/*This basically means choosing alpha and beta from random values */
void RandoStartClineVars(hyb_chain *C, cline_struct *L)
{
int l;
locline_struct *Loc;
int N,lo,hi;
if(L->NumLocales==0) {
return;
}
N = L->NumClineXs;
lo = (int)(.15 * N);
hi = (int)(.85 * N);
CYCLE_l(C->Dat) /* cycle over loci */
/* define this pointer to the current locline struct */
Loc = L->Locs[l];
Loc->alpha->v = L->ClineX[UniformRV(lo,hi)];
Loc->beta->v = ranf() * .1;
Loc->LogLike->v = LogistLogL(Loc->alpha->v,Loc->beta->v,Loc->N,Loc->Y,L->x,L->HasLocale,L->MaxLocaleIndex);
END1CYCLE
}
/* here we accumulate the averages of these cline vars */
void IncrementClineVars(hyb_chain *C, cline_struct *L)
{
int p,l,x;
if(L->NumLocales==0) {
return;
}
/* get the averages for Y and N and alpha and beta */
for(p=0;p<=L->MaxLocaleIndex;p++) {
if(L->HasLocale[p]) {
CYCLE_l(C->Dat)
IncrementIval(L->Locs[l]->Y[p]);
IncrementIval(L->Locs[l]->N[p]);
END1CYCLE
}
}
void gfnhDrawKullbLeib(void)
{
int l;
GLfloat x=0.0f,y,h=.7f,w,max=0.0f;
char S[100];
FILE *out;
gsSettings gsCS gsWoH;
CYCLE_l(gC->Dat)
/* set the height and the width */
y = (GLfloat)(gC->Dat->L - l);
if(Settings->GFNH_CURRENT_OR_AVES == GFNH_AVES)
w = (GLfloat)gC->Lat->Locus_KB[l]->Ave;
else if(Settings->GFNH_CURRENT_OR_AVES == GFNH_CURRENT)
w = (GLfloat)gC->Lat->Locus_KB[l]->v;
else {
out = fopen(gERROR_FILE,"a");
fprintf(out,"\nGFNH_CURRENT_OR_AVES set to neither GFNH_AVES or");
fprintf(out,"\nGFNH_CURRENT in gfnhDrawKullbLeib!! \n\n");
fclose(out);
}
if(w>max)
max = w;
/* set the string of the locus and print it */
sprintf(S,"%s ",gC->Dat->LocNames[l]);
glColor3fv(CS->Text);
gfmStrokeString(S, h*.85f ,x, y-h, 4, 0.0f, WoH);
/* then print the rectangle in the 3rd color of the series */
glColor3fv(CS->Series[5]);
glRectf(x,y,x+w,y-h);
END1CYCLE
gsHANDLE_EXTREMA(0,max,0,gC->Dat->L);
gfmDrawXYAxes();
}
void gfnhDrawAlleleFreqs(void)
{
int k,l;
GLfloat xs = 1.0f, ys = .5f;
int n;
GLfloat w,h,halfh;
GLfloat x, y;
int Aves = 0;
GLfloat cum0,cum1;
int CW = glutGetWindow();
char temp[200];
GLfloat WoH = gfmWoH();
int MC;
if(gWindowsSettings[CW]->GFNH_CURRENT_OR_AVES==GFNH_AVES)
Aves = 1;
/* record the max number of colors in the color scheme */
MC = gWindowsSettings[CW]->ColorScheme->N;
gfmSetParsForBarGraphs(gC->Dat->L, gWindowsSettings[CW]->NumCols, xs, ys, &n, &w, &h);
halfh = .5f * h;
gWindowsSettings[CW]->SelectedElement = gfmBarGraphIdxFromXY(n, gC->Dat->L, w, h, xs, ys,
gWindowsSettings[CW]->XCoord, gWindowsSettings[CW]->YCoord);
CYCLE_l(gC->Dat)
cum0 = 0.0f;
cum1 = 0.0f;
x = gfmBarGraphXCoord(n,w,xs,l);
y = gfmBarGraphYCoord(n,h,ys,l);
/* draw the locus name to the left of the locus */
sprintf(temp,"%s ",gC->Dat->LocNames[l]);
glColor3fv(gWindowsSettings[CW]->ColorScheme->Text);
if(l == gWindowsSettings[CW]->SelectedElement)
glColor3fv(gWindowsSettings[CW]->ColorScheme->Series[0]); /* make the selected one a different color */
gfmStrokeString(temp,h,x,y-h,3,0.0f,WoH);
CYCLE_k(gC->Dat)
gfmDrawRectLeaf6f(x,y,w,halfh, cum0, 1.0f, gWindowsSettings[CW]->ColorScheme->Series[k%MC]);
gfmDrawRectLeaf6f(x,y-halfh,w,halfh, cum1, 1.0f, gWindowsSettings[CW]->ColorScheme->Series[k%MC]);
if(Aves) {
cum0 += gC->Lat->Theta[0][l][k]->Ave;
cum1 += gC->Lat->Theta[1][l][k]->Ave;
}
else {
cum0 += gC->Lat->Theta[0][l][k]->v;
cum1 += gC->Lat->Theta[1][l][k]->v;
}
END1CYCLE
END1CYCLE
if(gWindowsSettings[CW]->SelectedElement >= 0) {
sprintf(temp,"Selected Locus = %s", gC->Dat->LocNames[gWindowsSettings[CW]->SelectedElement]);
glColor3fv(gWindowsSettings[CW]->ColorScheme->Text);
gfmRenderBitmapString(-.05f,1.1f,GLUT_BITMAP_HELVETICA_12,temp);
}
}
/* Horizontal lines between the individuals are toggled using the Xaxis DrawIt variable */
void gfnhDrawW_Aves(void)
{
int i,l,c;
GLfloat xs = .8f, ys = .8f;
GLfloat x,y, yy;
ColorScheme3f *CS = gWindowsSettings[glutGetWindow()]->ColorScheme;
XY_axis_struct *XA = gWindowsSettings[glutGetWindow()]->Xaxis;
clipping_struct *C = gWindowsSettings[glutGetWindow()]->Clips;
GLfloat WoH = gfmWoH();
char temp[100];
GLfloat texth;
/* lay down the locus names as rotated text at the top of each column */
/* set the top height of the bars */
y = 3.0f * (GLfloat)gC->Dat->M;
texth = xs * (C->yhi - C->ylo) / (C->xhi - C->xlo) ; /* for textheight */
CYCLE_l(gC->Dat) /* cycle over the loci */
x = (GLfloat)l; /* set the "cursor" to the left edge of each locus rectangle */
sprintf(temp," %s",gC->Dat->LocNames[l]);
glColor3fv(CS->Text);
gfmStrokeString(temp,texth,x+.5f*xs,y,1,-45.0f,WoH);
END1CYCLE
CYCLE_i(gC->Dat)
y = 3.0f * (GLfloat)gC->Dat->M - (3.0f * (GLfloat)i);
/* draw text telling the individual's number */
glColor3fv(CS->Text);
sprintf(temp,"%d",i+1);
gfmStrokeString(temp, 1.9f ,-.1f, y-1.8f, 4, 0.0f,WoH);
CYCLE_l(gC->Dat)
x = (GLfloat)l;
yy = y;
if(1) { /* draw alleles if they are codominant OR if they are AFLP */
for(c=0;c<2;c++) {
if(gC->Dat->Yobs[i][l][c]->v >= 0) { /* if it is not missing draw the square */
glColor3fv(CS->Series[0]); /* set the color for the whole underlying rectangle */
glRectf(x,yy,x+xs,yy-ys);
glColor3fv(CS->Series[1]); /* then set the color for the Species=1 part. */
glRectf(x+xs*(1.0-gC->Lat->Ind[i]->W[l][c]->Ave),yy,x+xs,yy-ys);
}
if(gC->Dat->Yobs[i][l][c]->v == -1) { /* if it is missing, then draw an empty box in axis color, slightly larger than the allele box */
glColor3fv(CS->Axes); /* set the color */
glBegin(GL_LINE_LOOP);
glVertex2f(x,yy);
glVertex2f(x+xs,yy);
glVertex2f(x+xs,yy-ys);
glVertex2f(x,yy-ys);
glEnd();
}
/* move the second allele down one unit: */
yy -= 1.0f;
}
}
END1CYCLE
/* draw a separating line */
if(XA->DrawIt==1) {
glColor3fv(CS->Axes);
glBegin(GL_LINES);
glVertex2f(0.0f,y-2.5f);
glVertex2f((GLfloat)gC->Dat->L-(1.0f-xs),y-2.5f);
glEnd();
}
END1CYCLE
gsHANDLE_EXTREMA(0.0f,(GLfloat)gC->Dat->L,0.0f, 3.0f * (GLfloat)gC->Dat->M);
}
/* Horizontal lines between the individuals are toggled using the Xaxis DrawIt variable */
void gfnhDrawObservedData(void)
{
int i,l,c;
GLfloat xs = .8f, ys = .8f;
GLfloat x,y, yy;
ColorScheme3f *CS = gWindowsSettings[glutGetWindow()]->ColorScheme;
XY_axis_struct *XA = gWindowsSettings[glutGetWindow()]->Xaxis;
clipping_struct *C = gWindowsSettings[glutGetWindow()]->Clips;
GLfloat WoH = gfmWoH();
char temp[100];
GLfloat texth;
/* lay down the locus names as rotated text at the top of each column */
/* set the top height of the bars */
y = 3.0f * (GLfloat)gC->Dat->M;
texth = xs * (C->yhi - C->ylo) / (C->xhi - C->xlo) ; /* for textheight */
CYCLE_l(gC->Dat) /* cycle over the loci */
x = (GLfloat)l; /* set the "cursor" to the left edge of each locus rectangle */
sprintf(temp," %s",gC->Dat->LocNames[l]);
glColor3fv(CS->Text);
gfmStrokeString(temp,texth,x+.5f*xs,y,1,-45.0f,WoH);
END1CYCLE
CYCLE_i(gC->Dat)
y = 3.0f * (GLfloat)gC->Dat->M - (3.0f * (GLfloat)i);
/* draw text telling the individual's number */
glColor3fv(CS->Text);
sprintf(temp,"%d",i+1);
gfmStrokeString(temp, 1.9f ,-.1f, y-1.8f, 4, 0.0f,WoH);
CYCLE_l(gC->Dat)
x = (GLfloat)l;
yy = y;
if(gC->Dat->LocTypes[l] == CODOM) { /* draw alleles if they are codominant */
for(c=0;c<2;c++) {
if(gC->Dat->Yobs[i][l][c]->v >= 0) { /* if it is not missing data draw the square */
glColor3fv(CS->Series[gC->Dat->Yobs[i][l][c]->v % CS->N]); /* set the color */
glRectf(x,yy,x+xs,yy-ys);
}
else { /* if it is missing, then draw an empty box in axis color */
glColor3fv(CS->Axes); /* set the color */
glBegin(GL_LINE_LOOP);
glVertex2f(x,yy);
glVertex2f(x+xs,yy);
glVertex2f(x+xs,yy-ys);
glVertex2f(x,yy-ys);
glEnd();
}
/* move the second allele down one unit: */
yy -= 1.0f;
}
}
/* now, if the locus is an AFLP locus, we draw a plus or a zero */
if(gC->Dat->LocTypes[l] == AFLP) {
if(gC->Dat->Yobs[i][l][0]->v == 1) {
sprintf(temp,"+");
glColor3fv(CS->Series[0]);
gfmStrokeString(temp,3.0f,x + (.5f * xs),y-2.4f + .3f * ys, 2,0.0f,WoH);
}
else if(gC->Dat->Yobs[i][l][0]->v == 0) {
sprintf(temp,"-");
glColor3fv(CS->Series[1]);
gfmStrokeString(temp,2.2f,x + (.5f * xs),y-2.2f + .3f * ys, 2,0.0f,WoH);
}
else if(gC->Dat->Yobs[i][l][0]->v == -1) { /* draw an axis-colored, solid rectangle if it is missing */
glColor3fv(CS->Axes); /* set the color */
glRectf(x,yy,x+xs,yy-1.0-ys);
}
}
END1CYCLE
/* draw a separating line */
if(XA->DrawIt==1) {
glColor3fv(CS->Axes);
glBegin(GL_LINES);
glVertex2f(0.0f,y-2.5f);
glVertex2f((GLfloat)gC->Dat->L-(1.0f-xs),y-2.5f);
glEnd();
}
END1CYCLE
gsHANDLE_EXTREMA(0.0f,(GLfloat)gC->Dat->L,0.0f, 3.0f * (GLfloat)gC->Dat->M);
}
