@@ -6,7 +6,7 @@

 #' @rdname cover

 #' @aliases cover

 #' 

-setGeneric("cover", function(data, ...) standardGeneric("cover"))

+setGeneric("cover", function(.data, ...) standardGeneric("cover"))

 #' Method map

 #' 

@@ -27,7 +27,7 @@ setGeneric("map", function(x, y, ...) standardGeneric("map"))

 #' @rdname take

 #' @aliases take,GMQLDataset-method

 #' 

-setGeneric("take", function(data, ...) standardGeneric("take"))

+setGeneric("take", function(.data, ...) standardGeneric("take"))

 #' Method extend

@@ -4,29 +4,27 @@

 #' Condition evaluation functions

 #'

-#' These functions are used to support joinBy and/or groupBy function parameter.

-#' They create a 2-D array made up by two coloumn:

-#' type of condition evaluation and the metadata attribute name

+#' This function is used to support joinBy and/or groupBy function parameter.

 #'

-#'

-#' @param default series of string identifying a name of metadata attribute 

-#' to be evaluated.

-#' It defines a DEFAULT evaluation of the input values.

+#' @param 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.

 #' 

-#' @param full series of string identifying a name of metadata attribute 

-#' to be evaluated.

+#' @param 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.

 #' 

-#' @param exact series of string identifying a name of metadata attribute 

-#' to be evaluated.

+#' @param 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. 

 #' 

-#' @return list of 2-D array containing method of evaluation and metadata

+#' @return list of 2-D array containing method of evaluation and metadata 

+#' attribute name

 #' 

 #' @examples

 #' 

@@ -41,7 +39,7 @@ condition_evaluation <- function(default = c(""), full = c(""), exact = c(""))

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

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

     ex <- .condition("EXACT",exact)

-    list("def" = df, "full" = fn, "exact" = ex)

+    list("condition" = list("def" = df, "full" = fn, "exact" = ex))

 }

 .condition <- function(cond, array)

@@ -21,7 +21,7 @@

 #' if NULL no filtering action occures

 #' (i.e every sample is taken for region filtering)

 #' @param metadata_prefix vector of strings that will support the metadata

-#' filtering. If defined every defined 'metadata' are concatenated with the 

+#' filtering. If defined, each 'metadata' are concatenated with the 

 #' corresponding prefix.

 #' @param regions vector of strings that extracts only region attribute 

 #' specified; if NULL no regions attribute is taken and the output is only 

@@ -27,7 +27,7 @@

 #' @importFrom methods is

 #' @importFrom rJava J .jnull .jarray

 #' 

-#' @param data GMQLDataset class object

+#' @param .data GMQLDataset class object

 #' @param min_acc minimum number of overlapping regions to be considered 

 #' during execution. It is an integer number, declared also as string.

 #' minAcc accepts also:

@@ -124,10 +124,10 @@

 #' @aliases cover-method

 #' @export

 setMethod("cover", "GMQLDataset",

-            function(data, min_acc, max_acc, groupBy = NULL, 

+            function(.data, min_acc, max_acc, groupBy = NULL, 

                     variation = "cover", ...)

             {

-                val <- data@value

+                val <- value(.data)

                 s_min <- substitute(min_acc)

                 s_min <- .trasform_cover(deparse(s_min))                

                 s_max <- substitute(max_acc)

@@ -143,19 +143,23 @@ setMethod("cover", "GMQLDataset",

-gmql_cover <- function(data, min_acc, max_acc, groupBy, aggregates, flag)

+gmql_cover <- function(input_data, min_acc, max_acc, groupBy, aggregates, flag)

 {

-    

     if(!is.null(groupBy))

     {

-        cond <- .join_condition(groupBy)

-        if(is.null(cond))

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

+        if("condition" %in% names(groupBy))

+        {

+            cond <- .join_condition(groupBy)

+            if(is.null(cond))

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

+            else

+                join_matrix <- .jarray(cond, dispatch = TRUE)

+        }

         else

-            join_condition_matrix <- .jarray(cond, dispatch = TRUE)

+            stop("use function condition_evaluation()")

     }

     else

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

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

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

     {

@@ -167,33 +171,33 @@ gmql_cover <- function(data, min_acc, max_acc, groupBy, aggregates, flag)

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

     response <- switch(flag,

-        "COVER" = WrappeR$cover(min_acc, max_acc, join_condition_matrix,

-                                    metadata_matrix, data),

-        "FLAT" = WrappeR$flat(min_acc, max_acc, join_condition_matrix,

-                                    metadata_matrix, data),

-        "SUMMIT" = WrappeR$summit(min_acc,max_acc, join_condition_matrix,

-                                    metadata_matrix, data),

-        "HISTOGRAM" = WrappeR$histogram(min_acc, max_acc, 

-                        join_condition_matrix, metadata_matrix, data))

+        "COVER" = WrappeR$cover(min_acc, max_acc, join_matrix,

+                                    metadata_matrix, input_data),

+        "FLAT" = WrappeR$flat(min_acc, max_acc, join_matrix,

+                                    metadata_matrix, input_data),

+        "SUMMIT" = WrappeR$summit(min_acc,max_acc, join_matrix,

+                                    metadata_matrix, input_data),

+        "HISTOGRAM" = WrappeR$histogram(min_acc, max_acc, join_matrix, 

+                                    metadata_matrix, input_data))

     if(is.null(response))

         stop("no admissible variation: cover, flat, summit, histogram")

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

 .check_cover_param <- function(param, is_min)

 {

-    if(length(param)>1)

+    if(length(param))

         stop("length > 1")

     if(is.numeric(param))

     {

-        if(param<=0)

+        if(param <= 0)

             stop("No negative value")

         else

             return(as.character(param))

@@ -17,16 +17,9 @@

 #' 

 #' @param x GMQLDataset class object

 #' @param y GMQLDataset class object

-#' @param joinBy list of evalation functions to define evaluation on metadata:

-#' \itemize{

-#' \item{\code{\link{FN}}(value): Fullname evaluation, two attributes match 

-#' if they both end with \emph{value} and, if they have further prefixes,

-#' the two prefix sequence are identical}

-#' \item{\code{\link{EX}}(value): Exact evaluation, only attributes exactly 

-#' 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}.}

-#' }

+#' @param joinBy \code{\link{condition_evaluation}} function to support 

+#' methods with groupBy or JoinBy input paramter

+#' 

 #' @param is_exact single logical value: TRUE means that the region difference 

 #' is executed only on regions in left_input_data with exactly the same 

 #' coordinates of at least one region present in right_input_data; 

@@ -62,7 +55,7 @@

 #' ## do not overlap any region in s2; 

 #' ## metadata of the result are the same as the metadata of s1.

 #' 

-#' out_t = setdiff(data1, data2, DF("antibody_target"))

+#' out_t = setdiff(data1, data2, condition_evaluation(c("cell")))

 #'

 #' @name setdiff

 #' @aliases setdiff,GMQLDataset,GMQLDataset-method

@@ -71,33 +64,33 @@

 setMethod("setdiff", c("GMQLDataset","GMQLDataset"),

             function(x, y, joinBy = NULL, is_exact = FALSE)

             {

-                ptr_data_x = x@value

-                ptr_data_y = y@value

+                ptr_data_x = value(x)

+                ptr_data_y = value(y)

                 gmql_difference(ptr_data_x, ptr_data_y, is_exact, joinBy)

             })

 gmql_difference <- function(left_data, right_data, is_exact, joinBy)

 {

-    if(!is.list(joinBy))

-        stop("joinBy: must be a list")

-    

-    if(!is.null(joinBy) && !length(joinBy) == 0)

+    if(!is.null(joinBy))

     {

         cond <- .join_condition(joinBy)

-        join_condition_matrix <- .jarray(cond, dispatch = TRUE)

+        if(is.null(cond))

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

+        else

+            join_matrix <- .jarray(cond, dispatch = TRUE)

     }

     else

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

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

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

-    response <- WrappeR$difference(join_condition_matrix, right_data, 

-                                        left_data, is_exact)

+    response <- WrappeR$difference(join_matrix, left_data, right_data, 

+                                        is_exact)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -59,7 +59,7 @@

 #' @export

 setMethod("extend", "GMQLDataset", function(.data, ...)

             {

-                ptr_data = .data@value

+                ptr_data = value(.data)

                 meta <- list(...)

                 gmql_extend(ptr_data, meta)

             })

@@ -67,7 +67,7 @@ setMethod("extend", "GMQLDataset", function(.data, ...)

 gmql_extend <-function(input_data, meta)

 {

-    if(!is.null(meta) && !length(meta) == 0)

+    if(!is.null(meta) && length(meta))

     {

         aggr <- .aggregates(meta, "META_AGGREGATES")

         metadata_matrix <- .jarray(aggr, dispatch = TRUE)

@@ -78,9 +78,9 @@ gmql_extend <-function(input_data, meta)

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

     response <- WrappeR$extend(metadata_matrix, input_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -80,11 +80,20 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,

 {

     if(!is.null(group_meta))

     {

-        cond <- .join_condition(group_meta)

-        join_condition_matrix <- .jarray(cond, dispatch = TRUE)

+        if("condition" %in% names(group_meta))

+        {

+            cond <- .join_condition(group_meta)

+            if(is.null(cond))

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

+            else

+                join_matrix <- .jarray(cond, dispatch = TRUE)

+        }

+        else

+            stop("use function condition_evaluation()")

     }

     else

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

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

+    

     if(!is.null(group_reg))

     {

@@ -94,7 +103,7 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,

         group_reg <- group_reg[!group_reg %in% ""]

         group_reg <- group_reg[!duplicated(group_reg)]

-        if(length(group_reg)==0)

+        if(!length(group_reg))

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

         group_reg <- .jarray(metadata)

@@ -102,7 +111,7 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,

     else

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

-    if(!is.null(meta_aggregates) && !length(meta_aggregates) == 0)

+    if(!is.null(meta_aggregates) && length(meta_aggregates))

     {

         aggr <- .aggregates(meta_aggregates,"AGGREGATES")

         metadata_matrix <- .jarray(aggr, dispatch = TRUE)

@@ -110,7 +119,7 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,

     else

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

-    if(!is.null(region_aggregates) && !length(region_aggregates) == 0)

+    if(!is.null(region_aggregates) && length(region_aggregates))

     {

         aggr <- .aggregates(region_aggregates,"AGGREGATES")

         region_matrix <- .jarray(aggr, dispatch = TRUE)

@@ -119,12 +128,12 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,

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

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

-    response <- WrappeR$group(join_condition_matrix, metadata_matrix, 

-                                group_reg, region_matrix, input_data)

+    response <- WrappeR$group(join_matrix, metadata_matrix, group_reg, 

+                                region_matrix, input_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -45,9 +45,9 @@ init_gmql <- function(output_format = "GTF", remote_processing = FALSE,

                     url = NULL, username = NULL, password = NULL)

 {

     out_format <- toupper(output_format)

-    if(!identical(out_format,"TAB") && !identical(out_format,"GTF") && 

-                !identical(out_format,"COLLECT"))

-        stop("output_format must be TAB, GTF or COLLECT")

+    if(!out_format %in% c("TAB", "GTF", "COLLECT"))

+        stop("output_format: must be TAB, GTF or COLLECT")

+    

     .check_logical(remote_processing)

     # mettere attesa da input keyboard, controllare se token già esiste 

@@ -81,10 +81,10 @@

 #' @export

 setMethod("merge", c("GMQLDataset","GMQLDataset"),

                 function(x, y, genometric_predicate = NULL, 

-                    region_output = "contig", joinBy = NULL)

+                    region_output = "CAT", joinBy = NULL)

                 {

-                    ptr_data_x <- x@value

-                    ptr_data_y <- y@value

+                    ptr_data_x <- value(x)

+                    ptr_data_y <- value(y)

                     gmql_join(ptr_data_x, ptr_data_y, genometric_predicate, 

                                 joinBy, region_output)

                 })

@@ -118,12 +118,12 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,

     {

         cond <- .join_condition(joinBy)

         if(is.null(cond))

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

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

         else

-            join_condition_matrix <- .jarray(cond, dispatch = TRUE)

+            join_matrix <- .jarray(cond, dispatch = TRUE)

     }

     else

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

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

     ouput <- toupper(region_output)

     if(!ouput %in% c("CAT", "LEFT", "RIGHT", "INT", "BOTH", "RIGHT_DIST", 

@@ -132,12 +132,12 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,

                 or int (intersection)")

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

-    response <- WrappeR$join(genomatrix,join_condition_matrix, 

-                                ouput,right_data, left_data)

+    response <- WrappeR$join(genomatrix, join_matrix, ouput, left_data, 

+                                right_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -86,34 +86,40 @@

 setMethod("map", "GMQLDataset",

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

             {

-                r_data <- x@value

-                l_data <- y@value

+                left_data <- value(x)

+                right_data <- value(y)

                 aggregates = list(...)

-                gmql_map(r_data, l_data, aggregates, joinBy)

+                gmql_map(left_data, right_data, aggregates, joinBy)

             })

-gmql_map <- function(l_data, r_data, aggregates, joinBy)

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

 {

-    if(!is.null(aggregates) && !length(aggregates) == 0)

-        metadata_matrix <- .jarray(.aggregates(aggregates,"AGGREGATES"),

-                                    dispatch = TRUE)

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

+    {

+        aggr <- .aggregates(aggregates, "META_AGGREGATES")

+        metadata_matrix <- .jarray(aggr, dispatch = TRUE)

+    }

     else

-        metadata_matrix = .jnull("java/lang/String")

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

     if(!is.null(joinBy))

-        join_condition_matrix <- .jarray(.join_condition(joinBy),

-                                            dispatch = TRUE)

+    {

+        cond <- .join_condition(joinBy)

+        if(is.null(cond))

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

+        else

+            join_matrix <- .jarray(cond, dispatch = TRUE)

+    }

     else

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

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

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

-    response<-WrappeR$map(join_condition_matrix, metadata_matrix, l_data, 

-                            r_data)

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

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -39,16 +39,16 @@ execute <- function()

     response <- WrappeR$execute()

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

     {

         if(remote_proc)

         {

             url <- WrappeR$get_url()

             .download_or_upload()

-            res <- serialize_query(url,FALSE,data)

+            res <- serialize_query(url,FALSE,val)

         }

     }

 }

@@ -56,8 +56,8 @@ execute <- function()

 .download_or_upload <- function()

 {

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

-    data <- .jevalArray(WrappeR$get_dataset_list(),simplify = TRUE)

-    data_list <- apply(data, 1, as.list)

+    datasets <- .jevalArray(WrappeR$get_dataset_list(),simplify = TRUE)

+    data_list <- apply(datasets, 1, as.list)

     url <- WrappeR$get_url()

     remote <- WrappeR$is_remote_processing()

     if(remote)

@@ -76,7 +76,7 @@ execute <- function()

 collect.GMQLDataset <- function(x, dir_out = getwd(), name = "ds1")

 {

-    ptr_data <- x@value

+    ptr_data <- value(x)

     gmql_materialize(ptr_data, dir_out, name)

 }

@@ -146,9 +146,9 @@ gmql_materialize <- function(input_data, dir_out, name)

     response <- WrappeR$materialize(input_data, res_dir_out)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

         invisible(NULL)

 }

@@ -169,7 +169,7 @@ gmql_materialize <- function(input_data, dir_out, name)

 #' @importFrom rJava J .jevalArray

 #' @importFrom GenomicRanges GRangesList

 #' 

-#' @param data returned object from any GMQL function

+#' @param .data returned object from any GMQL function

 #' @param rows number of rows for each sample regions that you want to 

 #' retrieve and store in memory.

 #' By default it is 0 that means take all rows for each sample

@@ -198,9 +198,9 @@ gmql_materialize <- function(input_data, dir_out, name)

 #' @aliases take-method

 #' @export

 setMethod("take", "GMQLDataset",

-            function(data, rows = 0L)

+            function(.data, rows = 0L)

             {

-                ptr_data <- data@value

+                ptr_data <- value(.data)

                 gmql_take(ptr_data, rows)

             })

@@ -229,11 +229,11 @@ gmql_take <- function(input_data, rows = 0L)

     reg_data_frame <- as.data.frame(reg)

     list <- split(reg_data_frame, reg_data_frame[1])

-    names <- c("seqname","start","end","strand",schema)

+    seq_name <- c("seqname","start","end","strand",schema)

     sampleList <- lapply(list, function(x){

         x <- x[-1]

-        names(x) <- names

+        names(x) <- seq_name

         g <- GenomicRanges::makeGRangesFromDataFrame(x,

                                     keep.extra.columns = TRUE,

                                     start.field = "start",

@@ -51,7 +51,7 @@

 setMethod("aggregate", "GMQLDataset",

             function(x, groupBy = NULL)

             {

-                ptr_data = x@value

+                ptr_data = value(x)

                 gmql_merge(ptr_data, groupBy)

             })

@@ -61,20 +61,20 @@ gmql_merge <- function(input_data, groupBy)

     {

         cond <- .join_condition(groupBy)

         if(is.null(cond))

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

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

         else

-            join_condition_matrix <- .jarray(cond, dispatch = TRUE)

+            join_matrix <- .jarray(cond, dispatch = TRUE)

     }

     else

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

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

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

-    response <- WrappeR$merge(join_condition_matrix, input_data)

+    response <- WrappeR$merge(join_matrix, input_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -1,8 +1,8 @@

 arrange.GMQLDataset <- function(.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)

 {

-    ptr_data <- .data@value

+    ptr_data <- value(.data)

     gmql_order(ptr_data, metadata_ordering, regions_ordering, 

                 fetch_opt, num_fetch, reg_fetch_opt, reg_num_fetch)

 }

@@ -85,7 +85,7 @@ arrange.GMQLDataset <- function(.data, metadata_ordering = NULL,

 #' @export

 setMethod("arrange", "GMQLDataset", arrange.GMQLDataset)

-gmql_order <- function(data, metadata_ordering, regions_ordering,

+gmql_order <- function(input_data, metadata_ordering, regions_ordering,

                     fetch_opt, num_fetch, reg_fetch_opt, reg_num_fetch)

 {

     if(!is.null(fetch_opt))

@@ -96,12 +96,12 @@ gmql_order <- function(data, metadata_ordering, regions_ordering,

     if(!is.null(num_fetch))

         .check_opt_value(num_fetch)

     else

-        num_fetch <- 0

+        num_fetch <- 0L

     if(!is.null(reg_num_fetch))

         .check_opt_value(reg_num_fetch)

     else

-        reg_num_fetch <- 0  

+        reg_num_fetch <- 0L

     if(!is.null(reg_fetch_opt))

         reg_fetch_opt <- .check_option(reg_fetch_opt)

@@ -127,13 +127,13 @@ gmql_order <- function(data, metadata_ordering, regions_ordering,

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

     response <- WrappeR$order(meta_matrix, fetch_opt, as.integer(num_fetch), 

                         reg_fetch_opt, as.integer(reg_num_fetch), 

-                        region_matrix, data)

+                        region_matrix, input_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

@@ -146,9 +146,7 @@ gmql_order <- function(data, metadata_ordering, regions_ordering,

 .check_option <- function(opt)

 {

     opt <- tolower(opt)

-    if(!identical("mtop",opt) && !identical("mtopp",opt) && 

-        !identical("mtopg",opt) && !identical("rtop",opt) && 

-        !identical("rtopp",opt) && !identical("rtopg",opt))

+    if(!opt %in% c("mtop", "mtopp", "mtopg", "rtop", "rtopp", "rtopg"))

         stop("option not admissable")

     opt

 }

@@ -170,11 +170,11 @@ gmql_project <-function(input_data, metadata, metadata_update, all_but_meta,

     response <- WrappeR$project(metadata, metadata_update, all_but_meta, 

                     regions, regions_update, all_but_reg, input_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

 .trasform_update <- function(predicate=NULL)

@@ -112,8 +112,8 @@ read_dataset <- function(dataset, parser = "CustomParser", is_local=TRUE,

     }

     parser_name <- .check_parser(parser)

-    response <- WrappeR$readDataset(dataset,parser_name, is_local, is_GMQL, 

-                                        schema_matrix,schema_XML)

+    response <- WrappeR$readDataset(dataset, parser_name, is_local, is_GMQL, 

+                                        schema_matrix, schema_XML)

     error <- strtoi(response[1])

     data <- response[2]

     if(error!=0)

@@ -142,11 +142,10 @@ read <- function(samples)

     {

         #repeat meta for each sample in samples list

         len <- length(samples)

-        warning("GrangesList has no metadata.

-We provide two metadata for you")

-        index_meta <- rep(1:len,each = len)

+        warning("No metadata.\nWe provide two metadata for you")

+        index_meta <- rep(seq_len(len),each = len)

         rep_meta <- rep(c("provider","PoliMi", "application", "RGMQL"),

-                            times=len)

+                            times = len)

         meta_matrix <- matrix(rep_meta,ncol = 2,byrow = TRUE)

         meta_matrix <- cbind(index_meta,meta_matrix)

     }

@@ -199,12 +198,8 @@ We provide two metadata for you")

 .check_parser <- function(parser)

 {

     parser <- toupper(parser)

-    if(!identical(parser,"BEDPARSER") && !identical(parser,"ANNPARSER") &&

-        !identical(parser,"BROADPROJPARSER") && 

-        !identical(parser,"BASICPARSER") && 

-        !identical(parser,"NARROWPEAKPARSER") && 

-        !identical(parser,"RNASEQPARSER") && 

-        !identical(parser,"CUSTOMPARSER"))

+    if(!parser %in% c("BEDPARSER","ANNPARSER","BROADPROJPARSER","BASICPARSER",

+                "NARROWPEAKPARSER","RNASEQPARSER","CUSTOMPARSER"))

         stop("parser not defined")

     parser

@@ -137,7 +137,7 @@ gmql_select <- function(input_data, predicate, region_predicate, s_join)

 #' This function is used as support to the filter method to define 

 #' semijoin conditions on metadata  

 #' 

-#' @param data GMQLDataset class object

+#' @param .data GMQLDataset class object

 #' 

 #' @param 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 

@@ -189,7 +189,7 @@ gmql_select <- function(input_data, predicate, region_predicate, s_join)

 #' @return semijoin condition as list

 #' @export

 #' 

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

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

 {

     if(!is.list(groupBy))

         stop("groupBy: must be a list")

@@ -203,7 +203,7 @@ semijoin <- function(data, not_in = FALSE, groupBy = NULL)

         stop("data: Must be a GMQLDataset object") 

     .check_logical(not_in)

-    ptr_data <- data@value

+    ptr_data <- value(.data)

     data_cond <- cbind(ptr_data,not_in)

     cond <- .join_condition(semij_cond)

@@ -53,7 +53,6 @@

 setMethod("union", c("GMQLDataset","GMQLDataset"),

             function(x, y)

             {

-                

                 ptr_data_x = value(x)

                 ptr_data_y = value(y)

                 gmql_union(ptr_data_x, ptr_data_y)

@@ -64,9 +63,9 @@ gmql_union <- function(left_data, right_data)

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

     response <- WrappeR$union(left_data, right_data)

     error <- strtoi(response[1])

-    data <- response[2]

+    val <- response[2]

     if(error!=0)

-        stop(data)

+        stop(val)

     else

-        GMQLDataset(data)

+        GMQLDataset(val)

 }

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

@@ -11,16 +11,8 @@

 \arguments{

 \item{x}{GMQLDataset class object}

-\item{groupBy}{list of evalation functions to define evaluation on metadata:

-\itemize{

-\item{\code{\link{FN}}(value): Fullname evaluation, two attributes match 

-if they both end with \emph{value} and, if they have further prefixes,

-the two prefix sequences are identical}

-\item{\code{\link{EX}}(value): Exact evaluation, only attributes exactly 

-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{groupBy}{\code{\link{condition_evaluation}} function to support 

+methods with groupBy or JoinBy input paramter}

 }

 \value{

 GMQLDataset object. It contains the value to use as input 

@@ -57,6 +49,6 @@ exp = read_dataset(test_path)

 ## antibody_target and cell metadata

 ## attributes.

-merged = aggregate(exp, list(DF("antibody_target","cell")))

+merged = aggregate(exp, condition_evaluation(c("antibody_target","cell")))

 }

@@ -2,46 +2,35 @@

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

 \name{Evaluation-Function}

 \alias{Evaluation-Function}

-\alias{FN}

-\alias{Evaluation-Function}

-\alias{EX}

-\alias{Evaluation-Function}

-\alias{DF}

-\alias{Evaluation-Function}

 \alias{condition_evaluation}

 \title{Condition evaluation functions}

 \usage{

-FN(...)

-

-EX(...)

-

-DF(...)

-

-condition_evaluation(...)

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

 }

 \arguments{

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

-to be evaluated}

+\item{default}{series 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.

+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.

+It defines a EXACT evaluation of the input values.

+EXACT evaluation: only attributes exactly as value match; 

+no further prefixes are allowed.}

 }

 \value{

-2-D array containing method of evaluation and metadata

+list of 2-D array containing method of evaluation and metadata 

+attribute name

 }

 \description{

-These functions are used to support joinBy and/or groupBy function parameter.

-They create a 2-D array made up by two coloumn:

-type of condition evaluation and the metadata attribute name

-}

-\details{

-\itemize{

-\item{FN: 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{EX: It defines a EXACT evaluation of the input values.

-EXACT evaluation: only attributes exactly as value match; 

-no further prefixes are allowed. }

-\item{DF: It defines a DEFAULT evaluation of the input values.

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

-}

+This function is used to support joinBy and/or groupBy function parameter.

 }

 \examples{

@@ -54,16 +54,8 @@ considering any amount of overlapping regions.

 ALL() / K, with N and K integer values  }

 }}

-\item{groupBy}{list of evalation functions to define evaluation on metadata:

-\itemize{

-\item{\code{\link{FN}}(value): Fullname evaluation, two attributes match 

-if they both end with \emph{value} and, if they have further prefixes,

-the two prefix sequence are identical}

-\item{\code{\link{EX}}(value): Exact evaluation, only attributes exactly 

-as \emph{value} match; no further prefixes are allowed. }