TIN::TIN() : mMesh(NULL), mBehavior(NULL), mRecentTri(NULL), mMinZ(std::numeric_limits<double>::max()), mMaxZ(-1 * std::numeric_limits<double>::max())
{
mMesh = new TMesh;
mBehavior = new TBehavior;
mRecentTri = new TOrientedTriangle;
// Using incremental algorithm for triangulation
char * switches = {"zQ"};
triangleinit(mMesh);
parsecommandline(1, &switches, mBehavior);
mRecentTri->tri = NULL;
mRecentTri->orient = 0;
}
/* This function should be called from main() to configure the program.
* After the configurations have been initialized the command line is
* parsed. Then the configuration file is read and after that if any
* parameter has not been set the defaults are used. */
int
opt_configure(int argc, const char *argv[])
{
initconfig();
parsecommandline(argc, argv);
if(readconfigfile()) {
xerror("Unable to read configuration running with defaults");
}
setdefaults();
// xlog(LOG_CONFIG, "Daemonize set to %d", _daemonize);
// xlog(LOG_CONFIG, "Status Tagname is set to %s", _statustag);
// xlog(LOG_CONFIG, "PID File Name set to %s", _pidfile);
return 0;
}
int cmd_call(char *param)
{
/*
* Perform CALL command.
*
* Allocate a new batch context and add it to the current chain.
* Call parsecommandline passing in our param string
* If No batch file was opened then remove our newly allocted
* context block.
*/
struct bcontext *n = newBatchContext();
int ec;
if (n == 0) {
/* Not in a batch file */
return 1;
}
optS = optN = 0;
if((ec = leadOptions(¶m, opt_call, 0)) != E_None)
return ec;
if(swapOnExec != ERROR) {
if(optS)
swapOnExec = TRUE;
if(optN)
swapOnExec = FALSE;
}
parsecommandline(param, FALSE);
if(swapOnExec != ERROR)
swapOnExec = FALSE;
if (bc->bfile == 0
&& bc->bfnam == 0) { /* Wasn't a batch file so remove context */
bc = bc->prev;
free(n);
}
return 0;
}
/*
* do the prompt/input/process loop
*
* If xflg is true, the function will not go interactive, but returns.
* If commandline != NULL, this command is processed first.
*
* Return: 0: on success
*/
int process_input(int xflag, char *commandline)
{
/* Dimensionate parsedline that no sprintf() can overflow the buffer
*/
char parsedline[MAX_INTERNAL_COMMAND_SIZE + sizeof(errorlevel) * 8]
, *readline;
/* Return the maximum pointer into parsedline to add 'numbytes' bytes */
#define parsedMax(numbytes) \
(parsedline + MAX_INTERNAL_COMMAND_SIZE - 1 - (numbytes))
char *evar;
char *tp;
char *ip;
char *cp;
char forvar;
int echothisline;
int tracethisline;
do
{
interactive_command = 0; /* not directly entered by user */
echothisline = tracethisline = 0;
if(commandline) {
ip = commandline;
readline = commandline = NULL;
} else {
if ((readline = malloc(MAX_INTERNAL_COMMAND_SIZE + 1)) == NULL)
{
error_out_of_memory();
return 1;
}
if (NULL == (ip = readbatchline(&echothisline, readline,
MAX_INTERNAL_COMMAND_SIZE)))
{ /* if no batch input then... */
if (xflag /* must not go interactive */
|| (fdattr(0) & 0x84) == 0x84 /* input is NUL device */
|| feof(stdin)) /* no further input */
{
free(readline);
break;
}
/* Go Interactive */
interactive_command = 1; /* directly entered by user */
readcommand(ip = readline, MAX_INTERNAL_COMMAND_SIZE);
tracemode = 0; /* reset trace mode */
}
}
/*
* The question mark '?' has a double meaning:
* C:\> ?
* ==> Display short help
*
* C:\> ? command arguments
* ==> enable tracemode for just this line
*/
if(*(ip = trim(ip)) == '?') {
ip = trim(ip + 1);
if(!*ip) { /* is short help command */
#ifdef INCLUDE_CMD_QUESTION
showcmds(ip);
#endif
free(readline);
continue;
}
/* this-line-tracemode */
echothisline = 0;
tracethisline = 1;
}
/* The FOR hack
If the line matches /^\s*for\s+\%[a-z]\s/, the FOR hack
becomes active, because FOR requires the sequence "%<ch>"
in its input.
When the percent (%) expansion is made later on, any
sequence "%<ch>" is retained.
*/
cp = ip;
if(matchtok(cp, "for") && *cp == '%' && isalpha(cp[1])
&& isspace(cp[2])) /* activate FOR hack */
forvar = toupper(cp[1]);
else forvar = 0;
cp = parsedline;
while (*ip)
{
/* Assume that at least one character is added, place the
test here to simplify the switch() statement */
if(cp >= parsedMax(1)) {
cp = NULL; /* error condition */
break;
}
if (*ip == '%')
{
switch (*++ip)
{
case '\0': /* FOR hack forvar == 0 if no FOR is active */
*cp++ = '%';
break;
case '%':
*cp++ = *ip++;
break;
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
if (NULL != (tp = find_arg(*ip - '0')))
{
if(cp >= parsedMax(strlen(tp))) {
cp = NULL;
goto intBufOver;
}
cp = stpcpy(cp, tp);
ip++;
}
else
*cp++ = '%';
/* Let the digit be copied in the cycle */
break;
case '?':
/* overflow check: parsedline has that many character
"on reserve" */
cp += sprintf(cp, "%u", errorlevel);
ip++;
break;
default:
if(forvar == toupper(*ip)) { /* FOR hack */
*cp++ = '%'; /* let the var be copied in next cycle */
break;
}
if ((tp = strchr(ip, '%')) != NULL)
{
*tp = '\0';
if ((evar = getEnv(ip)) != NULL) {
if(cp >= parsedMax(strlen(evar))) {
cp = NULL;
goto intBufOver;
}
cp = stpcpy(cp, evar);
}
ip = tp + 1;
}
break;
}
continue;
}
if (iscntrl(*ip))
*cp = ' ';
else
*cp++ = *ip++;
}
intBufOver:
free(readline);
if(!cp) { /* internal buffer overflow */
error_line_too_long();
continue;
}
*cp = '\0'; /* terminate copied string */
if (echothisline) /* Echo batch file line */
{
printprompt();
puts(parsedline);
}
if (*parsedline)
{
if(tracethisline)
++tracemode;
parsecommandline(parsedline);
if(tracethisline)
--tracemode;
if (echothisline || echo)
putchar('\n');
}
}
while (!canexit || !exitflag);
return 0;
}
int cmd_if(char *param)
{
#define X_EXEC 1
char *pp;
int x_flag = 0; /* when set cause 'then' clause to be exec'ed */
int negate = 0; /* NOT keyword present */
int ignore_case = 0; /* /I option, case insensitive compare */
/* First check if param exists */
assert(param);
/* check for options, note non-options must be treated as part of comparision */
if (matchtok(param, "/I")||matchtok(param, "/i"))
ignore_case++;
/* next check if param string begins with word 'not' */
if(matchtok(param, "not"))
negate = X_EXEC; /* Remember 'NOT' */
/* Check for 'exist' form */
if(matchtok(param, "exist")) {
struct dos_ffblk f;
isr olderrhandler;
if(!*param) {
/* syntax error */
error_if_exist();
return 0;
}
pp = skip_word(param);
*pp++ = '\0';
/* don't show abort/retry/fail if no disk in drive */
get_isr(0x24, olderrhandler);
#ifdef XMS_SWAP
set_isrfct(0x24, autofail_err_handler); /* always fails */
#else
set_isrfct(0x24, dummy_criter_handler); /* always fails */
#endif
if(dos_findfirst(param, &f, FA_NORMAL|FA_ARCH|FA_SYSTEM|FA_RDONLY|FA_HIDDEN) == 0)
x_flag = X_EXEC;
dos_findclose(&f);
/* restore critical error handler */
set_isrfct(0x24, olderrhandler);
}
/* Check for 'errorlevel' form */
else if(matchtok(param, "errorlevel")) {
int n = 0;
#if 0
if(!isdigit(*param)) {
error_if_errorlevel();
return 0;
}
pp = param;
do n = n * 10 + (*pp - '0');
while (isdigit(*++pp));
if(*pp && !isargdelim(*pp)) {
error_if_errorlevel_number();
return 0;
}
#else
/* Add this COMMAND bug as someone tries to use:
IF ERRORLEVEL H<upper-case_letter>
-or-
IF ERRORLEVEL x<lower-case_letter>
to match the errorlevel against drive letters.
NOT supported by 4dos or WinNT.
HA --> maps to errorlevel 1
xa --> same
HB & xb --> to 2
a.s.o.
*/
if(!*param) {
error_if_errorlevel();
return 0;
}
pp = param;
do n = n * 10 + (*pp - '0');
while(*++pp && !isargdelim(*pp));
n &= 255;
dprintf( ("IF: checking for ERRORLEVEL >= %u\n", n) );
#endif
if(errorlevel >= n)
x_flag = X_EXEC;
}
/* Check that '==' is present, syntax error if not */
else {
size_t len;
char *r; /* right operand */
pp = skipqword(param, "==");
if(*pp != '=' || pp[1] != '=') {
error_syntax(0);
return 0;
}
*pp = '\0'; /* param[] points to the left operand */
/* skip over the '==' and subsquent spaces and
assign the end of the right operator to pp */
pp = skipqword(r = ltrimcl(pp + 2), 0);
/* now: param := beginning of the left operand
r := beginning of the right operand
pp := end of right operand
*/
rtrimcl(param); /* ensure that spurious whitespaces are ignored */
len = strlen(param);
/* check if strings differ */
if ( ((pp - r) == len) &&
((ignore_case && strnicmp(param, r, len) == 0) ||
(memcmp(param, r, len) == 0)) )
x_flag = X_EXEC;
}
if(x_flag ^ negate) /* perform the command */
if(!*(pp = ltrimcl(pp)))
error_if_command();
else
parsecommandline(pp, FALSE);
return 0;
}
// Customized triangulation call.
void custom_triangulate(char *triswitches, struct triangulateio *in, struct triangulateio *out, struct triangulateio *vorout, const int *outside, const int *inside)
{
struct mesh m;
struct behavior b;
//REAL *holearray;
//REAL *regionarray;
triangleinit(& m);
parsecommandline(1, & triswitches, & b);
//b.verbose=2;
m.steinerleft = b.steiner;
transfernodes(& m, & b, in->pointlist, in->pointattributelist,
in->pointmarkerlist, in->numberofpoints,
in->numberofpointattributes);
if ( b.refine ) {
m.hullsize = reconstruct(& m, & b, in->trianglelist,
in->triangleattributelist, in->trianglearealist,
in->numberoftriangles, in->numberofcorners,
in->numberoftriangleattributes,
in->segmentlist, in->segmentmarkerlist,
in->numberofsegments);
} else {
m.hullsize = delaunay(& m, & b);
}
m.infvertex1 = ( vertex ) NULL;
m.infvertex2 = ( vertex ) NULL;
m.infvertex3 = ( vertex ) NULL;
if ( b.usesegments ) {
m.checksegments = 1;
if ( !b.refine ) {
formskeleton(& m, & b, in->segmentlist,
in->segmentmarkerlist, in->numberofsegments);
}
}
#if 0
struct osub subsegloop;
traversalinit(& m.subsegs);
subsegloop.ss = subsegtraverse(& m);
subsegloop.ssorient = 0;
while ( subsegloop.ss != ( subseg * ) NULL ) {
if ( subsegloop.ss != m.dummysub ) {
REAL *p1, *p2;
sorg(subsegloop, p1);
sdest(subsegloop, p2);
printf(" Connected (%f,%f) to (%f,%f)\n", p1 [ 0 ], p1 [ 1 ], p2 [ 0 ], p2 [ 1 ]);
subsegloop.ss = subsegtraverse(& m);
}
}
#endif
if ( b.poly && ( m.triangles.items > 0 ) ) {
//holearray = in->holelist;
m.holes = in->numberofholes;
//regionarray = in->regionlist;
m.regions = in->numberofregions;
if ( !b.refine ) {
/* Only increase quality if the regions are properly defined. */
int sane = custom_carveholes(& m, & b, outside, inside);
b.quality *= sane;
if ( sane == 0 ) {
printf("Probably bad PSLG\n");
exit(-1);
}
}
} else {
m.holes = 0;
m.regions = 0;
}
if ( b.quality && ( m.triangles.items > 0 ) ) {
enforcequality(& m, & b);
}
m.edges = ( 3l * m.triangles.items + m.hullsize ) / 2l;
if ( b.order > 1 ) {
highorder(& m, & b);
}
if ( !b.quiet ) {
printf("\n");
}
if ( b.jettison ) {
out->numberofpoints = m.vertices.items - m.undeads;
} else {
out->numberofpoints = m.vertices.items;
}
out->numberofpointattributes = m.nextras;
out->numberoftriangles = m.triangles.items;
out->numberofcorners = ( b.order + 1 ) * ( b.order + 2 ) / 2;
out->numberoftriangleattributes = m.eextras;
out->numberofedges = m.edges;
if ( b.usesegments ) {
out->numberofsegments = m.subsegs.items;
} else {
out->numberofsegments = m.hullsize;
}
if ( vorout != ( struct triangulateio * ) NULL ) {
vorout->numberofpoints = m.triangles.items;
vorout->numberofpointattributes = m.nextras;
vorout->numberofedges = m.edges;
}
if ( b.nonodewritten || ( b.noiterationnum && m.readnodefile ) ) {
if ( !b.quiet ) {
printf("NOT writing vertices.\n");
}
numbernodes(& m, & b);
} else {
writenodes(& m, & b, & out->pointlist, & out->pointattributelist,
& out->pointmarkerlist);
}
// Simp. always write the triangles.
writeelements(& m, & b, & out->trianglelist, & out->triangleattributelist);
if ( b.poly || b.convex ) {
writepoly(& m, & b, & out->segmentlist, & out->segmentmarkerlist);
out->numberofholes = m.holes;
out->numberofregions = m.regions;
if ( b.poly ) {
out->holelist = in->holelist;
out->regionlist = in->regionlist;
} else {
out->holelist = ( REAL * ) NULL;
out->regionlist = ( REAL * ) NULL;
}
}
if ( b.edgesout ) {
writeedges(& m, & b, & out->edgelist, & out->edgemarkerlist);
}
// Simp. no voronoi
if ( b.neighbors ) {
writeneighbors(& m, & b, & out->neighborlist);
}
// Simp. No statistics.
if ( b.docheck ) {
checkmesh(& m, & b);
checkdelaunay(& m, & b);
}
triangledeinit(& m, & b);
}
int _Cdecl my2e_parsecommandline( char *s ) {
s[ (unsigned char)s[ 0 ] ] = '\0';
/* printf("_my2e_parsecommandline( %s )\n", s );*/
parsecommandline( &s[ 1 ], 1 );
return( errorlevel );
}
/*
* do the prompt/input/process loop
*
* If xflg is true, the function will not go interactive, but returns.
* If commandline != NULL, this command is processed first.
*
* Return: 0: on success
*/
int process_input(int xflag, char *commandline)
{
/* Dimensionate parsedline that no sprintf() can overflow the buffer
*/
char parsedline[MAX_INTERNAL_COMMAND_SIZE + sizeof(errorlevel) * 8]
, *readline;
#if 0
/* Return the maximum pointer into parsedline to add 'numbytes' bytes */
#define parsedMax(numbytes) \
(parsedline + MAX_INTERNAL_COMMAND_SIZE - 1 - (numbytes))
char *evar;
char *tp;
char *cp;
#endif
char *ip;
#if 0
char forvar;
#endif
int echothisline;
int tracethisline;
do
{
#ifdef FEATURE_LONG_FILENAMES
if( toupper( *getEnv( "LFN" ) ) == 'N' )
__supportlfns = 0;
else __supportlfns = 1;
#endif
interactive_command = 0; /* not directly entered by user */
echothisline = tracethisline = 0;
if(commandline) {
ip = commandline;
readline = commandline = 0;
} else {
if ((readline = malloc(MAX_INTERNAL_COMMAND_SIZE + 1)) == 0)
{
error_out_of_memory();
return 1;
}
if (0 == (ip = readbatchline(&echothisline, readline,
MAX_INTERNAL_COMMAND_SIZE)))
{ /* if no batch input then... */
if (xflag /* must not go interactive */
|| (fdattr(0) & 0x84) == 0x84 /* input is NUL device */
|| feof(stdin)) /* no further input */
{
free(readline);
break;
}
/* Go Interactive */
interactive_command = 1; /* directly entered by user */
/* Ensure the prompt starts at column #0 */
if(echo && (mywherex()>1))
outc('\n');
readcommand(ip = readline, MAX_INTERNAL_COMMAND_SIZE);
tracemode = 0; /* reset trace mode */
}
}
/* Make sure there is no left-over from last run */
currCmdHelpScreen = 0;
/*
* The question mark '?' has a double meaning:
* C:\> ?
* ==> Display short help
*
* C:\> ? command arguments
* ==> enable tracemode for just this line
*/
if(*(ip = ltrimcl(ip)) == '?') {
ip = ltrimcl(ip + 1);
if(!*ip) { /* is short help command */
#ifdef INCLUDE_CMD_QUESTION
showcmds(ip);
#endif
free(readline);
continue;
}
/* this-line-tracemode */
echothisline = 0;
tracethisline = 1;
}
#if 0
/* The FOR hack
If the line matches /^\s*for\s+\%[a-z]\s/, the FOR hack
becomes active, because FOR requires the sequence "%<ch>"
in its input.
When the percent (%) expansion is made later on, any
sequence "%<ch>" is retained.
*/
cp = ip;
if(matchtok(cp, "for") && *cp == '%' && isalpha(cp[1])
&& isargdelim(cp[2])) /* activate FOR hack */
forvar = toupper(cp[1]);
else forvar = 0;
#else
if(cmd_for_hackery(ip)) {
free(readline);
continue;
}
#endif
{ int rc = expandEnvVars(ip, parsedline);
free(readline);
if(!rc) {
error_line_too_long();
continue;
}
}
if (echothisline) /* Echo batch file line */
{
printprompt();
puts(parsedline);
}
if (*parsedline)
{
if(swapOnExec != ERROR)
swapOnExec = defaultToSwap;
if(tracethisline)
++tracemode;
parsecommandline(parsedline, TRUE);
if(tracethisline)
--tracemode;
}
}
while (!canexit || !exitflag);
return 0;
}
int cmd_set(char *param)
{ char *value;
char *promptBuf = 0, tempcmd[255];
int ret;
optC = promptUser = upCaseValue = optExecute = 0;
if(leadOptions(¶m, opt_set, 0) != E_None)
return 1;
switch(breakVarAssign(ctxtEnvironment, param, &value)) {
case 1: /* no equal sign */
#ifdef FEATURE_CMD_SET_PRINT
if( ( value = getEnv( param ) ) != NULL ) printf( "%s\n", value );
else {
error_env_var_not_found( param );
return( 1 );
}
return( 0 );
#else
error_syntax(0);
return 1;
#endif
case 0: /* displayed */
return 0;
#ifdef DEBUG
case 2: break;
default:
dprintf(("[SET: Invalid response from breakVarAssign()]\n"));
return 1;
#endif
}
if(promptUser) { /* -> Display the value, then read and assign */
assert(value);
fputs(value, stdout);
promptBuf = malloc(promptBuffer);
if(!promptBuf) {
error_out_of_memory();
return E_NoMem;
}
fgets(promptBuf, promptBuffer, stdin);
if(cbreak) {
free(promptBuf);
return E_CBreak;
}
value = strchr(promptBuf, '\0');
while(--value >= promptBuf && (*value == '\n' || *value == '\r'));
value[1] = '\0'; /* strip trailing newlines */
value = promptBuf;
}
if (optExecute) {
char *tempfile = tmpfn();
FILE *fhandle;
if (!tempfile) return (1);
sprintf (tempcmd, "%s>%s", value, tempfile);
parsecommandline (tempcmd, TRUE);
fhandle = fopen (tempfile, "r");
if (!fhandle) {
unlink (tempfile);
free (tempfile);
return (1);
}
fgets (tempcmd, 255, fhandle);
value = strchr(tempcmd, '\n');
if (value) *value = '\0';
value = tempcmd;
fclose (fhandle);
unlink (tempfile);
free (tempfile);
}
/* If the value is just blanks, it means to delete the value;
but otherwise even leading and trailing spaces must be kept */
if(is_empty(value))
value = 0;
if (upCaseValue) StrUpr(value); /* set value as upper case, eg for if testing */
ret = chgEnvCase(optC, param, value);
free(promptBuf);
return ret;
}
int main (int argc, char * argv[])
{
// Plant frequencies... (zeroed here just to suppress a -Wall warning)
float f_AA_MM = 0;
float f_AA_Mm = 0;
float f_AA_mm = 0;
float f_Aa_MM = 0;
float f_Aa_Mm = 0;
float f_Aa_mm = 0;
float f_aa_MM = 0;
float f_aa_Mm = 0;
float f_aa_mm = 0;
float next_f_AA_MM;
float next_f_AA_Mm;
float next_f_AA_mm;
float next_f_Aa_MM;
float next_f_Aa_Mm;
float next_f_Aa_mm;
float next_f_aa_MM;
float next_f_aa_Mm;
float next_f_aa_mm;
// Pollen frequencies...
float p_A_M;
float p_A_m;
float p_a_M;
float p_a_m;
// Egg frequencies...
float e_A_M;
float e_A_m;
float e_a_M;
float e_a_m;
float male = 0;
float female = 0;
float inconstant = 0;
float PSatC; // Pollen saturation point for cosex receivers
float K;
float k;
float totalpollen;
float totalplants;
int n;
int x;
int y;
char bmp_filename[1024];
char txt_filename[1024];
FILE * textfile = NULL;
parsecommandline(argc, argv);
result = malloc(subdivisions * sizeof(int*));
if (result == NULL)
{
printf("Out of memory!\n");
exit(1);
}
for (n = 0; n < subdivisions; n++)
{
result[n] = malloc(subdivisions * sizeof(int));
if (result[n] == NULL)
{
printf("Out of memory!\n");
exit(1);
}
}
// Print all settings...
printf("\nModel %d\n\n", MODEL);
if (onerun)
{
printf("Q = %G (K = %G, pi = %G)\n", Q, (1 / Q) - 1, 1 / Q);
printf("F = %G (k = %G, \"omega\" = %G)\n\n", F, (1 / F) - 1, 1 / F);
}
printf("h = %G\n", h);
printf("Selfing rate = %G\n", S);
printf("Inbreeding depression = %G\n", d);
printf("YY viability = %G (YY penalty = %G)\n", V, 1 - V);
printf("PSatF = %G\n\n", PSatF);
printf("Iterations = %d\n\n", endpoint);
if (onerun == 0)
{
printf("Warning: --onerun option not received, therefore program will\n");
printf("use %d Q and F combinations and produce a graph. This may\n", subdivisions * subdivisions);
printf("take a long time. If this was not your intention, terminate now.\n\n");
printf(" %d |\n", oldformat ? oldformatlimit : 1);
printf("Output format: %s |\n", oldformat ? "k" : "F");
printf(" 0 |\n");
printf(" -----\n");
printf(" 0 %d\n", oldformat ? oldformatlimit : 1);
printf(" %s\n\n", oldformat ? "K" : "Q");
}
// Choose names for .bmp and .txt output files (if needed)...
sprintf(bmp_filename, "model%d_start%s_V%G_S%G_d%G_h%G_PSatF%G_ppY%G.bmp", MODEL, pgd ? "PGD" : "DIO", V, S, d, h, PSatF, ppY);
sprintf(txt_filename, "model%d_start%s_V%G_S%G_d%G_h%G_PSatF%G_ppY%G.txt", MODEL, pgd ? "PGD" : "DIO", V, S, d, h, PSatF, ppY);
// Open .txt output file (if needed)...
if (onerun == 0 && gnuplot)
{
textfile = fopen(txt_filename, "w");
}
for (y = 0; y < subdivisions; y++)
{
for (x = 0; x < subdivisions; x++)
{
if (onerun == 0)
{
// Here we map the X,Y coordinates of our output .bmp file onto Q and F parameters...
if (oldformat == 0)
{
Q = (float) x / (subdivisions - 1); // X axis: Q values 0 to 1
F = (float) y / (subdivisions - 1); // Y axis: F values 0 to 1
} else {
K = ((float) x / (subdivisions - 1)) * oldformatlimit; // X axis: K values 0 to oldformatlimit
k = ((float) y / (subdivisions - 1)) * oldformatlimit; // Y axis: k values 0 to oldformatlimit
// But Q and F are the parameters actually used by the code, so calculate them:
Q = 1 / (1 + K);
F = 1 / (1 + k);
}
}
// Set start plant frequencies...
if (pgd == 0) // Start with DIOECY, try inconstant invasion
{
f_AA_MM = 0;
f_AA_Mm = 0;
f_AA_mm = 0.499;
f_Aa_MM = 0;
f_Aa_Mm = 0.002;
f_Aa_mm = 0.499;
f_aa_MM = 0;
f_aa_Mm = 0;
f_aa_mm = 0;
} else { // Start with PSEUDO-GYNODIOECY, try male invasion
f_AA_MM = 0.499;
f_AA_Mm = 0;
f_AA_mm = 0;
f_Aa_MM = 0.499;
f_Aa_Mm = 0;
f_Aa_mm = 0.002;
f_aa_MM = 0;
f_aa_Mm = 0;
f_aa_mm = 0;
}
for (n = 0; n < endpoint; n++)
{
// Outcrossed pollen frequencies....................................................
//
// Here we sum up the 4 types of pollen (containing the 4 possible allele combinations)
// from the various possible sources. We could do this in 4 equations (as in the paper)
// but it's simpler to consider each source in turn and add to the totals.
p_A_M = 0;
p_A_m = 0;
p_a_M = 0;
p_a_m = 0;
// From AA MM pure females (genotype 1)
;
// From AA Mm pure females (genotype 2)
;
// From AA mm pure females (genotype 3)
;
// From Aa MM inconstants (genotype 4) as cosexes
p_A_M += f_Aa_MM * 0.5 * h * Q;
p_a_M += f_Aa_MM * 0.5 * h * Q;
// From Aa MM inconstants (genotype 4) as males
p_A_M += f_Aa_MM * 0.5 * (1 - h);
p_a_M += f_Aa_MM * 0.5 * (1 - h);
// From Aa Mm inconstants (genotype 5) as cosexes
p_A_M += f_Aa_Mm * 0.25 * h * Q;
p_A_m += f_Aa_Mm * 0.25 * h * Q;
p_a_M += f_Aa_Mm * 0.25 * h * Q;
p_a_m += f_Aa_Mm * 0.25 * h * Q;
// From Aa Mm inconstants (genotype 5) as males
p_A_M += f_Aa_Mm * 0.25 * (1 - h);
p_A_m += f_Aa_Mm * 0.25 * (1 - h);
p_a_M += f_Aa_Mm * 0.25 * (1 - h);
p_a_m += f_Aa_Mm * 0.25 * (1 - h);
// From Aa mm pure males (genotype 6)
p_A_m += f_Aa_mm * 0.5;
p_a_m += f_Aa_mm * 0.5;
// From aa MM inconstants (genotype 7) as cosexes
p_a_M += f_aa_MM * h * Q;
// From aa MM inconstants (genotype 7) as males
p_a_M += f_aa_MM * (1 - h);
// From aa Mm inconstants (genotype 8) as cosexes
p_a_M += f_aa_Mm * 0.5 * h * Q;
p_a_m += f_aa_Mm * 0.5 * h * Q;
// From aa Mm inconstants (genotype 8) as males
p_a_M += f_aa_Mm * 0.5 * (1 - h);
p_a_m += f_aa_Mm * 0.5 * (1 - h);
// From aa mm pure males (genotype 9)
p_a_m += f_aa_mm;
// Normalise pollen frequencies to add up to 1......................................
totalpollen = p_A_M + p_A_m + p_a_M + p_a_m;
if (totalpollen > 0)
{
p_A_M /= totalpollen;
p_A_m /= totalpollen;
p_a_M /= totalpollen;
p_a_m /= totalpollen;
}
// Outcrossed egg frequencies.......................................................
// Calculate pollen required to fertilise a cosex's outcrossing ovules:
PSatC = PSatF * F * (1 - S);
e_A_M = 0;
e_A_m = 0;
e_a_M = 0;
e_a_m = 0;
// From AA MM pure females (genotype 1)
if (totalpollen >= PSatF)
{
e_A_M += f_AA_MM;
} else {
e_A_M += f_AA_MM * totalpollen / PSatF;
}
// From AA Mm pure females (genotype 2)
if (totalpollen >= PSatF)
{
e_A_M += f_AA_Mm * 0.5;
e_A_m += f_AA_Mm * 0.5;
} else {
e_A_M += f_AA_Mm * 0.5 * totalpollen / PSatF;
e_A_m += f_AA_Mm * 0.5 * totalpollen / PSatF;
}
// From AA mm pure females (genotype 3)
if (totalpollen >= PSatF)
{
e_A_m += f_AA_mm;
} else {
e_A_m += f_AA_mm * totalpollen / PSatF;
}
// From Aa MM inconstants (genotype 4) as cosexes
if (totalpollen >= PSatC)
{
e_A_M += f_Aa_MM * h * 0.5 * (1 - S) * F;
e_a_M += f_Aa_MM * h * 0.5 * (1 - S) * F;
} else {
e_A_M += f_Aa_MM * h * 0.5 * (1 - S) * F * totalpollen / PSatC;
e_a_M += f_Aa_MM * h * 0.5 * (1 - S) * F * totalpollen / PSatC;
}
// From Aa Mm inconstants (genotype 5) as cosexes
if (totalpollen >= PSatC)
{
e_A_M += f_Aa_Mm * h * 0.25 * (1 - S) * F;
e_A_m += f_Aa_Mm * h * 0.25 * (1 - S) * F;
e_a_M += f_Aa_Mm * h * 0.25 * (1 - S) * F;
e_a_m += f_Aa_Mm * h * 0.25 * (1 - S) * F;
} else {
e_A_M += f_Aa_Mm * h * 0.25 * (1 - S) * F * totalpollen / PSatC;
e_A_m += f_Aa_Mm * h * 0.25 * (1 - S) * F * totalpollen / PSatC;
e_a_M += f_Aa_Mm * h * 0.25 * (1 - S) * F * totalpollen / PSatC;
e_a_m += f_Aa_Mm * h * 0.25 * (1 - S) * F * totalpollen / PSatC;
}
// From Aa mm pure males (genotype 6)
;
// From aa MM inconstants (genotype 7) as cosexes
if (totalpollen >= PSatC)
{
e_a_M += f_aa_MM * h * (1 - S) * F;
} else {
e_a_M += f_aa_MM * h * (1 - S) * F * totalpollen / PSatC;
}
// From aa Mm inconstants (genotype 8) as cosexes
if (totalpollen >= PSatC)
{
e_a_M += f_aa_Mm * h * 0.5 * (1 - S) * F;
e_a_m += f_aa_Mm * h * 0.5 * (1 - S) * F;
} else {
e_a_M += f_aa_Mm * h * 0.5 * (1 - S) * F * totalpollen / PSatC;
e_a_m += f_aa_Mm * h * 0.5 * (1 - S) * F * totalpollen / PSatC;
}
// From aa mm pure males (genotype 9)
;
// WE CANNOT AND MUST NOT NORMALISE THE EGG FREQUENCIES, AS WE HAVEN'T
// YET CONSIDERED THE SELFED EGGS. BUT WE DON'T NEED TO NORMALISE.
// Plant frequencies from outcrossing...............................................
next_f_AA_MM = p_A_M * e_A_M;
next_f_AA_Mm = p_A_M * e_A_m + p_A_m * e_A_M;
next_f_AA_mm = p_A_m * e_A_m;
next_f_Aa_MM = p_A_M * e_a_M + p_a_M * e_A_M;
next_f_Aa_Mm = p_A_M * e_a_m + p_A_m * e_a_M + p_a_M * e_A_m + p_a_m * e_A_M;
next_f_Aa_mm = p_A_m * e_a_m + p_a_m * e_A_m;
next_f_aa_MM = p_a_M * e_a_M;
next_f_aa_Mm = p_a_M * e_a_m + p_a_m * e_a_M;
next_f_aa_mm = p_a_m * e_a_m;
// Additional plants from selfing...................................................
// From AA MM pure females (genotype 1)
;
// From AA Mm pure females (genotype 2)
;
// From AA mm pure females (genotype 3)
;
// From Aa MM inconstants (genotype 4)
next_f_AA_MM += f_Aa_MM * 0.25 * S * (1 - d) * h * F;
next_f_Aa_MM += f_Aa_MM * 0.5 * S * (1 - d) * h * F;
next_f_aa_MM += f_Aa_MM * 0.25 * S * (1 - d) * h * F;
// From Aa Mm inconstants (genotype 5)
next_f_AA_MM += f_Aa_Mm * 0.0625 * S * (1 - d) * h * F;
next_f_AA_Mm += f_Aa_Mm * 0.125 * S * (1 - d) * h * F;
next_f_AA_mm += f_Aa_Mm * 0.0625 * S * (1 - d) * h * F;
next_f_Aa_MM += f_Aa_Mm * 0.125 * S * (1 - d) * h * F;
next_f_Aa_Mm += f_Aa_Mm * 0.25 * S * (1 - d) * h * F;
next_f_Aa_mm += f_Aa_Mm * 0.125 * S * (1 - d) * h * F;
next_f_aa_MM += f_Aa_Mm * 0.0625 * S * (1 - d) * h * F;
next_f_aa_Mm += f_Aa_Mm * 0.125 * S * (1 - d) * h * F;
next_f_aa_mm += f_Aa_Mm * 0.0625 * S * (1 - d) * h * F;
// From Aa mm pure males (genotype 6)
;
// From aa MM inconstants (genotype 7)
next_f_aa_MM += f_aa_MM * S * (1 - d) * h * F;
// From aa Mm inconstants (genotype 8)
next_f_aa_MM += f_aa_Mm * 0.25 * S * (1 - d) * h * F;
next_f_aa_Mm += f_aa_Mm * 0.5 * S * (1 - d) * h * F;
next_f_aa_mm += f_aa_Mm * 0.25 * S * (1 - d) * h * F;
// From aa mm pure males (genotype 9)
;
// Apply YY penalty.................................................................
next_f_aa_MM *= V;
next_f_aa_Mm *= V;
next_f_aa_mm *= V;
// Copy.............................................................................
f_AA_MM = next_f_AA_MM;
f_AA_Mm = next_f_AA_Mm;
f_AA_mm = next_f_AA_mm;
f_Aa_MM = next_f_Aa_MM;
f_Aa_Mm = next_f_Aa_Mm;
f_Aa_mm = next_f_Aa_mm;
f_aa_MM = next_f_aa_MM;
f_aa_Mm = next_f_aa_Mm;
f_aa_mm = next_f_aa_mm;
// Normalise plant frequencies to add up to 1.......................................
totalplants = f_AA_MM + f_AA_Mm + f_AA_mm + f_Aa_MM + f_Aa_Mm + f_Aa_mm + f_aa_MM + f_aa_Mm + f_aa_mm;
if (totalplants > 0)
{
f_AA_MM /= totalplants;
f_AA_Mm /= totalplants;
f_AA_mm /= totalplants;
f_Aa_MM /= totalplants;
f_Aa_Mm /= totalplants;
f_Aa_mm /= totalplants;
f_aa_MM /= totalplants;
f_aa_Mm /= totalplants;
f_aa_mm /= totalplants;
}
}
// Calculate and save results...
female = f_AA_MM + f_AA_Mm + f_AA_mm;
male = f_Aa_mm + f_aa_mm;
inconstant = f_Aa_MM + f_Aa_Mm + f_aa_MM + f_aa_Mm;
if (male > threshold && female > threshold && inconstant > threshold)
{
result[x][y] = SSD;
} else if (male > threshold && female > threshold) {
result[x][y] = DIO;
} else if (female > threshold && inconstant > threshold) {
result[x][y] = PGD;
} else if (male > threshold && inconstant > threshold) {
result[x][y] = PAD;
} else if (inconstant > threshold) {
result[x][y] = INC;
} else {
result[x][y] = 0;
}
if (onerun == 0 && gnuplot)
{
fprintf(textfile, "%f", female);
if (x == subdivisions - 1)
{
fprintf(textfile, "\n");
} else {
fprintf(textfile, "\t");
}
}
if (onerun) break;
}
if (onerun) break;
}
if (onerun == 0)
{
drawbmp(bmp_filename, 1);
printf("Saved %s\n", bmp_filename);
} else {
printf("Females Males Inconstants\n");
printf("%.6f %.6f %.6f\n\n", female, male, inconstant);
printf("Genotype frequencies, as notated by E&B (2007), or C&C (2012):\n\n");
printf("E&B: AA MM AA Mm AA mm Aa MM Aa Mm Aa mm aa MM aa Mm aa mm\n");
printf("C&C: mm AA mm Aa mm aa Mm AA Mm Aa Mm aa MM AA MM Aa MM aa\n");
printf(" %.6f %.6f %.6f %.6f %.6f %.6f %.6f %.6f %.6f\n\n", f_AA_MM, f_AA_Mm, f_AA_mm, f_Aa_MM, f_Aa_Mm, f_Aa_mm, f_aa_MM, f_aa_Mm, f_aa_mm);
if (male > threshold && female > threshold && inconstant > threshold)
{
printf("Final state: SSD\n");
} else if (male > threshold && female > threshold) {
printf("Final state: DIO\n");
} else if (female > threshold && inconstant > threshold) {
printf("Final state: PGD\n");
} else if (male > threshold && inconstant > threshold) {
printf("Final state: PAD\n");
} else if (inconstant > threshold) {
printf("Final state: INC\n");
} else {
printf("Final state: ???\n");
}
}
return 0;
}
