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; }
static void dottup_stretchplot(AjPGraph graph, const AjPList matchlist, const AjPSeq seq1, const AjPSeq seq2, ajint begin1, ajint begin2, ajint end1, ajint end2) { EmbPWordMatch wmp = NULL; float xa[1]; float ya[2]; AjPGraphdata gdata = NULL; AjPStr tit = NULL; float x1; float y1; float x2; float y2; AjIList iter = NULL; tit = ajStrNew(); ajFmtPrintS(&tit,"%S",ajGraphGetTitleS(graph)); gdata = ajGraphdataNewI(1); xa[0] = (float)begin1; ya[0] = (float)begin2; ajGraphSetTitleC(graph,ajStrGetPtr(tit)); ajGraphSetXlabelC(graph,ajSeqGetNameC(seq1)); ajGraphSetYlabelC(graph,ajSeqGetNameC(seq2)); ajGraphdataSetTypeC(gdata,"2D Plot Float"); ajGraphdataSetMinmax(gdata,(float)begin1,(float)end1,(float)begin2, (float)end2); ajGraphdataSetTruescale(gdata,(float)begin1,(float)end1,(float)begin2, (float)end2); ajGraphxySetXstartF(graph,(float)begin1); ajGraphxySetXendF(graph,(float)end1); ajGraphxySetYstartF(graph,(float)begin2); ajGraphxySetYendF(graph,(float)end2); ajGraphxySetXrangeII(graph,begin1,end1); ajGraphxySetYrangeII(graph,begin2,end2); if(matchlist) { iter = ajListIterNewread(matchlist); while((wmp = ajListIterGet(iter))) { x1 = x2 = (float) (wmp->seq1start + begin1); y1 = y2 = (float) (wmp->seq2start + begin2); x2 += (float) wmp->length-1; y2 += (float) wmp->length-1; ajGraphAddLine(graph,x1,y1,x2,y2,0); } ajListIterDel(&iter); } ajGraphdataAddXY(gdata,xa,ya); ajGraphDataReplace(graph,gdata); ajGraphxyDisplay(graph,ajFalse); ajGraphicsClose(); ajStrDel(&tit); return; }
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) { 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; }