@@ -28,7 +28,7 @@ export(SUM)

 export(UP)

 export(compile_query)

 export(compile_query_fromfile)

-export(condition_evaluation)

+export(conds)

 export(delete_dataset)

 export(download_as_GRangesList)

 export(download_dataset)

@@ -34,7 +34,7 @@

 #' @aliases condition_evaluation

 #' @rdname condition_eval_func

 #' @export

-condition_evaluation <- function(default = c(""), full = c(""), exact = c(""))

+conds <- function(default = c(""), full = c(""), exact = c(""))

 {

     df <- .condition("DEF",default)

     fn <- .condition("FULL",full)

@@ -43,6 +43,20 @@

 #' having left (right) coordinates equal to the minimum (maximum) of the 

 #' corresponding coordinate values in the 'x' and 'y' regions satisfying 

 #' the genometric predicate)}

+#' \item{LEFT_DISTINCT: It outputs the duplicate elimination of "x" output 

+#' regions with the same values, regardless the "y" paired region and its 

+#' values. In this case, the output regions attributes and their values are 

+#' all those of "x", and the output metadata are equal to the "x" metadata, 

+#' without additional prefixes}

+#' \item{RIGHT_DISTINCT: It outputs the duplicate elimination of "y" output 

+#' regions with the same values, regardless the "x" paired region and its 

+#' values. In this case, the output regions attributes and their values are 

+#' all those of "y", and the output metadata are equal to the "y" metadata, 

+#' without additional prefixes}

+#' \item{BOTH: It outputs the same regions as LEFT, but it adds in the output 

+#' region attributes the coordinates of the "y" dataset region that, 

+#' together with the output "x" dataset region, satisfies the equi predicate 

+#' and the genometric predicate}

 #' }

 #'

 #' @return GMQLDataset object. It contains the value to use as input 

@@ -85,13 +99,13 @@ setMethod("merge", c("GMQLDataset","GMQLDataset"),

                 {

                     ptr_data_x <- value(x)

                     ptr_data_y <- value(y)

-                    gmql_join(ptr_data_x, ptr_data_y, genometric_predicate, 

-                                joinBy, region_output, reg_attr)

+                    gmql_join(ptr_data_x, ptr_data_y, 

+                        genometric_predicate, joinBy, region_output, reg_attr)

                 })

 gmql_join <- function(left_data, right_data, genometric_predicate, joinBy, 

-                            region_output, reg_attributes)

+                        region_output, reg_attributes)

 {

     if(!is.null(genometric_predicate))

     {

@@ -49,6 +49,8 @@

 #' \item{ \code{\link{DF}}(value): Default evaluation, the two attributes match 

 #' if both end with \emph{value}.}

 #' }

+#' @param count_name string defining the metadata count name; if it is 

+#' not specifying the name is "count_left_right" 

 #' 

 #' @return GMQLDataset object. It contains the value to use as input 

 #' for the subsequent GMQLDataset method

@@ -84,16 +86,16 @@

 #' @aliases map-method

 #' @export

 setMethod("map", "GMQLDataset",

-            function(x, y, ..., joinBy = NULL)

+            function(x, y, ..., joinBy = NULL, count_name = NULL)

             {

                 left_data <- value(x)

                 right_data <- value(y)

                 aggregates = list(...)

-                gmql_map(left_data, right_data, aggregates, joinBy)

+                gmql_map(left_data, right_data,aggregates, joinBy, count_name)

             })

-gmql_map <- function(left_data, right_data, aggregates, joinBy)

+gmql_map <- function(left_data, right_data, aggregates, joinBy, count_name)

 {

     if(!is.null(aggregates) && length(aggregates))

     {

@@ -114,8 +116,17 @@ gmql_map <- function(left_data, right_data, aggregates, joinBy)

     else

         join_matrix <- .jnull("java/lang/String")

+    if(!is.null(count_name))

+    {

+        if(!is.character(count_name))

+            stop("count_name: must be string")

+    }

+    else

+        count_name <- .jnull("java/lang/String")

+    

     WrappeR <- J("it/polimi/genomics/r/Wrapper")

-    response<-WrappeR$map(join_matrix, metadata_matrix, left_data, right_data)

+    response<-WrappeR$map(join_matrix, metadata_matrix, count_name, left_data, 

+                            right_data)

     error <- strtoi(response[1])

     val <- response[2]

     if(error!=0)

@@ -32,8 +32,8 @@ arrange.GMQLDataset <- function(.data, metadata_ordering = NULL,

 #' first k samples; it can assume the values:

 #' \itemize{

 #' \item{mtop: it fetches the first k samples}

-#' \item{mtopg: it fetches the percentage of samples.}

-#' \item{mtopp: it fetches the first k samples in each group.}

+#' \item{mtopp: it fetches the first k percentage of samples.}

+#' \item{mtopg: it fetches the first k samples in each group.}

 #' 

 #' }

 #' if NULL, \emph{num_fetch} is not considered 

@@ -49,8 +49,8 @@ arrange.GMQLDataset <- function(.data, metadata_ordering = NULL,

 #' first k regions; it can assume the values:

 #' \itemize{

 #' \item{rtop: it fetches the first k regions.}

-#' \item{rtopg: it fetches the first k percentage of regions.}

-#' \item{rtopp: it fetches the first k regions in each group.}

+#' \item{rtopp: it fetches the first k percentage of regions.}

+#' \item{rtopg: it fetches the first k regions in each group.}

 #' }

 #' if NULL, \emph{reg_num_fetch} is not considered 

 #' 

Binary files a/inst/java/GMQL.jar and b/inst/java/GMQL.jar differ

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

 \title{Method arrange}

 \usage{

 \S4method{arrange}{GMQLDataset}(.data, metadata_ordering = NULL,

-  regions_ordering = NULL, fetch_opt = NULL, num_fetch = 0,

-  reg_fetch_opt = NULL, reg_num_fetch = 0)

+  regions_ordering = NULL, fetch_opt = NULL, num_fetch = 0L,

+  reg_fetch_opt = NULL, reg_num_fetch = 0L)

 }

 \arguments{

 \item{.data}{GMQLDataset class object}

@@ -2,25 +2,26 @@

 % Please edit documentation in R/evaluation-functions.R

 \name{Evaluation-Function}

 \alias{Evaluation-Function}

+\alias{conds}

 \alias{condition_evaluation}

 \title{Condition evaluation functions}

 \usage{

-condition_evaluation(default = c(""), full = c(""), exact = c(""))

+conds(default = c(""), full = c(""), exact = c(""))

 }

 \arguments{

-\item{default}{series of string identifying a name of metadata attribute 

-to be evaluated.

-It defines a DEFAULT evaluation of the input values.

+\item{default}{concatenation of string identifying a name of metadata 

+attribute to be evaluated. 

+It defines a DEFAULT evaluation of the input values. 

 DEFAULT evaluation: the two attributes match if both end with value.}

-\item{full}{series of string identifying a name of metadata attribute 

-to be evaluated.

+\item{full}{concatenation of string identifying a name of metadata 

+attribute to be evaluated.

 It defines a FULL (FULLNAME) evaluation of the input values.

 FULL evaluation: two attributes match if they both end with value and,

 if they have further prefixes, the two prefix sequences are identical.}

-\item{exact}{series of string identifying a name of metadata attribute 

-to be evaluated.

+\item{exact}{concatenation of string identifying a name of metadata 

+attribute to be evaluated.

 It defines a EXACT evaluation of the input values.

 EXACT evaluation: only attributes exactly as value match; 

 no further prefixes are allowed.}

@@ -7,13 +7,13 @@

 \alias{cover,GMQLDataset-method}

 \title{Method cover}

 \usage{

-cover(data, ...)

+cover(.data, ...)

-\S4method{cover}{GMQLDataset}(data, min_acc, max_acc, groupBy = NULL,

+\S4method{cover}{GMQLDataset}(.data, min_acc, max_acc, groupBy = NULL,

   variation = "cover", ...)

 }

 \arguments{

-\item{data}{GMQLDataset class object}

+\item{.data}{GMQLDataset class object}

 \item{...}{a series of expressions separated by comma in the form 

 \emph{key} = \emph{aggregate}. The \emph{aggregate} is an object of 

@@ -10,7 +10,7 @@

 \usage{

 map(x, y, ...)

-\S4method{map}{GMQLDataset}(x, y, ..., joinBy = NULL)

+\S4method{map}{GMQLDataset}(x, y, ..., joinBy = NULL, count_name = NULL)

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -44,6 +44,9 @@ as \emph{value} match; no further prefixes are allowed.}

 \item{ \code{\link{DF}}(value): Default evaluation, the two attributes match 

 if both end with \emph{value}.}

 }}

+

+\item{count_name}{string defining the metadata count name; if it is 

+not specifying the name is "count_left_right"}

 }

 \value{

 GMQLDataset object. It contains the value to use as input 

@@ -7,7 +7,7 @@

 \title{Method merge}

 \usage{

 \S4method{merge}{GMQLDataset,GMQLDataset}(x, y, genometric_predicate = NULL,

-  region_output = "contig", joinBy = NULL)

+  region_output = "CAT", joinBy = NULL, reg_attr = NULL)

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -35,10 +35,26 @@ that satisfy the genometric predicate, (i.e. the output regionis defined as

 having left (right) coordinates equal to the minimum (maximum) of the 

 corresponding coordinate values in the 'x' and 'y' regions satisfying 

 the genometric predicate)}

+\item{LEFT_DISTINCT: It outputs the duplicate elimination of "x" output 

+regions with the same values, regardless the "y" paired region and its 

+values. In this case, the output regions attributes and their values are 

+all those of "x", and the output metadata are equal to the "x" metadata, 

+without additional prefixes}

+\item{RIGHT_DISTINCT: It outputs the duplicate elimination of "y" output 

+regions with the same values, regardless the "x" paired region and its 

+values. In this case, the output regions attributes and their values are 

+all those of "y", and the output metadata are equal to the "y" metadata, 

+without additional prefixes}

+\item{BOTH: outputs the same regions as LEFT, but it adds in the output 

+region attributes the coordinates of the "y" dataset region that, 

+together with the output "x" dataset region, satisfies the equi predicate 

+and the genometric predicate}

 }}

 \item{joinBy}{\code{\link{condition_evaluation}} function to support 

 methods with groupBy or JoinBy input paramter}

+

+\item{reg_attr}{vector of string made up by schema field attribute}

 }

 \value{

 GMQLDataset object. It contains the value to use as input 

@@ -4,10 +4,10 @@

 \alias{semijoin}

 \title{Semijoin condtion}

 \usage{

-semijoin(data, not_in = FALSE, groupBy = NULL)

+semijoin(.data, not_in = FALSE, groupBy = NULL)

 }

 \arguments{

-\item{data}{GMQLDataset class object}

+\item{.data}{GMQLDataset class object}

 \item{not_in}{logical value: TRUE => for a given sample of input dataset

 ".data" in \code{\link{filter}} method if and only if there exists at 

@@ -8,12 +8,12 @@

 \alias{take-method}

 \title{Method take}

 \usage{

-take(data, ...)

+take(.data, ...)

-\S4method{take}{GMQLDataset}(data, rows = 0L)

+\S4method{take}{GMQLDataset}(.data, rows = 0L)

 }

 \arguments{

-\item{data}{returned object from any GMQL function}

+\item{.data}{returned object from any GMQL function}

 \item{...}{Additional arguments for use in other specific methods of the 

 generic take function}