void RTTIBuilder::push_void_array(llvm::Constant* CI, Type* valtype, Dsymbol* mangle_sym)
{
std::string initname(mangle_sym->mangle());
initname.append(".rtti.voidarr.data");
LLGlobalVariable* G = new llvm::GlobalVariable(
*gIR->module, CI->getType(), true, TYPEINFO_LINKAGE_TYPE, CI, initname);
G->setAlignment(valtype->alignsize());
push_void_array(getTypePaddedSize(CI->getType()), G);
}
LLGlobalVariable * IrStruct::getClassInfoSymbol()
{
if (classInfo)
return classInfo;
// create the initZ symbol
std::string initname("_D");
initname.append(aggrdecl->mangle());
if (aggrdecl->isInterfaceDeclaration())
initname.append("11__InterfaceZ");
else
initname.append("7__ClassZ");
llvm::GlobalValue::LinkageTypes _linkage = DtoExternalLinkage(aggrdecl);
ClassDeclaration* cinfo = ClassDeclaration::classinfo;
DtoType(cinfo->type);
IrTypeClass* tc = stripModifiers(cinfo->type)->irtype->isClass();
assert(tc && "invalid ClassInfo type");
// classinfos cannot be constants since they're used as locks for synchronized
classInfo = new llvm::GlobalVariable(
*gIR->module, tc->getMemoryLLType(), false, _linkage, NULL, initname);
#if USE_METADATA
// Generate some metadata on this ClassInfo if it's for a class.
ClassDeclaration* classdecl = aggrdecl->isClassDeclaration();
if (classdecl && !aggrdecl->isInterfaceDeclaration()) {
// Gather information
LLType* type = DtoType(aggrdecl->type);
LLType* bodyType = llvm::cast<LLPointerType>(type)->getElementType();
bool hasDestructor = (classdecl->dtor != NULL);
bool hasCustomDelete = (classdecl->aggDelete != NULL);
// Construct the fields
MDNodeField* mdVals[CD_NumFields];
mdVals[CD_BodyType] = llvm::UndefValue::get(bodyType);
mdVals[CD_Finalize] = LLConstantInt::get(LLType::getInt1Ty(gIR->context()), hasDestructor);
mdVals[CD_CustomDelete] = LLConstantInt::get(LLType::getInt1Ty(gIR->context()), hasCustomDelete);
// Construct the metadata and insert it into the module.
llvm::SmallString<64> name;
llvm::NamedMDNode* node = gIR->module->getOrInsertNamedMetadata(
llvm::Twine(CD_PREFIX, initname).toStringRef(name));
node->addOperand(llvm::MDNode::get(gIR->context(),
llvm::makeArrayRef(mdVals, CD_NumFields)));
}
#endif // USE_METADATA
return classInfo;
}
void RTTIBuilder::push_void_array(llvm::Constant *CI, Type *valtype,
Dsymbol *mangle_sym) {
std::string initname(mangle(mangle_sym));
initname.append(".rtti.voidarr.data");
const LinkageWithCOMDAT lwc(TYPEINFO_LINKAGE_TYPE, supportsCOMDAT());
auto G = new LLGlobalVariable(gIR->module, CI->getType(), true,
lwc.first, CI, initname);
setLinkage(lwc, G);
G->setAlignment(DtoAlignment(valtype));
push_void_array(getTypeAllocSize(CI->getType()), G);
}
void RTTIBuilder::push_array(llvm::Constant * CI, uint64_t dim, Type* valtype, Dsymbol * mangle_sym)
{
std::string tmpStr(valtype->arrayOf()->toChars());
tmpStr.erase( remove( tmpStr.begin(), tmpStr.end(), '[' ), tmpStr.end() );
tmpStr.erase( remove( tmpStr.begin(), tmpStr.end(), ']' ), tmpStr.end() );
tmpStr.append("arr");
std::string initname(mangle_sym?mangle_sym->mangle():".ldc");
initname.append(".rtti.");
initname.append(tmpStr);
initname.append(".data");
LLGlobalVariable* G = new llvm::GlobalVariable(
*gIR->module, CI->getType(), true, TYPEINFO_LINKAGE_TYPE, CI, initname);
G->setAlignment(valtype->alignsize());
push_array(dim, DtoBitCast(G, DtoType(valtype->pointerTo())));
}
LLGlobalVariable * IrStruct::getVtblSymbol()
{
if (vtbl)
return vtbl;
// create the initZ symbol
std::string initname("_D");
initname.append(aggrdecl->mangle());
initname.append("6__vtblZ");
llvm::GlobalValue::LinkageTypes _linkage = DtoExternalLinkage(aggrdecl);
LLType* vtblTy = stripModifiers(type)->irtype->isClass()->getVtbl();
vtbl = new llvm::GlobalVariable(
*gIR->module, vtblTy, true, _linkage, NULL, initname);
return vtbl;
}
LLGlobalVariable * IrAggr::getInitSymbol()
{
if (init)
return init;
// create the initZ symbol
std::string initname("_D");
initname.append(mangle(aggrdecl));
initname.append("6__initZ");
init = getOrCreateGlobal(aggrdecl->loc,
gIR->module, init_type, true, llvm::GlobalValue::ExternalLinkage, NULL, initname);
// set alignment
init->setAlignment(type->alignsize());
StructDeclaration *sd = aggrdecl->isStructDeclaration();
if (sd && sd->alignment != STRUCTALIGN_DEFAULT)
init->setAlignment(sd->alignment);
return init;
}
void RTTIBuilder::push_array(llvm::Constant *CI, uint64_t dim, Type *valtype,
Dsymbol *mangle_sym) {
std::string tmpStr(valtype->arrayOf()->toChars());
tmpStr.erase(remove(tmpStr.begin(), tmpStr.end(), '['), tmpStr.end());
tmpStr.erase(remove(tmpStr.begin(), tmpStr.end(), ']'), tmpStr.end());
tmpStr.append("arr");
std::string initname(mangle_sym ? mangle(mangle_sym) : ".ldc");
initname.append(".rtti.");
initname.append(tmpStr);
initname.append(".data");
const LinkageWithCOMDAT lwc(TYPEINFO_LINKAGE_TYPE, supportsCOMDAT());
auto G = new LLGlobalVariable(gIR->module, CI->getType(), true,
lwc.first, CI, initname);
setLinkage(lwc, G);
G->setAlignment(DtoAlignment(valtype));
push_array(dim, DtoBitCast(G, DtoType(valtype->pointerTo())));
}
void inputdata()
{ /* read species data */
long i, j, k, l, m, m0, n, p;
double sum;
if (printdata) {
fprintf(outfile, "\nName");
if (contchars)
fprintf(outfile, " Phenotypes\n");
else
fprintf(outfile, " Gene Frequencies\n");
fprintf(outfile, "----");
if (contchars)
fprintf(outfile, " ----------\n");
else
fprintf(outfile, " ---- -----------\n");
putc('\n', outfile);
if (!contchars) {
for (j = 1; j <= nmlngth - 8; j++)
putc(' ', outfile);
fprintf(outfile, "locus:");
p = 1;
for (j = 1; j <= loci; j++) {
if (all)
n = alleles[j - 1];
else
n = alleles[j - 1] - 1;
for (k = 1; k <= n; k++) {
fprintf(outfile, "%10ld", j);
if (p % 6 == 0 && (all || p < df)) {
putc('\n', outfile);
for (l = 1; l <= nmlngth - 2; l++)
putc(' ', outfile);
}
p++;
}
}
fprintf(outfile, "\n\n");
}
}
for (i = 0; i < spp; i++) {
scan_eoln(infile);
initname(i);
if (printdata)
for (j = 0; j < nmlngth; j++)
putc(nayme[i][j], outfile);
m = 1;
p = 1;
for (j = 1; j <= loci; j++) {
m0 = m;
sum = 0.0;
if (contchars)
n = 1;
else if (all)
n = alleles[j - 1];
else
n = alleles[j - 1] - 1;
for (k = 1; k <= n; k++) {
if (eoln(infile))
scan_eoln(infile);
if (fscanf(infile, "%lf", &x[i][m - 1]) != 1) {
printf("ERROR: unable to read allele frequency"
"for species %ld, locus %ld\n", i+1, j);
exxit(-1);
}
sum += x[i][m - 1];
if (!contchars && x[i][m - 1] < 0.0) {
printf("\n\nERROR: locus %ld in species %ld: an allele", j, i+1);
printf(" frequency is negative\n");
exxit(-1);
}
if (printdata) {
fprintf(outfile, "%10.5f", x[i][m - 1]);
if (p % 6 == 0 && (all || p < df)) {
putc('\n', outfile);
for (l = 1; l <= nmlngth; l++)
putc(' ', outfile);
}
}
p++;
m++;
}
if (all && !contchars) {
if (fabs(sum - 1.0) > epsilon2) {
printf(
"\n\nERROR: Locus %ld in species %ld: frequencies do not add up to 1\n",
j, i + 1);
printf("\nFrequencies are:\n");
for (l = m0; l <= m-3; l++)
printf("%f+", x[i][l]);
printf("%f = %f\n\n", x[i][m-2], sum);
exxit(-1);
} else {
for (l = 0; l <= m-2; l++)
x[i][l] /= sum;
}
}
if (!all && !contchars) {
x[i][m-1] = 1.0 - sum;
if (x[i][m-1] < 0.0) {
if (x[i][m-1] > -epsilon2) {
for (l = 0; l <= m-2; l++)
x[i][l] /= sum;
x[i][m-1] = 0.0;
} else {
printf("\n\nERROR: Locus %ld in species %ld: ", j, i + 1);
printf("frequencies add up to more than 1\n");
printf("\nFrequencies are:\n");
for (l = m0-1; l <= m-3; l++)
printf("%f+", x[i][l]);
printf("%f = %f\n\n", x[i][m-2], sum);
exxit(-1);
}
}
m++;
}
}
if (printdata)
putc('\n', outfile);
}
scan_eoln(infile);
if (printdata)
putc('\n', outfile);
} /* inputdata */
void inputdata(boolean replicates, boolean printdata, boolean lower,
boolean upper, vector *x, intvector *reps)
{
/* read in distance matrix */
/* used in fitch & neighbor */
long i=0, j=0, k=0, columns=0;
boolean skipit=false, skipother=false;
if (replicates)
columns = 4;
else
columns = 6;
if (printdata) {
fprintf(outfile, "\nName Distances");
if (replicates)
fprintf(outfile, " (replicates)");
fprintf(outfile, "\n---- ---------");
if (replicates)
fprintf(outfile, "-------------");
fprintf(outfile, "\n\n");
}
for (i = 0; i < spp; i++) {
x[i][i] = 0.0;
scan_eoln(infile);
initname(i);
for (j = 0; j < spp; j++) {
skipit = ((lower && j + 1 >= i + 1) || (upper && j + 1 <= i + 1));
skipother = ((lower && i + 1 >= j + 1) || (upper && i + 1 <= j + 1));
if (!skipit) {
if (eoln(infile))
scan_eoln(infile);
if (fscanf(infile, "%lf", &x[i][j]) != 1) {
printf("The infile is of the wrong type\n");
exxit(-1);
}
if (replicates) {
if (eoln(infile))
scan_eoln(infile);
if (fscanf(infile, "%ld", &reps[i][j]) != 1) {
printf("The infile is of the wrong type\n");
exxit(-1);
}
} else
reps[i][j] = 1;
}
if (!skipit && skipother) {
x[j][i] = x[i][j];
reps[j][i] = reps[i][j];
}
if ((i == j) && (fabs(x[i][j]) > 0.000000001)) {
printf("\nERROR: diagonal element of row %ld of distance matrix ", i+1);
printf("is not zero.\n");
printf(" Is it a distance matrix?\n\n");
exxit(-1);
}
if ((j < i) && (fabs(x[i][j]-x[j][i]) > 0.000000001)) {
printf("ERROR: distance matrix is not symmetric:\n");
printf(" (%ld,%ld) element and (%ld,%ld) element are unequal.\n",
i+1, j+1, j+1, i+1);
printf(" They are %10.6f and %10.6f, respectively.\n",
x[i][j], x[j][i]);
printf(" Is it a distance matrix?\n\n");
exxit(-1);
}
}
}
scan_eoln(infile);
if (!printdata)
return;
for (i = 0; i < spp; i++) {
for (j = 0; j < nmlngth; j++)
putc(nayme[i][j], outfile);
putc(' ', outfile);
for (j = 1; j <= spp; j++) {
fprintf(outfile, "%10.5f", x[i][j - 1]);
if (replicates)
fprintf(outfile, " (%3ld)", reps[i][j - 1]);
if (j % columns == 0 && j < spp) {
putc('\n', outfile);
for (k = 1; k <= nmlngth + 1; k++)
putc(' ', outfile);
}
}
putc('\n', outfile);
}
putc('\n', outfile);
} /* inputdata */
int
main(int argc, char **argv) {
char *algname = NULL, *classname = NULL;
char *filename = NULL, *dir = NULL, *namestr;
char *lookaside = NULL;
char *endp;
int ch;
unsigned int dtype = DNS_DSDIGEST_SHA1;
isc_boolean_t both = ISC_TRUE;
isc_boolean_t usekeyset = ISC_FALSE;
isc_boolean_t showall = ISC_FALSE;
isc_result_t result;
isc_log_t *log = NULL;
isc_entropy_t *ectx = NULL;
dns_rdataset_t rdataset;
dns_rdata_t rdata;
dns_rdata_init(&rdata);
if (argc == 1)
usage();
result = isc_mem_create(0, 0, &mctx);
if (result != ISC_R_SUCCESS)
fatal("out of memory");
dns_result_register();
isc_commandline_errprint = ISC_FALSE;
while ((ch = isc_commandline_parse(argc, argv,
"12Aa:c:d:Ff:K:l:sv:h")) != -1) {
switch (ch) {
case '1':
dtype = DNS_DSDIGEST_SHA1;
both = ISC_FALSE;
break;
case '2':
dtype = DNS_DSDIGEST_SHA256;
both = ISC_FALSE;
break;
case 'A':
showall = ISC_TRUE;
break;
case 'a':
algname = isc_commandline_argument;
both = ISC_FALSE;
break;
case 'c':
classname = isc_commandline_argument;
break;
case 'd':
fprintf(stderr, "%s: the -d option is deprecated; "
"use -K\n", program);
/* fall through */
case 'K':
dir = isc_commandline_argument;
if (strlen(dir) == 0U)
fatal("directory must be non-empty string");
break;
case 'f':
filename = isc_commandline_argument;
break;
case 'l':
lookaside = isc_commandline_argument;
if (strlen(lookaside) == 0U)
fatal("lookaside must be a non-empty string");
break;
case 's':
usekeyset = ISC_TRUE;
break;
case 'v':
verbose = strtol(isc_commandline_argument, &endp, 0);
if (*endp != '\0')
fatal("-v must be followed by a number");
break;
case 'F':
/* Reserved for FIPS mode */
/* FALLTHROUGH */
case '?':
if (isc_commandline_option != '?')
fprintf(stderr, "%s: invalid argument -%c\n",
program, isc_commandline_option);
/* FALLTHROUGH */
case 'h':
usage();
default:
fprintf(stderr, "%s: unhandled option -%c\n",
program, isc_commandline_option);
exit(1);
}
}
if (algname != NULL) {
if (strcasecmp(algname, "SHA1") == 0 ||
strcasecmp(algname, "SHA-1") == 0)
dtype = DNS_DSDIGEST_SHA1;
else if (strcasecmp(algname, "SHA256") == 0 ||
strcasecmp(algname, "SHA-256") == 0)
dtype = DNS_DSDIGEST_SHA256;
#ifdef HAVE_OPENSSL_GOST
else if (strcasecmp(algname, "GOST") == 0)
dtype = DNS_DSDIGEST_GOST;
#endif
else if (strcasecmp(algname, "SHA384") == 0 ||
strcasecmp(algname, "SHA-384") == 0)
dtype = DNS_DSDIGEST_SHA384;
else
fatal("unknown algorithm %s", algname);
}
rdclass = strtoclass(classname);
if (usekeyset && filename != NULL)
fatal("cannot use both -s and -f");
/* When not using -f, -A is implicit */
if (filename == NULL)
showall = ISC_TRUE;
if (argc < isc_commandline_index + 1 && filename == NULL)
fatal("the key file name was not specified");
if (argc > isc_commandline_index + 1)
fatal("extraneous arguments");
if (ectx == NULL)
setup_entropy(mctx, NULL, &ectx);
result = isc_hash_create(mctx, ectx, DNS_NAME_MAXWIRE);
if (result != ISC_R_SUCCESS)
fatal("could not initialize hash");
result = dst_lib_init(mctx, ectx,
ISC_ENTROPY_BLOCKING | ISC_ENTROPY_GOODONLY);
if (result != ISC_R_SUCCESS)
fatal("could not initialize dst: %s",
isc_result_totext(result));
isc_entropy_stopcallbacksources(ectx);
setup_logging(verbose, mctx, &log);
dns_rdataset_init(&rdataset);
if (usekeyset || filename != NULL) {
if (argc < isc_commandline_index + 1 && filename != NULL) {
/* using zone name as the zone file name */
namestr = filename;
} else
namestr = argv[isc_commandline_index];
result = initname(namestr);
if (result != ISC_R_SUCCESS)
fatal("could not initialize name %s", namestr);
if (usekeyset)
result = loadkeyset(dir, &rdataset);
else
result = loadsetfromfile(filename, &rdataset);
if (result != ISC_R_SUCCESS)
fatal("could not load DNSKEY set: %s\n",
isc_result_totext(result));
for (result = dns_rdataset_first(&rdataset);
result == ISC_R_SUCCESS;
result = dns_rdataset_next(&rdataset)) {
dns_rdata_init(&rdata);
dns_rdataset_current(&rdataset, &rdata);
if (verbose > 2)
logkey(&rdata);
if (both) {
emit(DNS_DSDIGEST_SHA1, showall, lookaside,
&rdata);
emit(DNS_DSDIGEST_SHA256, showall, lookaside,
&rdata);
} else
emit(dtype, showall, lookaside, &rdata);
}
} else {
unsigned char key_buf[DST_KEY_MAXSIZE];
loadkey(argv[isc_commandline_index], key_buf,
DST_KEY_MAXSIZE, &rdata);
if (both) {
emit(DNS_DSDIGEST_SHA1, showall, lookaside, &rdata);
emit(DNS_DSDIGEST_SHA256, showall, lookaside, &rdata);
} else
emit(dtype, showall, lookaside, &rdata);
}
if (dns_rdataset_isassociated(&rdataset))
dns_rdataset_disassociate(&rdataset);
cleanup_logging(&log);
dst_lib_destroy();
isc_hash_destroy();
cleanup_entropy(&ectx);
dns_name_destroy();
if (verbose > 10)
isc_mem_stats(mctx, stdout);
isc_mem_destroy(&mctx);
fflush(stdout);
if (ferror(stdout)) {
fprintf(stderr, "write error\n");
return (1);
} else
return (0);
}
void seqboot_inputdata()
{
/* input the names and sequences for each species */
long i, j, k, l, m, n, basesread, basesnew=0;
double x;
Char charstate;
boolean allread, done;
nodep = matrix_char_new(spp, sites);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 37)
j = 37;
interleaved = (interleaved && ((data == seqs) || (data == restsites)));
basesread = 0;
allread = false;
while (!allread) {
/* eat white space -- if the separator line has spaces on it*/
do {
charstate = gettc(infile);
} while (charstate == ' ' || charstate == '\t');
ungetc(charstate, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp) {
if ((interleaved && basesread == 0) || !interleaved)
initname(i-1);
j = interleaved ? basesread : 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) ||eoff(infile))) {
charstate = gettc(infile);
if (charstate == '\n' || charstate == '\t')
charstate = ' ';
if (charstate == ' ' ||
(data == seqs && charstate >= '0' && charstate <= '9'))
continue;
uppercase(&charstate);
j++;
if (charstate == '.')
charstate = nodep[0][j-1];
nodep[i-1][j-1] = charstate;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
basesnew = j;
scan_eoln(infile);
if ((interleaved && j != basesnew) || ((!interleaved) && j != sites)) {
printf("\n\nERROR: sequences out of alignment at site %ld", j+1);
printf(" of species %ld\n\n", i);
exxit(-1);
}
i++;
}
if (interleaved) {
basesread = basesnew;
allread = (basesread == sites);
} else
allread = (i > spp);
}
if (!printdata)
return;
} /* seqboot_inputdata */
void seqboot_inputdata()
{
/* input the names and sequences for each species */
long i, j, k, l, m, n, basesread, basesnew=0;
double x;
Char charstate;
boolean allread, done;
if (data == genefreqs) {
nodef = matrix_double_new(spp, sites);
} else {
nodep = matrix_char_new(spp, sites);
}
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 37)
j = 37;
if (printdata) {
fprintf(outfile, "\nBootstrapping algorithm, version %s\n\n\n",VERSION);
if (bootstrap) {
if (blocksize > 1) {
if (regular)
fprintf(outfile, "Block-bootstrap with block size %ld\n\n", blocksize);
else
fprintf(outfile, "Partial (%2.0f%%) block-bootstrap with block size %ld\n\n",
100*fracsample, blocksize);
} else {
if (regular)
fprintf(outfile, "Bootstrap\n\n");
else
fprintf(outfile, "Partial (%2.0f%%) bootstrap\n\n", 100*fracsample);
}
} else {
if (jackknife) {
if (regular)
fprintf(outfile, "Delete-half Jackknife\n\n");
else
fprintf(outfile, "Delete-%2.0f%% Jackknife\n\n", 100*(1.0-fracsample));
} else {
if (permute) {
fprintf(outfile, "Species order permuted separately for each");
if (data == genefreqs)
fprintf(outfile, " locus\n\n");
if (data == seqs)
fprintf(outfile, " site\n\n");
if (data == morphology)
fprintf(outfile, " character\n\n");
if (data == restsites)
fprintf(outfile, " site\n\n");
}
else {
if (ild) {
if (data == genefreqs)
fprintf(outfile, "Locus");
if (data == seqs)
fprintf(outfile, "Site");
if (data == morphology)
fprintf(outfile, "Character");
if (data == restsites)
fprintf(outfile, "Site");
fprintf(outfile, " order permuted\n\n");
} else {
if (lockhart)
if (data == genefreqs)
fprintf(outfile, "Locus");
if (data == seqs)
fprintf(outfile, "Site");
if (data == morphology)
fprintf(outfile, "Character");
if (data == restsites)
fprintf(outfile, "Site");
fprintf(outfile, " order permuted separately for each species\n\n");
}
}
}
}
if (data == genefreqs)
fprintf(outfile, "%3ld species, %3ld loci\n\n", spp, loci);
else {
fprintf(outfile, "%3ld species, ", spp);
if (data == seqs)
fprintf(outfile, "%3ld sites\n\n", sites);
else if (data == morphology)
fprintf(outfile, "%3ld characters\n\n", sites);
else if (data == restsites)
fprintf(outfile, "%3ld sites\n\n", sites);
}
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Data\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "----\n\n");
}
interleaved = (interleaved && ((data == seqs) || (data == restsites)));
if (data == genefreqs) {
for (i = 1; i <= (spp); i++) {
initname(i - 1);
j = 1;
while (j <= sites && !eoff(infile)) {
if (eoln(infile))
scan_eoln(infile);
if ( fscanf(infile, "%lf", &x) != 1) {
printf("ERROR: Invalid value for locus %ld of species %ld\n", j, i);
exxit(-1);
} else if ((unsigned)x > 1.0) {
printf("GENE FREQ OUTSIDE [0,1] in species %ld\n", i);
exxit(-1);
} else {
nodef[i - 1][j - 1] = x;
j++;
}
}
scan_eoln(infile);
}
return;
}
basesread = 0;
allread = false;
while (!allread) {
/* eat white space -- if the separator line has spaces on it*/
do {
charstate = gettc(infile);
} while (charstate == ' ' || charstate == '\t');
ungetc(charstate, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp) {
if ((interleaved && basesread == 0) || !interleaved)
initname(i-1);
j = interleaved ? basesread : 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) ||eoff(infile))) {
charstate = gettc(infile);
if (charstate == '\n' || charstate == '\t')
charstate = ' ';
if (charstate == ' ' ||
(data == seqs && charstate >= '0' && charstate <= '9'))
continue;
uppercase(&charstate);
j++;
if (charstate == '.')
charstate = nodep[0][j-1];
nodep[i-1][j-1] = charstate;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
basesnew = j;
scan_eoln(infile);
if ((interleaved && j != basesnew) || ((!interleaved) && j != sites)){
printf("\n\nERROR: sequences out of alignment at site %ld", j+1);
printf(" of species %ld\n\n", i);
exxit(-1);}
i++;
}
if (interleaved) {
basesread = basesnew;
allread = (basesread == sites);
} else
allread = (i > spp);
}
if (!printdata)
return;
if (data == genefreqs)
m = (sites - 1) / 8 + 1;
else
m = (sites - 1) / 60 + 1;
for (i = 1; i <= m; i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
if (data == genefreqs)
l = i * 8;
else
l = i * 60;
if (l > sites)
l = sites;
if (data == genefreqs)
n = (i - 1) * 8;
else
n = (i - 1) * 60;
for (k = n; k < l; k++) {
if (data == genefreqs)
fprintf(outfile, "%8.5f", nodef[j][k]);
else {
if (j + 1 > 1 && nodep[j][k] == nodep[0][k])
charstate = '.';
else
charstate = nodep[j][k];
putc(charstate, outfile);
if ((k + 1) % 10 == 0 && (k + 1) % 60 != 0)
putc(' ', outfile);
}
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
} /* seqboot_inputdata */
void restdist_inputdata()
{
/* read the species and sites data */
long i, j, k, l, sitesread = 0, sitesnew = 0;
Char ch;
boolean allread, done;
if (printdata)
putc('\n', outfile);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 39)
j = 39;
if (printdata) {
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Sites\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "-----\n\n");
}
sitesread = 0;
allread = false;
while (!(allread)) {
allread = true;
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
i = 1;
while (i <= spp ) {
if ((interleaved && sitesread == 0) || !interleaved)
initname(i - 1);
if (interleaved)
j = sitesread;
else
j = 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) || eoff(infile))) {
ch = getc(infile);
if (ch == '\n')
ch = ' ';
if (ch == ' ')
continue;
uppercase(&ch);
if (ch != '1' && ch != '0' && ch != '+' && ch != '-' && ch != '?') {
printf(" WARNING -- BAD SYMBOL %c",ch);
printf(" AT POSITION %5ld OF SPECIES %3ld\n",j,i);
exxit(-1);
}
if (ch == '1')
ch = '+';
if (ch == '0')
ch = '-';
j++;
y[i - 1][j - 1] = ch;
}
if (interleaved)
continue;
if (j < sites) {
fscanf(infile, "%*[^\n]");
getc(infile);
} else if (j == sites)
done = true;
}
if (interleaved && i == 1)
sitesnew = j;
fscanf(infile, "%*[^\n]");
getc(infile);
if ((interleaved && j != sitesnew ) || ((!interleaved) && j != sites)){
printf("ERROR: SEQUENCES OUT OF ALIGNMENT\n");
exxit(-1);}
i++;
}
if (interleaved) {
sitesread = sitesnew;
allread = (sitesread == sites);
} else
allread = (i > spp);
}
if (printdata) {
for (i = 1; i <= ((sites - 1) / 60 + 1); i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
l = i * 60;
if (l > sites)
l = sites;
for (k = (i - 1) * 60 + 1; k <= l; k++) {
putc(y[j][k - 1], outfile);
if (k % 10 == 0 && k % 60 != 0)
putc(' ', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
} /* restdist_inputdata */
void inputdata2(pointptr2 treenode)
{
/* input the names and character state data for species */
/* used in Mix & Penny */
long i, j, l;
char k;
Char charstate;
/* possible states are '0', '1', 'P', 'B', and '?' */
if (printdata)
headings(chars, "Characters", "----------");
for (i = 0; i < (chars); i++)
extras[i] = 0;
for (i = 1; i <= spp; i++) {
initname(i-1);
if (printdata) {
for (j = 0; j < nmlngth; j++)
putc(nayme[i - 1][j], outfile);
}
fprintf(outfile, " ");
for (j = 0; j < (words); j++) {
treenode[i - 1]->fulstte1[j] = 0;
treenode[i - 1]->fulstte0[j] = 0;
treenode[i - 1]->empstte1[j] = 0;
treenode[i - 1]->empstte0[j] = 0;
}
for (j = 1; j <= (chars); j++) {
k = (j - 1) % bits + 1;
l = (j - 1) / bits + 1;
do {
if (eoln(infile))
scan_eoln(infile);
charstate = gettc(infile);
if (charstate == '\n' || charstate == '\t')
charstate = ' ';
} while (charstate == ' ');
if (charstate == 'b') charstate = 'B';
if (charstate == 'p') charstate = 'P';
if (charstate != '0' && charstate != '1' && charstate != '?' &&
charstate != 'P' && charstate != 'B') {
printf("\n\nERROR: Bad character state: %c ",charstate);
printf("at character %ld of species %ld\n\n", j, i);
exxit(-1);
}
if (printdata) {
newline(outfile, j, 55, nmlngth + 3);
putc(charstate, outfile);
if (j % 5 == 0)
putc(' ', outfile);
}
if (charstate == '1') {
treenode[i-1]->fulstte1[l-1] =
((long)treenode[i-1]->fulstte1[l-1]) | (1L << k);
treenode[i-1]->empstte1[l-1] =
treenode[i-1]->fulstte1[l-1];
}
if (charstate == '0') {
treenode[i-1]->fulstte0[l-1] =
((long)treenode[i-1]->fulstte0[l-1]) | (1L << k);
treenode[i-1]->empstte0[l-1] =
treenode[i-1]->fulstte0[l-1];
}
if (charstate == 'P' || charstate == 'B')
extras[j-1] += weight[j-1];
}
scan_eoln(infile);
if (printdata)
putc('\n', outfile);
}
fprintf(outfile, "\n\n");
} /* inputdata2 */
void inputdata(pointptr treenode,boolean dollo,boolean printdata,FILE *outfile)
{
/* input the names and character state data for species */
/* used in Dollop, Dolpenny, Dolmove, & Move */
long i, j, l;
char k;
Char charstate;
/* possible states are '0', '1', 'P', 'B', and '?' */
if (printdata)
headings(chars, "Characters", "----------");
for (i = 0; i < (chars); i++)
extras[i] = 0;
for (i = 1; i <= spp; i++) {
initname(i-1);
if (printdata) {
for (j = 0; j < nmlngth; j++)
putc(nayme[i - 1][j], outfile);
fprintf(outfile, " ");
}
for (j = 0; j < (words); j++) {
treenode[i - 1]->stateone[j] = 0;
treenode[i - 1]->statezero[j] = 0;
}
for (j = 1; j <= (chars); j++) {
k = (j - 1) % bits + 1;
l = (j - 1) / bits + 1;
do {
if (eoln(infile))
scan_eoln(infile);
charstate = gettc(infile);
} while (charstate == ' ' || charstate == '\t');
if (charstate == 'b')
charstate = 'B';
if (charstate == 'p')
charstate = 'P';
if (charstate != '0' && charstate != '1' && charstate != '?' &&
charstate != 'P' && charstate != 'B') {
printf("\n\nERROR: Bad character state: %c ",charstate);
printf("at character %ld of species %ld\n\n", j, i);
exxit(-1);
}
if (printdata) {
newline(outfile, j, 55, nmlngth + 3);
putc(charstate, outfile);
if (j % 5 == 0)
putc(' ', outfile);
}
if (charstate == '1')
treenode[i - 1]->stateone[l - 1] =
((long)treenode[i - 1]->stateone[l - 1]) | (1L << k);
if (charstate == '0')
treenode[i - 1]->statezero[l - 1] =
((long)treenode[i - 1]->statezero[l - 1]) | (1L << k);
if (charstate == 'P' || charstate == 'B') {
if (dollo)
extras[j - 1] += weight[j - 1];
else {
treenode[i - 1]->stateone[l - 1] =
((long)treenode[i - 1]->stateone[l - 1]) | (1L << k);
treenode[i - 1]->statezero[l - 1] =
((long)treenode[i - 1]->statezero[l - 1]) | (1L << k);
}
}
}
scan_eoln(infile);
if (printdata)
putc('\n', outfile);
}
if (printdata)
fprintf(outfile, "\n\n");
} /* inputdata */
void restdist_inputdata()
{
/* read the species and sites data */
long i, j, k, l, sitesread = 0, sitesnew = 0;
Char ch;
boolean allread, done;
if (printdata)
putc('\n', outfile);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 39)
j = 39;
if (printdata) {
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Sites\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "-----\n\n");
}
sitesread = 0;
allread = false;
while (!(allread)) {
/* eat white space -- if the separator line has spaces on it*/
do {
ch = gettc(infile);
} while (ch == ' ' || ch == '\t');
ungetc(ch, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp ) {
if ((interleaved && sitesread == 0) || !interleaved)
initname(i - 1);
if (interleaved)
j = sitesread;
else
j = 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) || eoff(infile))) {
ch = gettc(infile);
if (ch == '\n' || ch == '\t')
ch = ' ';
if (ch == ' ')
continue;
uppercase(&ch);
if (ch != '1' && ch != '0' && ch != '+' && ch != '-' && ch != '?') {
printf(" ERROR -- Bad symbol %c",ch);
printf(" at position %ld of species %ld\n", j+1, i);
exxit(-1);
}
if (ch == '1')
ch = '+';
if (ch == '0')
ch = '-';
j++;
y[i - 1][j - 1] = ch;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
sitesnew = j;
scan_eoln(infile);
if ((interleaved && j != sitesnew ) || ((!interleaved) && j != sites)){
printf("ERROR: SEQUENCES OUT OF ALIGNMENT\n");
exxit(-1);}
i++;
}
if (interleaved) {
sitesread = sitesnew;
allread = (sitesread == sites);
} else
allread = (i > spp);
}
if (printdata) {
for (i = 1; i <= ((sites - 1) / 60 + 1); i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
l = i * 60;
if (l > sites)
l = sites;
for (k = (i - 1) * 60 + 1; k <= l; k++) {
putc(y[j][k - 1], outfile);
if (k % 10 == 0 && k % 60 != 0)
putc(' ', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
} /* restdist_inputdata */
