@@ -18,7 +18,8 @@

 #  \item{readBases}{If @TRUE, cell P and T bases are retrieved, otherwise not.}

 #  \item{readExpos}{If @TRUE, cell "expos" values are retrieved, otherwise not.}

 #  \item{readType}{If @TRUE, unit types are retrieved, otherwise not.}

-#  \item{readDirection}{If @TRUE, unit directions are retrieved, otherwise not.}

+#  \item{readDirection}{If @TRUE, unit \emph{and} group directions are

+#    retrieved, otherwise not.}

 #  \item{stratifyBy}{A @character string specifying which and how

 #    elements in group fields are returned.

 #    If \code{"nothing"}, elements are returned as is, i.e. as @vectors.

@@ -44,8 +45,13 @@

 #  @list structure with three components:

 #  \item{groups}{A @list with one component for each group 

 #   (also called block). The information on each group is a 

-#   @list with five components: \code{x}, \code{y}, 

-#   \code{pbase}, \code{tbase}, \code{expos}, and \code{indices}.}

+#   @list of up to seven components: \code{x}, \code{y}, 

+#   \code{pbase}, \code{tbase}, \code{expos}, \code{indices},

+#   and \code{direction}.

+#   All fields but the latter have the same number of values as 

+#   there are cells in the group.  The latter field has only

+#   one value indicating the direction for the whole group.

+#  }

 #  \item{type}{An @integer specifying the type of the

 #    unit, where 1 is "expression", 2 is "genotyping", 3 is "CustomSeq", 

 #    and 4 "tag".}

@@ -242,6 +248,8 @@ readCdfUnits <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE, read

 ############################################################################

 # HISTORY:

+# 2006-12-30

+# o Now 'readDirection=TRUE' also return group directions.

 # 2006-03-28

 # o Unit indices are now one-based. /HB

 # o Renamed argument 'readCells' to 'readIndices'. /HB

@@ -1360,7 +1360,8 @@ extern "C" {

     PROTECT(unitNames = NEW_CHARACTER(nbrOfUnits));

     int nbrOfUnitElements = i_readGroups + i_readType + i_readDirection;

-    int nbrOfGroupElements = 2*i_readXY + 2*i_readBases + i_readExpos + i_readIndices;

+    int nbrOfGroupElements = 2*i_readXY + 2*i_readBases + i_readExpos 

+                                          + i_readIndices + i_readDirection;

     /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -1392,6 +1393,10 @@ extern "C" {

       if (i_readExpos) {

         SET_STRING_ELT(cell_list_names, fieldIdx++, mkChar("expos"));

       }

+

+      if (i_readDirection) {

+        SET_STRING_ELT(cell_list_names, fieldIdx++, mkChar("direction"));

+      }

     }

@@ -1573,6 +1578,14 @@ extern "C" {

            * Assign field values

 					 * - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

           fieldIdx = 0;

+

+          if (i_readDirection) {

+            PROTECT(tmp = allocVector(INTSXP, 1));

+            INTEGER(tmp)[0] = group.GetDirection();

+            UNPROTECT(1);

+            SET_VECTOR_ELT(cell_list, fieldIdx++, tmp);

+          }

+

           /** do I have to make the attribute vector everytime? **/

           if (i_readXY) {

             SET_VECTOR_ELT(cell_list, fieldIdx++, xvals);

@@ -1750,6 +1763,9 @@ extern "C" {

 /***************************************************************************

  * HISTORY:

+ * 2006-12-30

+ * o Added group directions to R_affx_get_cdf_units() too.  That is the

+ *   most important group element missing. /HB

  * 2006-08-28

  * o If a unit index is out of range, the error now show the invalid index.

  * 2006-04-02