#include "FusionCDFData.h"
#include <iostream>
#include "R_affx_constants.h"
using namespace std;
using namespace affymetrix_fusion_io;
#include <R.h>
#include <Rdefines.h>
#include <wchar.h>
#include <wctype.h>
extern "C" {
/************************************************************************
*
* R_affx_cdf_nbrOfCellsPerUnitGroup()
*
************************************************************************/
SEXP R_affx_cdf_nbrOfCellsPerUnitGroup(SEXP fname, SEXP units, SEXP verbose)
{
FusionCDFData cdf;
FusionCDFFileHeader header;
string str;
int str_length;
char* cstr;
SEXP names = R_NilValue,
probe_sets = R_NilValue,
r_groups = R_NilValue,
r_group_names = R_NilValue;
bool readAll = true;
int nsets = 0, nunits = 0;
int iset = 0;
const char* cdfFileName = CHAR(STRING_ELT(fname, 0));
int i_verboseFlag = INTEGER(verbose)[0];
FusionCDFProbeSetInformation probeset;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Opens file
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
cdf.SetFileName(cdfFileName);
if (i_verboseFlag >= R_AFFX_VERBOSE) {
Rprintf("Attempting to read CDF File: %s\n", cdf.GetFileName().c_str());
}
if (cdf.Read() == false) {
error("Failed to read the CDF file.");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Read header and get unit indices to be read
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
header = cdf.GetHeader();
nsets = header.GetNumProbeSets();
nunits = length(units);
if (nunits == 0) {
nunits = nsets;
} else {
readAll = false;
/* Validate argument 'units': */
for (int ii = 0; ii < nunits; ii++) {
iset = INTEGER(units)[ii];
if (iset < 1 || iset > nsets) {
error("Argument 'units' contains an element out of range.");
}
}
}
/* Allocate R character vector and R list for the names and units */
PROTECT(names = NEW_CHARACTER(nunits));
PROTECT(probe_sets = NEW_LIST(nunits));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Access information for the requested units one by one
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int ii = 0; ii < nunits; ii++) {
if (readAll) {
iset = ii;
} else {
/* Unit indices are zero-based in Fusion SDK. */
iset = INTEGER(units)[ii] - 1;
}
/* Retrieve the current unit */
cdf.GetProbeSetInformation(iset, probeset);
/* Record its name */
str = cdf.GetProbeSetName(iset);
str_length = str.size();
cstr = Calloc(str_length+1, char);
strncpy(cstr, str.c_str(), str_length);
cstr[str_length] = '\0';
SET_STRING_ELT(names, ii, mkChar(cstr));
Free(cstr);
/* Get the number of groups in the unit */
int ngroups = probeset.GetNumGroups();
/* Allocate an R list and a vector of names for the groups */
PROTECT(r_groups = NEW_INTEGER(ngroups));
PROTECT(r_group_names = NEW_CHARACTER(ngroups));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* For each group, query the number of cells (probes)
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int igroup = 0; igroup < ngroups; igroup++) {
FusionCDFProbeGroupInformation group;
/* Get the current group */
probeset.GetGroupInformation(igroup, group);
/* Get the name of the group */
str = group.GetName();
str_length = str.size();
cstr = Calloc(str_length+1, char);
strncpy(cstr, str.c_str(), str_length);
cstr[str_length] = '\0';
SET_STRING_ELT(r_group_names, igroup, mkChar(cstr));
Free(cstr);
/* Get the number of cells (probes) in the group */
int ncells = group.GetNumCells();
INTEGER(r_groups)[igroup] = ncells;
}
/** set the group names. **/
setAttrib(r_groups, R_NamesSymbol, r_group_names);
/** now set the probe_set in the main probe_set list. **/
SET_VECTOR_ELT(probe_sets, ii, r_groups);
/** pop the group list and group names of the stack. **/
UNPROTECT(2); /* 'r_group_names' and then 'r_groups' */
}
/** set the names down here at the end. **/
setAttrib(probe_sets, R_NamesSymbol, names);
/** unprotect the names and the main probe set list.**/
UNPROTECT(2); /* 'names' and then 'probe_sets' */
return probe_sets;
}
/************************************************************************
*
* R_affx_cdf_groupNames()
*
************************************************************************/
SEXP R_affx_cdf_groupNames(SEXP fname, SEXP units, SEXP truncateGroupNames, SEXP verbose)
{
FusionCDFData cdf;
FusionCDFFileHeader header;
string str;
int str_length;
char* cstr;
SEXP names = R_NilValue,
probe_sets = R_NilValue,
r_group_names = R_NilValue;
bool readAll = true;
int nsets = 0, nunits = 0;
int iset = 0;
const char* cdfFileName = CHAR(STRING_ELT(fname, 0));
int i_truncateGroupNames = INTEGER(truncateGroupNames)[0];
int i_verboseFlag = INTEGER(verbose)[0];
/** pointer to the name of the probeset. **/
char* name;
char bfr[512];
FusionCDFProbeSetInformation probeset;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Opens file
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
cdf.SetFileName(cdfFileName);
if (i_verboseFlag >= R_AFFX_VERBOSE) {
Rprintf("Attempting to read CDF File: %s\n", cdf.GetFileName().c_str());
}
if (cdf.Read() == false) {
error("Failed to read the CDF file.");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Read header and get unit indices to be read
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
header = cdf.GetHeader();
nsets = header.GetNumProbeSets();
nunits = length(units);
if (nunits == 0) {
nunits = nsets;
} else {
readAll = false;
/* Validate argument 'units': */
for (int ii = 0; ii < nunits; ii++) {
iset = INTEGER(units)[ii];
if (iset < 1 || iset > nsets) {
error("Argument 'units' contains an element out of range.");
}
}
}
/* Allocate R character vector and R list for the names and units */
PROTECT(probe_sets = NEW_LIST(nunits));
PROTECT(names = NEW_CHARACTER(nunits));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Access information for the requested units one by one
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int ii = 0; ii < nunits; ii++) {
if (readAll) {
iset = ii;
} else {
/* Unit indices are zero-based in Fusion SDK. */
iset = INTEGER(units)[ii] - 1;
}
/* Retrieve the current unit */
cdf.GetProbeSetInformation(iset, probeset);
/* Record its name */
str = cdf.GetProbeSetName(iset);
str_length = str.size();
name = Calloc(str_length+1, char);
strncpy(name, str.c_str(), str_length);
name[str_length] = '\0';
SET_STRING_ELT(names, ii, mkChar(name));
/* Get the number of groups in the unit */
int ngroups = probeset.GetNumGroups();
/* Allocate a vector of names for the groups */
PROTECT(r_group_names = NEW_CHARACTER(ngroups));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* For each group, query the number of cells (probes)
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int igroup = 0; igroup < ngroups; igroup++) {
FusionCDFProbeGroupInformation group;
/* Get the current group */
probeset.GetGroupInformation(igroup, group);
/* Get the name of the group */
str = group.GetName();
str_length = str.size();
cstr = Calloc(str_length+1, char);
strncpy(cstr, str.c_str(), str_length);
cstr[str_length] = '\0';
/* If group name starts with the unit name, and i_truncateGroupNames
is TRUE, strip it off. */
int len = strlen(name);
int res = strncmp(cstr, name, len);
if (res == 0 && i_truncateGroupNames) {
int last = strlen(cstr)-len;
for (int kk = 0; kk < last; kk++)
bfr[kk] = cstr[len+kk];
bfr[last] = '\0';
SET_STRING_ELT(r_group_names, igroup, mkChar(bfr));
} else {
SET_STRING_ELT(r_group_names, igroup, mkChar(cstr));
}
Free(cstr);
}
/** now set the probe_set in the main probe_set list. **/
SET_VECTOR_ELT(probe_sets, ii, r_group_names);
/** pop the group list and group names of the stack. **/
UNPROTECT(1); /* 'r_group_names' */
Free(name);
} /* for (int ii=0 ...) */
/** set the names down here at the end. **/
setAttrib(probe_sets, R_NamesSymbol, names);
/** unprotect the names and the main probe set list.**/
UNPROTECT(2); /* 'names' and then 'probe_sets' */
return probe_sets;
} /* R_affx_cdf_groupNames() */
/************************************************************************
*
* R_affx_pt_base_is_pm
*
* Return 1 if p_base/t_base pair is PM (complementary), 0 otherwise.
*
************************************************************************/
int R_affx_pt_base_is_pm(char p_base, char t_base)
{
int is_pm = 0; /* 0 is false, 1 is true */
if (p_base == t_base) {
is_pm = 0;
} else {
if ((p_base == 'a' || p_base == 'A') &&
(t_base == 't' || t_base == 'T')) {
is_pm = 1;
} else if ((p_base == 't' || p_base == 'T') &&
(t_base == 'a' || t_base == 'A')) {
is_pm = 1;
} else if ((p_base == 'c' || p_base == 'C') &&
(t_base == 'g' || t_base == 'G')) {
is_pm = 1;
} else if ((p_base == 'g' || p_base == 'G') &&
(t_base == 'c' || t_base == 'C')) {
is_pm = 1;
} else {
is_pm = 0;
}
}
return is_pm;
} /* R_affx_pt_base_is_pm() */
/************************************************************************
*
* R_affx_cdf_isPm()
*
************************************************************************/
SEXP R_affx_cdf_isPm(SEXP fname, SEXP units, SEXP verbose)
{
FusionCDFData cdf;
FusionCDFFileHeader header;
string str;
int str_length;
char* cstr;
SEXP names = R_NilValue,
probe_sets = R_NilValue,
r_groups = R_NilValue,
r_group_names = R_NilValue,
isPm = R_NilValue;
bool readAll = true;
int nsets = 0, nunits = 0;
int iset = 0;
const char* cdfFileName = CHAR(STRING_ELT(fname, 0));
int i_verboseFlag = INTEGER(verbose)[0];
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Opens file
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
cdf.SetFileName(cdfFileName);
if (i_verboseFlag >= R_AFFX_VERBOSE) {
Rprintf("Attempting to read CDF File: %s\n", cdf.GetFileName().c_str());
}
if (cdf.Read() == false) {
error("Failed to read the CDF file.");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Read header and get unit indices to be read
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
header = cdf.GetHeader();
nsets = header.GetNumProbeSets();
nunits = length(units);
if (nunits == 0) {
nunits = nsets;
} else {
readAll = false;
/* Validate argument 'units': */
for (int ii = 0; ii < nunits; ii++) {
iset = INTEGER(units)[ii];
if (iset < 1 || iset > nsets) {
error("Argument 'units' contains an element out of range.");
}
}
}
/* Allocate R character vector and R list for the names and units */
PROTECT(probe_sets = NEW_LIST(nunits));
PROTECT(names = NEW_CHARACTER(nunits));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* Access information for the requested units one by one
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int ii = 0; ii < nunits; ii++) {
FusionCDFProbeSetInformation probeset;
if (readAll) {
iset = ii;
} else {
/* Unit indices are zero-based in Fusion SDK. */
iset = INTEGER(units)[ii] - 1;
}
/* Retrieve the current unit */
cdf.GetProbeSetInformation(iset, probeset);
/* Record its name */
str = cdf.GetProbeSetName(iset);
str_length = str.size();
cstr = Calloc(str_length+1, char);
strncpy(cstr, str.c_str(), str_length);
cstr[str_length] = '\0';
SET_STRING_ELT(names, ii, mkChar(cstr));
Free(cstr);
/* Get the number of groups in the unit */
int ngroups = probeset.GetNumGroups();
/* Allocate an R list and a vector of names for the groups */
PROTECT(r_groups = NEW_LIST(ngroups));
PROTECT(r_group_names = NEW_CHARACTER(ngroups));
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* For each group, query the number of cells (probes)
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
for (int igroup = 0; igroup < ngroups; igroup++) {
FusionCDFProbeGroupInformation group;
/* Get the current group */
probeset.GetGroupInformation(igroup, group);
/* Get the name of the group */
str = group.GetName();
str_length = str.size();
cstr = Calloc(str_length+1, char);
strncpy(cstr, str.c_str(), str_length);
cstr[str_length] = '\0';
SET_STRING_ELT(r_group_names, igroup, mkChar(cstr));
Free(cstr);
/* Get the number of cells (probes) in the group */
int ncells = group.GetNumCells();
PROTECT(isPm = NEW_LOGICAL(ncells));
/* For each cell, record if it is an mis-match probe or not */
for (int icell = 0; icell < ncells; icell++) {
FusionCDFProbeInformation probe;
group.GetCell(icell, probe);
char p_base = probe.GetPBase();
char t_base = probe.GetTBase();
LOGICAL(isPm)[icell] = R_affx_pt_base_is_pm(p_base, t_base);
} /* for (int icell ...) */
SET_VECTOR_ELT(r_groups, igroup, isPm);
UNPROTECT(1); /* 'isPm' */
}
/** set the group names. **/
setAttrib(r_groups, R_NamesSymbol, r_group_names);
/** now set the probe_set in the main probe_set list. **/
SET_VECTOR_ELT(probe_sets, ii, r_groups);
/** pop the group list and group names of the stack. **/
UNPROTECT(2); /* 'r_group_names' and then 'r_groups' */
}
/** set the names down here at the end. **/
setAttrib(probe_sets, R_NamesSymbol, names);
/** unprotect the names and the main probe set list.**/
UNPROTECT(2); /* 'names' and then 'probe_sets' */
return probe_sets;
} /* R_affx_cdf_isPm() */
} /** end extern C **/
/***************************************************************************
* HISTORY:
* 2007-03-05
* o Added argument 'truncateGroupNames' to R_affx_cdf_group_names().
* 2006-11-27
* o Added Seth Falcon's help function R_affx_pt_base_is_pm().
* o Made R_affx_cdf_isMm() & R_affx_cdf_isPmOrMm() deprecated, because
* they've never been used. /HB
* 2006-03-28
* o Unit indices are now one-based. /HB
* 2006-01-15
* 2006-01-15
* o It is now possible to specify what readCdfUnits() should return. /HB
* 2006-01-12
* o BUG FIX: The check of the upper-limit of unit indicies was done
* assuming one-based indices. /HB
* o Added R_affx_cdf_isMm(), R_affx_cdf_isPm() & R_affx_cdf_isPmOrMm(). /HB
* 2006-01-11
* o Added R_affx_cdf_nbrOfCellsPerUnitGroup() /HB
* 2006-01-10
* o Updated the "units" code to be more similar to the corresponding code
* for CEL files. /HB
* o Added a return value to non-void function R_affx_get_cdf_file_qc(). /HB
* 2006-01-09
* o Added R_affx_get_cdf_units() and R_affx_get_cdf_unit.names(). /HB
* o Created. The purpose was to make it possible to read subsets of units
* and not just all units at once. /HB
**************************************************************************/
