/**
Turn a variant into an S object with a special class
such as COMDate or COMCurrency which is simply an extension
of numeric.
*/
SEXP
numberFromVariant(VARIANT *var, VARTYPE type)
{
SEXP ans;
SEXP klass;
const char *tmpName = NULL;
switch(type) {
case VT_CY:
tmpName = "COMCurrency";
break;
case VT_DATE:
tmpName = (char *) "COMDate";
break;
case VT_HRESULT:
tmpName = (char *) "HResult";
break;
case VT_DECIMAL:
tmpName = (char *) "COMDecimal";
break;
default:
PROBLEM "numberFromVariant called with unsupported variant type."
ERROR;
}
PROTECT(klass = MAKE_CLASS(tmpName));
PROTECT(ans = NEW(klass));
ans = R_do_slot_assign(ans, mkString(".Data"), R_scalarReal(V_R8(var)));
// SET_SLOT(ans, Rf_install(".Data"), R_scalarReal(V_R8(var)));
UNPROTECT(2);
return(ans);
}
SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
const SEXP Diploid, const SEXP Fields,
const SEXP Codes, const SEXP Threshold, const SEXP Lower,
const SEXP Sep, const SEXP Comment, const SEXP Skip,
const SEXP Simplify, const SEXP Verbose,
const SEXP In_order, const SEXP Every){
/* Process arguments */
if (TYPEOF(Verbose)!=LGLSXP)
error("Argument type error: Verbose");
if (length(Verbose)>1)
warning("Only first element of argument used: Verbose");
int verbose = *INTEGER(Verbose);
if (TYPEOF(In_order)!=LGLSXP)
error("Argument type error: In_order");
if (length(In_order)>1)
warning("Only first element of argument used: In_order");
int in_order = *INTEGER(In_order);
if (TYPEOF(Filenames)!=STRSXP)
error("Argument type error: Filenames");
int Nfile = length(Filenames);
int Nsample=0;
if (TYPEOF(Sample_id)==STRSXP)
Nsample = length(Sample_id);
else if (TYPEOF(Sample_id)!=NILSXP)
error("Argument type error: Sample_id");
int Nsnp=0;
if (TYPEOF(Snp_id)==STRSXP)
Nsnp = length(Snp_id);
else if (TYPEOF(Snp_id)!=NILSXP)
error("Argument type error: Snp_id");
/* file is 1 = sample, 2 = snp, 0 = irrelevant */
int file_is = 0;
if (!Nsample) {
if (Nsnp) {
Nsample = Nfile;
Rprintf("Each file is assumed to concern a single sample\n");
Rprintf("(Sample IDs are assumed to be included in filenames)\n");
file_is = 1;
}
else
error("No sample or SNP IDs specified");
}
else if (!Nsnp) {
Nsnp = Nfile;
Rprintf("Each file is assumed to concern a single SNP\n");
Rprintf("(SNP IDs are assumed to be included in filenames)\n");
file_is = 2;
}
/* If not in order, set up hash tables */
index_db sample_index = NULL;
index_db snp_index = NULL;
if (!in_order) {
if (file_is != 1)
sample_index = create_name_index(Sample_id);
if (file_is != 2)
snp_index = create_name_index(Snp_id);
}
int *diploid=NULL;
if (TYPEOF(Diploid)==LGLSXP) {
if (length(Diploid)!=Nsample)
error("Argument length error: diploid argument");
diploid = LOGICAL(Diploid);
}
else if (TYPEOF(Diploid)!=NILSXP)
error("Argument type error: diploid argument");
if (TYPEOF(Fields)!=INTSXP)
error("Argument type error: Fields");
int *fields = INTEGER(Fields);
int fsamp=0, fsnp=0, fgt=0, fa1=0, fa2=0, fconf=0;
SEXP Fnames = getAttrib(Fields, R_NamesSymbol);
if (TYPEOF(Fnames)==NILSXP)
error("Argument error: Fields argument has no names");
int fmax = 0;
int Nfield = length(Fields);
for (int i=0; i<Nfield; i++) {
const char *fname = CHAR(STRING_ELT(Fnames, i));
int fi = fields[i];
if (!strcmp(fname, "sample"))
fsamp = fi;
else if (!strcmp(fname, "snp"))
fsnp = fi;
else if (!strcmp(fname, "genotype"))
fgt = fi;
else if (!strcmp(fname, "allele1"))
fa1 = fi;
else if (!strcmp(fname, "allele2"))
fa2 = fi;
else if (!strcmp(fname, "confidence"))
fconf = fi;
else
error("Unrecognized input field name: %s", fname);
if (fi>fmax)
fmax = fi;
}
if (verbose) {
Rprintf("Reading one call per input line\n");
if (fsamp) {
Rprintf(" Sample id is in field %d", fsamp);
if (file_is==1)
Rprintf(" (ignored)\n");
else
Rprintf("\n");
}
if (fsnp) {
Rprintf(" SNP id is in field %d", fsnp);
if (file_is==2)
Rprintf(" (ignored)\n");
else
Rprintf("\n");
}
if (fgt)
Rprintf(" Genotype is in field %d\n", fgt);
if (fa1)
Rprintf(" Allele 1 is in field %d\n", fa1);
if (fa2)
Rprintf(" Allele 2 is in field %d\n", fa2);
if (fconf)
Rprintf(" Confidence score is in field %d\n", fconf);
}
if (file_is==1)
fsamp = 0;
else if (file_is==2)
fsnp = 0;
/* Allele or genotype coding? */
int gcoding;
if (fgt) {
if (fa1 || fa2)
error("Coding must be by genotype OR allele, not both");
gcoding = 1;
}
else {
if (!(fa1 && fa2))
error("No genotype or allele field(s) specified");
if (!(fa1 && fa2))
error("Field positions for both alleles must be specified");
gcoding = 0;
}
int nuc = 0;
if (TYPEOF(Codes)!=STRSXP)
error("Argument type error: Codes");
if (length(Codes)==1) {
SEXP Code = STRING_ELT(Codes, 0);
const char *code = CHAR(Code);
if (!strcmp(code, "nucleotide"))
nuc = 1;
else
error("Unrecognized coding: %s", code);
}
else {
int ncode = length(Codes);
if (gcoding) {
if (diploid) {
if (ncode!=5) {
if (ncode==3)
warning("Genotype coding for X: haploid genotypes are assumed to be coded as homozygous");
else
error("Genotype coding for X.snp: three or five genotype codes must be specified");
}
}
else {
if (ncode!=3)
error("Genotype coding: three genotype codes must be specified");
}
}
else {
if (ncode!=2)
error("Allele coding: two allele codes must be specified");
}
}
if (TYPEOF(Threshold)==NILSXP && !fconf)
error("Argument type error: no threshold argument");
if (TYPEOF(Threshold)!=REALSXP)
error("Argument type error: Threshold");
double threshold = *REAL(Threshold);
if (fconf && threshold==NA_REAL)
error("Confidence score is read but no threshold is set");
if (TYPEOF(Lower)!=LGLSXP)
error("Argument type error: Lower");
if (length(Lower)>1)
warning("Only first element of argument used: Lower");
int lower = *INTEGER(Lower);
char sep = ' ';
if (TYPEOF(Sep)==STRSXP) {
if (length(Sep)>1)
warning("Only first element of argument used: Sep");
const char *c = CHAR(STRING_ELT(Sep, 0));
if (strlen(c)>1)
warning("Only first character used: Sep");
sep = c[0];
}
else if (TYPEOF(Sep)!=NILSXP)
error("Argument type error: Sep");
char comment = (char) 0;
if (TYPEOF(Comment)==STRSXP) {
if (length(Sep)>1)
warning("Only first element of argument used: Comment");
const char *c = CHAR(STRING_ELT(Comment, 0));
if (strlen(c)>1)
warning("Only first character used: Comment");
comment = c[0];
}
else if (TYPEOF(Comment)!=NILSXP)
error("Argument type error: Comment");
int skip = 0;
if (TYPEOF(Skip)==INTSXP) {
if (length(Skip)>1)
warning("Only first element used: Skip");
skip = INTEGER(Skip)[0];
}
else if (TYPEOF(Skip)!=NILSXP)
error("Argument type error: Skip");
if (TYPEOF(Simplify)!=LGLSXP)
error("Argument type error: Simplify");
if (length(Simplify)>2)
error("Argument length error: Simplify");
int *simplify = INTEGER(Simplify);
if (length(Simplify)==1)
simplify[1] = simplify[0];
int every=0;
if (TYPEOF(Every)==INTSXP) {
if (length(Every)>1)
warning("Only first element used: Every");
every = INTEGER(Every)[0];
}
else if (TYPEOF(Every)!=NILSXP)
error("Argument type error: Every");
/* Create output object and initialise to zero */
if (verbose) {
if (diploid)
Rprintf("Reading XSnpMatrix with %d rows and %d columns\n",
Nsample, Nsnp);
else
Rprintf("Reading SnpMatrix with %d rows and %d columns\n",
Nsample, Nsnp);
}
SEXP Result, Dimnames, Package, Class;
PROTECT(Result = allocMatrix(RAWSXP, Nsample, Nsnp));
PROTECT(Dimnames = allocVector(VECSXP, 2));
if (simplify[0]) {
SET_VECTOR_ELT(Dimnames, 0,
simplify_names(file_is==1? Filenames: Sample_id));
}
else {
SET_VECTOR_ELT(Dimnames, 0,
duplicate(file_is==1? Filenames: Sample_id));
}
if (simplify[1]) {
SET_VECTOR_ELT(Dimnames, 1,
simplify_names(file_is==2? Filenames: Snp_id));
}
else {
SET_VECTOR_ELT(Dimnames, 1,
duplicate(file_is==2? Filenames: Snp_id));
}
setAttrib(Result, R_DimNamesSymbol, Dimnames);
/* Class */
PROTECT(Class = allocVector(STRSXP, 1));
if (diploid) {
R_do_slot_assign(Result, mkString("diploid"), Diploid);
SET_STRING_ELT(Class, 0, mkChar("XSnpMatrix"));
}
else {
SET_STRING_ELT(Class, 0, mkChar("SnpMatrix"));
}
PROTECT(Package = allocVector(STRSXP, 1));
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
setAttrib(Class, install("package"), Package);
classgets(Result, Class);
SET_S4_OBJECT(Result);
unsigned char *result = RAW(Result);
memset(result, 0x00, Nsample*Nsnp);
/* Read in data */
char field[MAX_FLD];
int Naccept = 0, Nreject = 0, Nocall = 0, Nskipped = 0, Nxerror = 0;
int i_this = 0, j_this = 0;
const char *this_sample=NULL, *this_snp=NULL;
if (fsamp) {
this_sample = CHAR(STRING_ELT(Sample_id, 0));
}
if (fsnp) {
this_snp = CHAR(STRING_ELT(Snp_id, 0));
}
if (verbose) {
Rprintf(" Cumulative totals\n");
Rprintf(" -----------------------------------\n");
Rprintf(" File Line Accepted Rejected No call Skipped File name\n");
}
/* slowest varying 0 = don't know, 1 = sample, 2 = snp */
int slowest = file_is, last=Nsample*Nsnp-1;
int advance = 0, finished=0;
for (int f=0; f<Nfile; f++) {
/* Open input file */
const char *filename = CHAR(STRING_ELT(Filenames, f));
if (verbose) {
int lfn = strlen(filename);
if (lfn > 20) {
Rprintf("%59s...%-17s\r", "", filename+lfn-17);
}
else
Rprintf("%59s%-20s\r", "", filename);
}
gzFile infile = gzopen(filename, "rb");
if (!infile) {
warning("Failure to open input file: %s", filename);
continue;
}
int fterm = 2, line = 0, found_in_file = 0;
/* Skip any header lines */
for (int i=0; i<skip; i++) {
line++;
if (skip_to_eol(infile)==3)
error("End-of-file reached on line %d", line);
}
Nskipped += skip;
/* Read data lines */
while (fterm!=3) {
/* Read a line */
line++;
if (verbose && every && !(line % every))
Rprintf("%8d %8d %10d %8d %8d %8d\r",
f+1, line, Naccept, Nreject, Nocall, Nskipped);
int genotype=0, allele1=0, allele2=0;
/* wanted is coded as:
1 if this call is to be accepted
0 if it is not wanted (or a comment line)
-1 if rejected due to insufficient confidence
-2 coded as no-call
*/
int wanted = 1;
char sampid[MAX_FLD], snpid[MAX_FLD];
char gtype1[MAX_FLD], gtype2[MAX_FLD];
char cscore[MAX_FLD];
sampid[0] = snpid[0] = cscore[0] = (char) 0;
for (int r=1; (r<=fmax); r++) {
fterm = next_field(infile, sep, comment, '_', field, MAX_FLD);
if (!fterm)
error("Field overflow: line %d, field %d", line, r);
if ((fterm>1) && (r<fmax)) {
if (r==1) {
if(!field[0]) {
/* Empty line or comment line */
wanted = 0;
if (fterm==2) {
Nskipped++;
continue;
}
else
break;
}
}
error("Incomplete line: %d (last field read: %d = %s)",
line, r, field);
}
/* Save fields */
if (r==fsamp) {
strncpy(sampid, field, MAX_FLD-1);
}
else if (r==fsnp) {
strncpy(snpid, field, MAX_FLD-1);
}
else if (r==fconf) {
strncpy(cscore, field, MAX_FLD-1);
}
else if (r==fgt)
strncpy(gtype1, field, MAX_FLD-1);
else if (r==fa1)
strncpy(gtype1, field, MAX_FLD-1);
else if (r==fa2)
strncpy(gtype2, field, MAX_FLD-1);
else {
/* skip field */
}
} /* Matches: for (int r=1; (r<=fmax); r++) { */
if (!wanted)
continue;
/* Discard any further fields */
if (fterm<2) {
fterm = skip_to_eol(infile);
}
/* Find next target and check matches */
int match_sample, match_snp;
if (in_order) {
/* Advance to next target read */
if (advance) {
/*
If unknown, determine sort order by seeing which indicator
has changed
*/
if (!slowest) {
if (strcmp(this_sample, sampid))
slowest = 2; /* sample fastest, SNP slowest */
else if (strcmp(this_snp, snpid))
slowest = 1; /* SNP fastest, sample slowest */
else
error("Error in input file sort order");
}
/* Now advance fastest varying indicator */
if (slowest==1) {
j_this++;
if (j_this==Nsnp) {
j_this = 0;
if (fsamp) {
i_this++;
if (i_this==Nsample) {
finished = 1;
break;
}
else
this_sample = CHAR(STRING_ELT(Sample_id, i_this));
}
}
this_snp = CHAR(STRING_ELT(Snp_id, j_this));
}
else {
i_this++;
if (i_this==Nsample) {
i_this = 0;
if (fsnp) {
j_this++;
if (j_this==Nsnp) {
finished = 1;
break;
}
else
this_snp = CHAR(STRING_ELT(Snp_id, j_this));
}
}
this_sample = CHAR(STRING_ELT(Sample_id, i_this));
}
}
/* Does current line match current target? */
match_sample = file_is==1 || !strcmp(this_sample, sampid);
match_snp = file_is==2 || !strcmp(this_snp, snpid);
}
else { /* Not in order */
if (file_is!=1) {
if (this_sample && strcmp(this_sample, sampid))
i_this = index_lookup(sample_index, sampid);
if (i_this >= 0) {
this_sample = CHAR(STRING_ELT(Sample_id, i_this));
match_sample = 1;
}
else {
this_sample = NULL;
match_sample = 0;
}
}
else {
match_sample = 1;
i_this = f;
}
if (file_is!=2) {
if (this_snp && strcmp(this_snp, snpid))
j_this = index_lookup(snp_index, snpid);
if (j_this >= 0) {
this_snp = CHAR(STRING_ELT(Snp_id, j_this));
match_snp = 1;
}
else {
this_snp = NULL;
match_snp = 0;
}
}
else {
match_snp = 1;
j_this = f;
}
}
if (match_sample && match_snp) {
/* Next target read found in file(s) */
found_in_file++;
int ij_this = j_this*Nsample + i_this;
finished = (ij_this==last);
/* Check confidence score */
if (fconf) {
double conf;
if (sscanf(cscore, "%lf", &conf)!=1)
error("Failure to read confidence score: line %d", line);
if ((lower && conf<threshold) || (!lower && conf>threshold)) {
wanted = -1;
Nreject++;
if (finished)
break;
else
advance = 1;
continue;
}
}
/* Decode genotype */
int which;
if (gcoding) {
if (nuc) {
switch (strlen(gtype1)) {
case 0:
allele1 = allele2 = 0;
break;
case 1:
allele1 = allele2 = nucleotide(gtype1[0]);
break;
case 2:
allele1 = nucleotide(gtype1[0]);
allele2 = nucleotide(gtype1[1]);
break;
default:
error("Nucleotide coded genotype should be 2 character string: line %d", line);
}
}
else {
which = str_inlist(Codes, gtype1);
if (!which)
genotype = 0;
else if (which>3)
genotype = 2*which - 7;
else
genotype = which;
}
}
else {
if (nuc) {
allele1 = nucleotide(gtype1[0]);
allele2 = nucleotide(gtype2[0]);
}
else {
allele1 = str_inlist(Codes, gtype1);
allele2 = str_inlist(Codes, gtype2);
}
}
/* Successful read, store genotype in result[i_this, j_this] */
if (nuc || !gcoding) {
if (allele2 < allele1) {
genotype = allele2;
allele2 = allele1;
allele1 = genotype;
}
if (allele1 && allele2)
genotype = allele1 + (allele2*(allele2-1))/2;
else
genotype = 0;
}
if (genotype) {
if (diploid && !diploid[i_this] && (genotype==2))
Nxerror++;
else {
Naccept++;
result[ij_this] = (unsigned char) genotype;
}
}
else {
wanted = -2;
Nocall++;
}
/* Flag need to advance to next target */
advance = 1;
} /* matches if (match_sample && match_snp) { */
else {
Nskipped++;
/* Flag no advance to next target */
advance = 0;
}
if (finished)
break;
} /* matches: while (fterm!=3) { */
if (file_is==1)
i_this++;
if (file_is==2)
j_this++;
if (verbose) {
Rprintf("%8d %8d %10d %8d %8d %8d\r", f+1, line, Naccept, Nreject, Nocall, Nskipped);
}
if(!found_in_file)
warning("No calls found in file %s", filename);
gzclose(infile);
if (finished)
break;
}
/* Warnings */
if (in_order && !finished)
warning("End of data reached before search completed");
if (Nxerror)
warning("%d haploid genotypes were coded as heterozygous; set to NA", Nxerror);
if (Nskipped)
warning("%d lines of input file(s) were skipped", Nskipped);
/* Report */
if (verbose)
Rprintf("\n");
Rprintf("%d genotypes successfully read\n", Naccept);
if (Nreject)
Rprintf("%d genotypes were rejected due to low confidence\n", Nreject);
if (Nocall)
Rprintf("%d genotypes were not called\n", Nocall);
if (Nsample*Nsnp > Naccept+Nxerror+Nreject+Nocall)
Rprintf("%d genotypes could not be found on input file(s)\n",
Nsample*Nsnp - Naccept - Nreject - Nxerror-Nocall);
if (nuc) {
if (verbose)
Rprintf("Recasting and checking nucleotide coding\n");
int none_snps = recode_snp(result, Nsample, Nsnp);
if (none_snps) {
Rprintf("%d polymorphisms were not SNPs and have been set to NA ",
none_snps);
Rprintf("(see warnings for details)\n");
}
}
UNPROTECT(4);
/* Destroy hash indexes */
if (sample_index)
index_destroy(sample_index);
if (snp_index)
index_destroy(snp_index);
return Result;
}
SEXP duplicateOrConvert(SEXP orig, int (*func)(MYSQL*,rdbVector*,rdbVector*), MYSQL *sqlconn, int needConvert)
{
SEXP x, tname;
rdbVector *info;
rdbVector *origInfo = getInfo(orig);
/* if this dbvector is shared by more than one variable
we should copy before set */
if (origInfo->sxp_spare > 1 || needConvert)
{
PROTECT(x = duplicate(orig));
Rprintf("new address %p \n",x);
SEXP s = R_do_slot(x,install("info"));
info = (rdbVector*)RAW(s);
initRDBVector(info);
info->sxp_spare = 0;
func(sqlconn, origInfo, info);
Rprintf("duplicated into table %s\n",info->tableName);
/* set tablename slot */
PROTECT(tname = ScalarString(mkChar(info->tableName)));
R_do_slot_assign(x, install("tablename"), tname);
free(info->tableName);
/* register finalizer for the new duplicate */
rdbVector *ptr = malloc(sizeof(rdbVector));
*ptr = *info;
SEXP rptr;
R_do_slot_assign(x, install("ext"), (rptr=R_MakeExternalPtr(ptr, R_NilValue, R_NilValue)));
R_RegisterCFinalizerEx(rptr, rdbVectorFinalizer, TRUE);
origInfo->sxp_spare--;
UNPROTECT(2);
}
else
{
x = orig;
/* set ref counter to 0 because it'll be incremented when the result is bound to a name */
origInfo->sxp_spare = 0;
/*
rdbVector oldInfo = *origInfo;
origInfo->tableName = calloc(MAX_TABLE_NAME, sizeof(char));
func(sqlconn, &oldInfo, origInfo);
*/
/* save new table name */
/*
PROTECT(tname = ScalarString(mkChar(origInfo->tableName)));
R_do_slot_assign(x, install("tablename"), tname);
UNPROTECT(1);
*/
/* update finalizer */
/*
SEXP rptr = R_do_slot(x, install("ext"));
rdbVector *ptr = R_ExternalPtrAddr(rptr);
rdbVector *ptr = malloc(sizeof(rdbVector));
*ptr = *info;
rep->tableName = calloc(MAX_TABLE_NAME, sizeof(char));
strcpy(ptr->tableName, info->tableName);
SEXP rptr;
R_do_slot_assign(x, install("ext"), (rptr=R_MakeExternalPtr(ptr, R_NilValue, R_NilValue)));
R_RegisterCFinalizerEx(rptr, rdbvectorFinalizer, TRUE);
*/
}
return x;
}
SEXP math_dbvector(SEXP x, SEXP op)
{
SEXP ans, rinfo, rtablename, rptr;
rdbVector *xinfo = getInfo(x);
MYSQL *sqlconn = NULL;
int success = connectToLocalDB(&sqlconn);
if(!success || sqlconn == NULL)
{
error("cannot connect to local db\n");
return R_NilValue;
}
PROTECT(ans = R_do_new_object(R_getClassDef("dbvector")));
PROTECT(rinfo = allocVector(RAWSXP,sizeof(rdbVector)));
rdbVector *vec = (rdbVector*)RAW(rinfo);
vec->tableName = malloc(MAX_TABLE_NAME*sizeof(char));
initRDBVector(&vec, 0, 0);
if (strcmp(CHAR(asChar(op)), "sin") == 0)
{
switch(xinfo->sxp_type)
{
case INTSXP:
case REALSXP:
performNumericSin(sqlconn, xinfo, vec);
break;
case CPLXSXP:
performComplexSin(sqlconn, xinfo, vec);
break;
default:
free(vec->tableName);
mysql_close(sqlconn);
UNPROTECT(2);
error("wrong type");
}
}
else if (strcmp(CHAR(asChar(op)), "cos") == 0)
{
switch(xinfo->sxp_type)
{
case INTSXP:
case REALSXP:
performNumericCos(sqlconn, xinfo, vec);
break;
case CPLXSXP:
performComplexCos(sqlconn, xinfo, vec);
break;
default:
free(vec->tableName);
mysql_close(sqlconn);
UNPROTECT(2);
error("wrong type");
}
}
else
{
free(vec->tableName);
mysql_close(sqlconn);
UNPROTECT(2);
error("wrong type");
}
PROTECT(rtablename= allocVector(STRSXP, 1));
SET_STRING_ELT(rtablename, 0, mkChar(vec->tableName));
R_do_slot_assign(ans, install("tablename"), rtablename);
R_do_slot_assign(ans, install("info"), rinfo);
/* register finalizer */
rdbVector *ptr = malloc(sizeof(rdbVector));
*ptr = *vec;
PROTECT(rptr = R_MakeExternalPtr(ptr, R_NilValue, R_NilValue));
R_do_slot_assign(ans, install("ext"), rptr);
R_RegisterCFinalizerEx(rptr, rdbVectorFinalizer, TRUE);
UNPROTECT(4);
return ans;
}
SEXP R_set_slot(SEXP obj, SEXP name, SEXP value)
{
return R_do_slot_assign(obj, name, value);
}
SEXP FLQuant_pointer::Return(void)
{
SEXP Quant, v,
d1, d2, d3, d4, d5, d6,
dim, dimnames, names;
int j, iAge, iYear, iUnit, iArea, iSeason, iIter;
//Create new S4 object
PROTECT(Quant = NEW_OBJECT(MAKE_CLASS("FLQuant")));
//Create array for slot
//Set dimensions of array
PROTECT(dim = allocVector(INTSXP, 6));
INTEGER(dim)[0] = maxquant()-minquant() +1;
INTEGER(dim)[1] = maxyr() -minyr() +1;
INTEGER(dim)[2] = nunits();
INTEGER(dim)[3] = nseasons();
INTEGER(dim)[4] = nareas();
INTEGER(dim)[5] = niters();
//allocate memory
PROTECT(v = Rf_allocArray(REALSXP, dim));
//Create dimension names
PROTECT(dimnames = allocVector(VECSXP, 6));
PROTECT(d1 = allocVector(INTSXP, maxquant()-minquant() +1));
for (iAge=minquant(),j=0; iAge<=maxquant(); iAge++, j++)
INTEGER(d1)[j] = iAge;
SET_VECTOR_ELT(dimnames, 0, d1);
PROTECT(d2 = allocVector(INTSXP, maxyr()-minyr()+1));
for (iYear=minyr(), j=0; iYear<=maxyr(); iYear++, j++)
INTEGER(d2)[j] = iYear;
SET_VECTOR_ELT(dimnames, 1, d2);
if (nunits()==1)
{
PROTECT(d3 = allocVector(STRSXP, nunits()));
SET_STRING_ELT(d3, 0, mkChar("unique"));
}
else
{
PROTECT(d3 = allocVector(INTSXP, nunits()));
for (iUnit=1, j=0; iUnit<=nunits(); iUnit++, j++)
INTEGER(d3)[j] = iUnit;
}
SET_VECTOR_ELT(dimnames, 2, d3);
if (nseasons()==1)
{
PROTECT(d4 = allocVector(STRSXP, nseasons()));
SET_STRING_ELT(d4, 0, mkChar("all"));
}
else
{
PROTECT(d4 = allocVector(INTSXP, nseasons()));
for (iSeason=1, j=0; iSeason<=nseasons(); iSeason++, j++)
INTEGER(d4)[j] = iSeason;
}
SET_VECTOR_ELT(dimnames, 3, d4);
if (nareas()==1)
{
PROTECT(d5 = allocVector(STRSXP, nareas()));
SET_STRING_ELT(d5, 0, mkChar("unique"));
}
else
{
PROTECT(d5 = allocVector(INTSXP, nareas()));
for (iArea=1, j=0; iArea<=nareas(); iArea++, j++)
INTEGER(d5)[j] = iArea;
}
SET_VECTOR_ELT(dimnames, 4, d5);
PROTECT(d6 = allocVector(INTSXP, niters()));
for (iIter=1, j=0; iIter<=niters(); iIter++, j++)
INTEGER(d6)[j] = iIter;
SET_VECTOR_ELT(dimnames, 5, d6);
//Create names for dimensions
PROTECT(names = allocVector(STRSXP, 6));
SET_STRING_ELT(names, 0, mkChar("age"));
SET_STRING_ELT(names, 1, mkChar("year"));
SET_STRING_ELT(names, 2, mkChar("unit"));
SET_STRING_ELT(names, 3, mkChar("season"));
SET_STRING_ELT(names, 4, mkChar("area"));
SET_STRING_ELT(names, 5, mkChar("iter"));
setAttrib(dimnames, R_NamesSymbol, names);
setAttrib(v, R_DimNamesSymbol, dimnames);
//Set data
j=0;
for(iIter = 1; iIter <= niters(); iIter++)
for (iArea = 1; iArea <= nareas(); iArea++)
for (iSeason = 1; iSeason <= nseasons(); iSeason++)
for (iUnit = 1; iUnit <= nunits(); iUnit++)
for (iYear = minyr(); iYear <= maxyr(); iYear++)
for (iAge = minquant(); iAge <= maxquant(); iAge++)
REAL(v)[j++] = data[i(iAge,iYear,iUnit,iSeason,iArea,iIter)];
//Set slot
Quant = R_do_slot_assign(Quant, install(".Data"), v);
UNPROTECT(11);
return Quant;
}
SEXP RErrorValue::FromValue (const com_opengamma_language_Value *pValue) {
if (!pValue) {
LOGWARN (TEXT ("NULL pointer"));
return R_NilValue;
}
if (!pValue->_errorValue) {
LOGWARN (TEXT ("NULL error value"));
return R_NilValue;
}
LOGDEBUG (TEXT ("Error ") << *pValue->_errorValue);
SEXP cls = R_getClassDef (R_ERRORVALUE_CLASS);
if (cls == R_NilValue) {
LOGFATAL (ERR_R_FUNCTION);
return R_NilValue;
}
PROTECT (cls);
SEXP obj = R_do_new_object (cls);
if (obj == R_NilValue) {
LOGFATAL (ERR_R_FUNCTION);
UNPROTECT (1);
return R_NilValue;
}
PROTECT (obj);
SEXP v = allocVector (INTSXP, 1);
if (v == R_NilValue) {
LOGFATAL (ERR_R_FUNCTION)
UNPROTECT (2);
return R_NilValue;
}
PROTECT (v);
*INTEGER(v) = *pValue->_errorValue;
SEXP f = mkString (R_ERRORVALUE_ERROR);
if (f == R_NilValue) {
LOGFATAL (ERR_R_FUNCTION);
UNPROTECT (3);
return R_NilValue;
}
PROTECT (f);
R_do_slot_assign (obj, f, v);
if (pValue->_intValue) {
LOGDEBUG (TEXT ("Int ") << *pValue->_intValue);
v = allocVector (INTSXP, 1);
if (v != R_NilValue) {
PROTECT (v);
*INTEGER(v) = *pValue->_intValue;
f = mkString (R_ERRORVALUE_INT);
if (f && (f != R_NilValue)) {
PROTECT (f);
R_do_slot_assign (obj, f, v);
UNPROTECT (2);
} else {
LOGERROR (ERR_R_FUNCTION);
UNPROTECT (1);
}
} else {
LOGERROR (ERR_R_FUNCTION);
}
}
if (pValue->_stringValue) {
LOGDEBUG (TEXT ("String ") << pValue->_stringValue);
#ifdef _UNICODE
char *pszStringValue = WideToAsciiDup (pValue->_stringValue);
if (pszStringValue) {
v = mkString (pszStringValue);
free (pszStringValue);
} else {
LOGFATAL (ERR_MEMORY);
return R_NilValue;
}
#else /* ifdef _UNICODE */
v = mkString (pValue->_stringValue);
#endif /* ifdef _UNICODE */
if (v != R_NilValue) {
PROTECT (v);
f = mkString (R_ERRORVALUE_STRING);
if (f != R_NilValue) {
PROTECT (f);
R_do_slot_assign (obj, f, v);
UNPROTECT (2);
} else {
LOGERROR (ERR_R_FUNCTION);
}
} else {
LOGERROR (ERR_R_FUNCTION);
}
}
TCHAR *psz = CError::ToString (pValue);
if (!psz) {
LOGFATAL (ERR_MEMORY);
UNPROTECT (4);
return R_NilValue;
}
LOGDEBUG (TEXT ("toString ") << psz);
#ifdef _UNICODE
char *pszAscii = WideToAsciiDup (psz);
if (pszAscii) {
v = mkString (pszAscii);
free (pszAscii);
} else {
LOGFATAL (ERR_MEMORY);
UNPROTECT (4);
return R_NilValue;
}
#else /* ifdef _UNICODE */
v = mkString (psz);
#endif /* ifdef _UNICODE */
delete psz;
if (v != R_NilValue) {
PROTECT (v);
f = mkString (R_ERRORVALUE_TOSTRING);
if (f != R_NilValue) {
PROTECT (f);
R_do_slot_assign (obj, f, v);
UNPROTECT (6);
} else {
LOGERROR (ERR_R_FUNCTION);
UNPROTECT (5);
}
} else {
LOGERROR (ERR_R_FUNCTION);
UNPROTECT (4);
}
return obj;
}
