr);
}
}
if(!stretch)
ajGraphicsClose();
else /* the xy graph for -stretch */
{
tit = ajStrNew();
ajFmtPrintS(&tit,"%S",ajGraphGetTitleS(xygraph));
gdata = ajGraphdataNewI(1);
xa[0] = (float)b1;
ya[0] = (float)b2;
ajGraphSetTitleC(xygraph,ajStrGetPtr(tit));
ajGraphSetXlabelC(xygraph,ajSeqGetNameC(seq));
ajGraphSetYlabelC(xygraph,ajSeqGetNameC(seq2));
ajGraphdataSetTypeC(gdata,"2D Plot Float");
ajGraphdataSetTitleS(gdata,subt);
ajGraphdataSetMinmax(gdata,(float)b1,(float)e1,(float)b2,
(float)e2);
ajGraphdataSetTruescale(gdata,(float)b1,(float)e1,(float)b2,
(float)e2);
ajGraphxySetXstartF(xygraph,(float)b1);
ajGraphxySetXendF(xygraph,(float)e1);
ajGraphxySetYstartF(xygraph,(float)b2);
ajGraphxySetYendF(xygraph,(float)e2);
ajGraphxySetXrangeII(xygraph,b1,e1);
ajGraphxySetYrangeII(xygraph,b2,e2);
if(list)
{
iter = ajListIterNewread(list);
while((ppt = ajListIterGet(iter)))
{
x1 = ppt->x1+b1-1;
y1 = ppt->y1+b2-1;
x2 = ppt->x2+b1-1;
y2 = ppt->y2+b2-1;
ajGraphAddLine(xygraph,x1,y1,x2,y2,0);
AJFREE(ppt);
}
ajListIterDel(&iter);
}
ajGraphdataAddXY(gdata,xa,ya);
ajGraphDataReplace(xygraph,gdata);
ajGraphxyDisplay(xygraph,ajFalse);
ajGraphicsClose();
ajStrDel(&tit);
}
ajListFree(&list);
ajSeqDel(&seq);
ajSeqDel(&seq2);
ajGraphxyDel(&graph);
ajGraphxyDel(&xygraph);
ajMatrixDel(&matrix);
ajTimeDel(&ajtime);
/* deallocate memory */
ajStrDel(&aa0str);
ajStrDel(&aa1str);
ajStrDel(&se1);
ajStrDel(&se2);
ajStrDel(&subt);
AJFREE(strret); /* created withing ajFmtString */
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("ggeneskew", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
ajint window = 0;
ajint slide = 0;
AjBool cumulative = ajFalse;
AjBool gc3 = ajFalse;
AjPStr basetype = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
window = ajAcdGetInt("window");
slide = ajAcdGetInt("slide");
cumulative = ajAcdGetBoolean("cumulative");
gc3 = ajAcdGetBoolean("gctri");
basetype = ajAcdGetSelectSingle("base");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
if(ajStrMatchC(base, "none"))
basetype = ajStrNewC("");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/geneskew/window=%d/slide=%d/"
"cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
base, restid, window, slide, cumulative, gc3, basetype);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("gene skew");
gpp.ylab = ajStrNewC("bp");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeq seq1;
AjPSeq seq2;
ajint wordlen;
AjPTable seq1MatchTable = 0;
AjPList matchlist = NULL;
AjPGraph graph = NULL;
AjPGraph xygraph = NULL;
AjBool boxit;
/*
** Different ticks as they need to be different for x and y due to
** length of string being important on x
*/
ajuint acceptableticksx[]=
{
1,10,50,100,500,1000,1500,10000,
500000,1000000,5000000
};
ajuint acceptableticks[]=
{
1,10,50,100,200,500,1000,2000,5000,10000,15000,
500000,1000000,5000000
};
ajint numbofticks = 10;
float xmargin;
float ymargin;
float ticklen;
float tickgap;
float onefifth = 0.0;
ajint i;
float k;
float max;
char ptr[10];
ajint begin1;
ajint begin2;
ajint end1;
ajint end2;
ajuint len1;
ajuint len2;
float fbegin1;
float fbegin2;
float fend1;
float fend2;
float flen1;
float flen2;
AjBool stretch;
embInit("dottup", argc, argv);
wordlen = ajAcdGetInt("wordsize");
seq1 = ajAcdGetSeq("asequence");
seq2 = ajAcdGetSeq("bsequence");
graph = ajAcdGetGraph("graph");
boxit = ajAcdGetBoolean("boxit");
stretch = ajAcdGetToggle("stretch");
xygraph = ajAcdGetGraphxy("xygraph");
begin1 = ajSeqGetBegin(seq1);
begin2 = ajSeqGetBegin(seq2);
end1 = ajSeqGetEnd(seq1);
end2 = ajSeqGetEnd(seq2);
len1 = end1 - begin1 + 1;
len2 = end2 - begin2 + 1;
flen1 = (float) len1;
flen2 = (float) len2;
fbegin1 = (float) begin1;
fbegin2 = (float) begin2;
fend1 = (float) end1;
fend2 = (float) end2;
offset1 = fbegin1;
offset2 = fbegin2;
ajSeqTrim(seq1);
ajSeqTrim(seq2);
embWordLength(wordlen);
if(embWordGetTable(&seq1MatchTable, seq1))
matchlist = embWordBuildMatchTable(seq1MatchTable, seq2, ajTrue);
if(stretch)
{
dottup_stretchplot(xygraph,matchlist,seq1,seq2,begin1,begin2,end1,
end2);
if(matchlist)
embWordMatchListDelete(&matchlist); /* free the match structures */
}
else
{
/* only here if stretch is false */
max= flen1;
if(flen2 > max)
max = flen2;
xmargin = ymargin = max * (float)0.15;
ajGraphOpenWin(graph, fbegin1-ymargin,fend1+ymargin,
fbegin2-xmargin,(float)fend2+xmargin);
ajGraphicsSetCharscale(0.5);
if(matchlist)
dottup_plotMatches(matchlist);
if(boxit)
{
ajGraphicsDrawposRect(fbegin1, fbegin2, fend1, fend2);
i = 0;
while(acceptableticksx[i]*numbofticks < len1)
i++;
if(i<=13)
tickgap = (float) acceptableticksx[i];
else
tickgap = (float) acceptableticksx[10];
ticklen = xmargin * (float) 0.1;
onefifth = xmargin * (float)0.2;
ajGraphicsDrawposTextAtmid(fbegin1+flen1*(float)0.5,
fbegin1-(onefifth*(float)3.0),
ajGraphGetYlabelC(graph));
if(len2/len1 > 10 )
{
/* a lot smaller then just label start and end */
ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1,
fbegin2-ticklen);
sprintf(ptr,"%u",ajSeqGetOffset(seq1));
ajGraphicsDrawposTextAtmid(fbegin1,fbegin2-(onefifth),ptr);
ajGraphicsDrawposLine(fend1,fbegin2,
fend1,fbegin2-ticklen);
sprintf(ptr,"%d",end1);
ajGraphicsDrawposTextAtmid(fend1,fbegin2-(onefifth),ptr);
}
else
for(k=fbegin1;k<fend1;k+=tickgap)
{
ajGraphicsDrawposLine(k,fbegin2,k,fbegin2-ticklen);
sprintf(ptr,"%d",(ajint)k);
ajGraphicsDrawposTextAtmid( k,fbegin2-(onefifth),ptr);
}
i = 0;
while(acceptableticks[i]*numbofticks < len2)
i++;
tickgap = (float) acceptableticks[i];
ticklen = ymargin*(float)0.1;
onefifth = ymargin*(float)0.2;
ajGraphicsDrawposTextAtlineJustify(fbegin1-(onefifth*(float)4.),
fbegin2+flen2*(float)0.5,
fbegin2-(onefifth*(float)4.),
fbegin2+flen2,
ajGraphGetXlabelC(graph),
0.5);
if(len1/len2 > 10 )
{
/* a lot smaller then just label start and end */
ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1-ticklen,
fbegin2);
sprintf(ptr,"%u",ajSeqGetOffset(seq2));
ajGraphicsDrawposTextAtend(fbegin1-(onefifth),fbegin2,ptr);
ajGraphicsDrawposLine(fbegin1,fend2,fbegin1-ticklen,
fend2);
sprintf(ptr,"%d",end2);
ajGraphicsDrawposTextAtend(fbegin2-(onefifth),fend2,ptr);
}
else
for(k=fbegin2;k<fend2;k+=tickgap)
{
ajGraphicsDrawposLine(fbegin1,k,fbegin1-ticklen,k);
sprintf(ptr,"%d",(ajint)k);
ajGraphicsDrawposTextAtend(fbegin1-(onefifth),k,ptr);
}
}
}
ajGraphicsClose();
ajSeqDel(&seq1);
ajSeqDel(&seq2);
ajGraphxyDel(&graph);
ajGraphxyDel(&xygraph);
embWordFreeTable(&seq1MatchTable);
if(matchlist)
embWordMatchListDelete(&matchlist); /* free the match structures */
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gviewcds", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
ajint length = 0;
ajint gap = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
AjPPStr names = NULL;
ajint i;
seqall = ajAcdGetSeqall("sequence");
length = ajAcdGetInt("length");
gap = ajAcdGetInt("gap");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(!ajStrGetLen(seqid))
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(seqid))
{
ajFmtError("No valid header information\n");
embExitBad();
}
ajStrAssignS(&restid, seqid);
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/"
"output=f/tag=gene", base, restid, length, gap);
if(plot)
{
if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
ajDie("Error in memory allocation, exiting\n");
}
names[0] = NULL;
names[1] = ajStrNewC("A");
names[2] = ajStrNewC("T");
names[3] = ajStrNewC("G");
names[4] = ajStrNewC("C");
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("position");
gpp.ylab = ajStrNewC("percentage");
gpp.names = names;
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
i = 0;
while(names[i])
{
AJFREE(names[i]);
++i;
}
AJFREE(names);
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPGraphdata graphdata;
ajint i;
AjPGraph mult;
AjBool overlap;
embInit("testplot", argc, argv);
mult = ajAcdGetGraphxy("graph");
ipoints = ajAcdGetInt("points");
overlap = ajAcdGetBoolean("overlap");
ajUser("Plotting sin, cos and tan for %d degrees",ipoints);
/* Create multiple graph store for a set of graphs */
/* This is used for drawing several graphs in one window */
/* create a new graph */
graphdata = ajGraphdataNewI(ipoints);
/* add graph to list in a multiple graph */
ajGraphDataAdd(mult,graphdata);
/* set overlap based on bool*/
ajGraphxySetflagOverlay(mult, overlap);
/* create the point values for this graph */
for(i=0;i<ipoints; i++)
{
graphdata->x[i] = (float)i;
graphdata->y[i] = sin(ajCvtDegToRad(i));
}
/* embGraphSetData(graphdata,&array[0][0]);*/
ajGraphdataSetYlabelC(graphdata,"SINE(degrees)");
ajGraphdataSetXlabelC(graphdata,"degrees");
ajGraphdataSetTitleC(graphdata,"hello");
ajGraphdataSetColour(graphdata,GREEN);
if(!overlap)
{
ajGraphdataAddposRect(graphdata,70.0,0.55,80.0,0.45,GREEN,1);
ajGraphdataAddposTextC(graphdata,82.0,0.5,GREEN,"Sine");
}
graphdata = ajGraphdataNewI(ipoints);
ajGraphDataAdd(mult,graphdata);
for(i=0;i<ipoints; i++)
{
graphdata->x[i] = (float)i;
graphdata->y[i] = cos(ajCvtDegToRad((float)i));
}
ajGraphdataSetXlabelC(graphdata,"degrees");
ajGraphdataSetYlabelC(graphdata,"COS(degrees)");
ajGraphdataSetTitleC(graphdata,"hello");
ajGraphdataSetColour(graphdata,RED);
if(!overlap)
{
ajGraphdataAddposLine(graphdata,5.0,0.1,15.0,0.1,RED);
ajGraphdataAddposTextC(graphdata,17.0,0.1,RED,"Cosine");
}
/* now set larger axis than needed */
ajGraphdataSetMinmax(graphdata,0.0,(float)ipoints,-0.5,1.5);
graphdata = ajGraphdataNewI(ipoints);
ajGraphdataSetLinetype(graphdata, 3);
ajGraphDataAdd(mult,graphdata);
for(i=0;i<ipoints; i++)
{
graphdata->x[i] = (float)i;
graphdata->y[i] = (tan(ajCvtDegToRad(i))*0.2);
}
ajGraphdataSetXlabelC(graphdata,"degrees");
ajGraphdataSetYlabelC(graphdata,"TAN(degrees)");
ajGraphdataSetTitleC(graphdata,"hello");
ajGraphdataSetLinetype(graphdata, 2);
ajGraphdataSetColour(graphdata,BLUE);
if(!overlap)
{
ajGraphdataAddposRect(graphdata,5.0,9.0,15.0,8.5,BLUE,0);
ajGraphdataAddposTextC(graphdata,17.0,8.75,BLUE,"Tangent");
}
ajGraphSetYlabelC(mult,"sin,cos,tan");
ajGraphSetXlabelC(mult,"degrees");
ajGraphSetTitleC(mult,"Trig functions");
ajGraphxySetYstartF(mult,0.0);
ajGraphxySetYendF(mult,2.0);
if(overlap)
{
ajGraphAddRect(mult,5.0,9.0,15.0,8.5,BLUE,0);
ajGraphAddRect(mult,5.0,8.0,15.0,7.5,GREEN,1);
ajGraphAddLine(mult,5.0,6.75,15.0,6.75,RED);
ajGraphAddTextC(mult,17.0,8.75,BLUE,"Tangent");
ajGraphAddTextC(mult,17.0,7.75,GREEN,"Sine");
ajGraphAddTextC(mult,17.0,6.75,RED,"Cosine");
}
ajGraphxyDisplay(mult,AJTRUE);
ajGraphxyDel(&mult);
embExit();
return 0;
}
