@@ -1,10 +1,10 @@

 Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

-Version: 0.99.31

+Version: 0.99.32

 Author: Simone Pallotta, Marco Masseroli

 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>

-Description: This RGMQL package brings the GenoMetric Query Language (GMQL)

+Description: This package brings the GenoMetric Query Language (GMQL)

     functionalities into the R environment. GMQL is a high-level, declarative

     language to query and compare multiple and heterogeneous genomic datasets

     for biomedical knowledge discovery. It allows expressing easily queries and

@@ -63,12 +63,47 @@ Imports:

     methods,

     S4Vectors,

     dplyr,

-    stats

+    stats,

+    BiocGenerics

 Depends:

     R(>= 3.4.2)

 VignetteBuilder: knitr

-Suggests:

+Suggests: 

     BiocStyle,

     knitr,

     rmarkdown

-biocViews: Software,Infrastructure,DataImport,Network,SingleCell

+biocViews:

+    Software,

+    Infrastructure,

+    DataImport,

+    Network,

+    SingleCell

+Collate: 

+    'GMQLDataset-class.R'

+    'Cover.R'

+    'Difference.R'

+    'Extend.R'

+    'GMQL4TFarm.R'

+    'GMQLtoGRanges.R'

+    'GRangesToGMQL.R'

+    'Join.R'

+    'Map.R'

+    'Materialize.R'

+    'Merge.R'

+    'Order.R'

+    'Project.R'

+    'Read.R'

+    'Select.R'

+    'Union.R'

+    'Utils.R'

+    'aggregate-class.R'

+    'authOp.R'

+    'browseOp.R'

+    'condition-class.R'

+    'cover_param-class.R'

+    'datasetOp.R'

+    'distal-class.R'

+    'onLoad.R'

+    'operator-class.R'

+    'ordering-class.R'

+    'queryOp.R'

@@ -30,7 +30,6 @@ export(SUM)

 export(UP)

 export(compile_query)

 export(compile_query_fromfile)

-export(cover)

 export(delete_dataset)

 export(download_as_GRangesList)

 export(download_dataset)

@@ -41,7 +40,6 @@ export(import_gmql)

 export(init_gmql)

 export(login_gmql)

 export(logout_gmql)

-export(map)

 export(materialize)

 export(read)

 export(read_dataset)

@@ -64,10 +62,11 @@ export(trace_job)

 export(upload_dataset)

 exportMethods(aggregate)

 exportMethods(cover)

+exportMethods(extend)

 exportMethods(filter)

 exportMethods(join)

+exportMethods(map)

 exportMethods(materialize)

-exportMethods(mutate)

 exportMethods(setdiff)

 exportMethods(sort)

 exportMethods(subset)

@@ -77,6 +76,7 @@ import(httr)

 import(xml2)

 importClassesFrom(GenomicRanges,GRangesList)

 importClassesFrom(S4Vectors,DataTable)

+importFrom(BiocGenerics,subset)

 importFrom(GenomicRanges,makeGRangesFromDataFrame)

 importFrom(S4Vectors,metadata)

 importFrom(data.table,fread)

@@ -21,14 +21,15 @@

 #' yielding to one sample in the result for each group.

 #' Input samples that do not satisfy the \emph{groupby} condition 

 #' are disregarded.

-#'

+#' 

+#' @include GMQLDataset-class.R

 #' @importFrom methods is

 #' @importFrom rJava J

 #' @importFrom rJava .jnull

 #' @importFrom rJava .jarray

 #' 

 #' @param data GMQLDataset class object

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

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

 #' during execution

 #' Is a integer number, declared also as string.

 #' minAcc accept also:

@@ -38,7 +39,7 @@

 #' \item{and expression built using PARAMETER object: (ALL() + N) / K or

 #' ALL() / K }

 #' }

-#' @param maxAcc maximum number of overlapping regions to be considered 

+#' @param max_acc maximum number of overlapping regions to be considered 

 #' during execution

 #' Is a integer number, declared also as string.

 #' maxAcc accept also:

@@ -99,7 +100,8 @@

 #' the AccIndex region attribute.}

 #' \item{cover: default value.}

 #' }

-#'

+#' @param ... Additional arguments for use in specific methods.

+#' 

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

 #' for the subsequent GMQL function

 #' 

@@ -113,7 +115,7 @@

 #' init_gmql()

 #' test_path <- system.file("example","DATASET",package = "RGMQL")

 #' exp = read_dataset(test_path)

-#' res = cover(exp, 2, ANY())

+#' res = cover(exp, 2, "ANY")

 #'

 #' \dontrun{

 #' ## This GMQL statement computes the result grouping the input exp samples 

@@ -129,44 +131,25 @@

 #' res = cover(exp, 2, 3, c("cell"), list(min_pValue = MIN("pvalue")))

 #' }

 #' 

-#' 

-#' @rdname GMQLDataset-class

-#' @aliases cover, GMQLDataset--method

-#' 

-#' @export

-#' 

-setGeneric("cover", function(data, minAcc, maxAcc, ...)

-{

-    minAcc <- .trasform_cover(deparse(substitute(minAcc)))

-    maxAcc <- .trasform_cover(deparse(substitute(maxAcc)))

-    

-    min <- .check_cover_param(minAcc,TRUE)

-    max <- .check_cover_param(maxAcc,FALSE)

-    

-    gmql_cover(data,min,max,NULL,NULL,"COVER")

-})

-

-#' @rdname GMQLDataset-class

-#' @aliases cover, GMQLDataset--method

+#' @aliases cover, cover-method

 #' @export

 setMethod("cover", "GMQLDataset",

-            function(data, minAcc, maxAcc, groupBy = NULL, aggregates = NULL, 

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

                         variation = "cover")

             {

-                minAcc <- .trasform_cover(deparse(substitute(minAcc)))

-                maxAcc <- .trasform_cover(deparse(substitute(maxAcc)))

-                

-                min <- .check_cover_param(minAcc,TRUE)

-                max <- .check_cover_param(maxAcc,FALSE)

+                val <- data@value

+                q_max <- .check_cover_param(max_acc,FALSE)

+                q_min <- .check_cover_param(min_acc,FALSE)

                 flag = toupper(variation)

-                

-                gmql_cover(data@value, min, max, groupBy, aggregates, 

-                           flag)

+                gmql_cover(val, q_min, q_max, groupBy, aggregates, flag)

             })

-gmql_cover <- function(data, minAcc, maxAcc, groupBy = NULL, 

+

+

+gmql_cover <- function(data, min_acc, max_acc, groupBy = NULL, 

                         aggregates = NULL, flag)

 {

+    

     if(!is.null(groupBy))

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

                                             dispatch = TRUE)

@@ -181,14 +164,14 @@ gmql_cover <- function(data, minAcc, maxAcc, groupBy = NULL,

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

     response <- switch(flag,

-                "COVER" = WrappeR$cover(minAcc, maxAcc, join_condition_matrix,

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

                                     metadata_matrix, data),

-                "FLAT" = WrappeR$flat(minAcc, maxAcc, join_condition_matrix,

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

                                     metadata_matrix, data),

-                "SUMMIT" = WrappeR$summit(minAcc,maxAcc, join_condition_matrix,

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

                                     metadata_matrix, data),

-                "HISTOGRAM" = WrappeR$histogram(minAcc, maxAcc, 

-                                join_condition_matrix, metadata_matrix, data))

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

+                        join_condition_matrix, metadata_matrix, data))

     if(is.null(response))

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

@@ -200,7 +183,7 @@ gmql_cover <- function(data, minAcc, maxAcc, groupBy = NULL,

         GMQLDataset(data)

 }

-.check_cover_param <- function(param,is_min)

+.check_cover_param <- function(param, is_min)

 {

     if(length(param)>1)

         stop("length > 1")

@@ -214,12 +197,19 @@ gmql_cover <- function(data, minAcc, maxAcc, groupBy = NULL,

     }

     else if(is.character(param))

     {

-        if(is_min && identical(param,"ANY"))

-            stop("min cannot assume ANY as value")

+        if(is.na(as.numeric(param)))

+        {

+            if(is_min && identical(param,"ANY"))

+                stop("min cannot assume ANY as value")

+            

+            if(!identical(param,"ANY") && !identical(param,"ALL"))

+                stop("invalid input data")

+        }

         return(param)

     }

     else

         stop("invalid input data")

+    

 }

 .trasform_cover <- function(predicate=NULL)

@@ -15,10 +15,10 @@

 #' @importFrom rJava .jnull

 #' @importFrom rJava .jarray

 #' 

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

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

-#' @param joinBy list of CONDITION objects where every object contains 

-#' the name of metadata to be used in semijoin, or simple string concatenation 

+#' @param x GMQLDataset class object

+#' @param y GMQLDataset class object

+#' @param joinBy vector of CONDITION objects where every object contains 

+#' the name of metadata to be used in semijoin, or string concatenation 

 #' of name of metadata, e.g. c("cell_type", "attribute_tag", "size") 

 #' without declaring condition.

 #' The CONDITION's available are:

@@ -30,9 +30,9 @@

 #' as value will match; no further prefixes are allowed. }

 #' }

 #' Every condition accepts only one string value. (e.g. FULL("cell_type") )

-#' In case of single concatenation with no CONDITION or list with some value 

-#' without conditon, the metadata are considered having default 

-#' evaluation: the two attributes match if both end with value.

+#' In case of single concatenation with no CONDITION the metadata are 

+#' considered having default evaluation: 

+#' the two attributes match if both end with value.

 #' 

 #' @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 

@@ -41,7 +41,7 @@

 #' left_input_data that overlap with at least one region in right_input_data 

 #' (even just one base).

 #'

-#' @return DataSet class object. It contains the value to use as input 

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

 #' for the subsequent GMQL function

 #' 

 #'

@@ -69,23 +69,21 @@

 #' test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")

 #' exp1 = read_dataset(test_path)

 #' exp2 = read_dataset(test_path2)

-#' out = setdiff(exp1, exp2, c("antibody_target"))

+#' out = setdiff(exp1, exp2, joinBy = c("antibody_target"))

 #'

 #' }

-#'

-#' @rdname setdiff-methods

-#' @aliases setdiff, setdiff-methods

+#' 

+#' @aliases setdiff, setdiff-method

 #' @export

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

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

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

             {

                 val_x = x@value

                 val_y = y@value

-                gmql_difference(val_x, val_y, joinBy, is_exact)

+                gmql_difference(val_x, val_y, is_exact, joinBy)

             })

-gmql_difference <- function(left_data, right_data, joinBy = NULL, 

-                                is_exact = FALSE)

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

 {

     if(!is.null(joinBy))

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

@@ -104,3 +102,4 @@ gmql_difference <- function(left_data, right_data, joinBy = NULL,

         GMQLDataset(data)

 }

+

@@ -1,3 +1,11 @@

+#' @name extend

+#' @rdname extend-GMQLDataset-method

+#' @aliases extend, GMQLDataset-method

+#' @exportMethod extend

+setGeneric("extend", function(.data, ...) 

+    standardGeneric("extend"))

+

+

 #' GMQL Operation: EXTEND

 #'

 #' It generates new metadata attributes as result of aggregate functions 

@@ -10,7 +18,9 @@

 #' @importFrom rJava .jarray

 #'

 #' @param .data GMQLDataset class object 

-#' @param metadata list of element in the form \emph{key} = \emph{aggregate}.

+#' @param ... Additional arguments for use in specific methods.

+#' 

+#' In this case a series of element in the form \emph{key} = \emph{aggregate}.

 #' The \emph{aggregate} is an object of class AGGREGATES

 #' The aggregate functions available are: \code{\link{SUM}}, 

 #' \code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}}, 

@@ -27,7 +37,7 @@

 #' }

 #' "mixed style" is not allowed

 #'

-#' @return DataSet class object. It contains the value to use as input 

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

 #' for the subsequent GMQL function

 #' 

 #' @examples

@@ -37,7 +47,7 @@

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' r <- read_dataset(test_path)

-#' e <- mutate(input_data = r, list(RegionCount = COUNT()))

+#' e <- extend(r, RegionCount = COUNT())

 #' 

 #' \dontrun{

 #' 

@@ -50,27 +60,25 @@

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' exp = read_dataset(test_path)

-#' res = mutate(input_data = exp, list(RegionCount = COUNT(),

-#' MinP = MIN("pvalue")))

+#' res = extend(exp, RegionCount = COUNT(), MinP = MIN("pvalue")))

 #' 

 #' }

-#' 

-#' @name mutate

-#' @rdname mutate-methods

-#' @aliases mutate, mutate-methods

+

+#' @aliases extend-method

 #' @export

-setMethod("mutate", "GMQLDataset",

-            function(.data, metadata = NULL)

+setMethod("extend", "GMQLDataset",

+            function(.data, ...)

             {

                 val_x = .data@value

-                gmql_extend(val_x, metadata)

+                meta <- list(...)

+                gmql_extend(val_x, meta)

             })

-gmql_extend <-function(input_data, metadata = NULL)

+gmql_extend <-function(input_data, meta)

 {

-    if(!is.null(metadata))

-        metadata_matrix <- .jarray(.aggregates(metadata,"META_AGGREGATES"),

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

+        metadata_matrix <- .jarray(.aggregates(meta,"META_AGGREGATES"),

                                     dispatch = TRUE)

     else

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

similarity index 62%

rename from R/Dataset-class.R

rename to R/GMQLDataset-class.R

@@ -7,6 +7,8 @@

 #' @name GMQLDataset-class

 #' @rdname GMQLDataset-class

 #' 

+#' @return instance of GMQL dataset

+

 setClass("GMQLDataset",

             contains = c("DataTable"),

             representation(value = "character"))

@@ -30,15 +32,6 @@ setMethod("show", "GMQLDataset",

             })

-#' Method mutate

-#' 

-#' Wrapper to GMQL extend function

-#' 

-#' @name mutate

-#' @rdname mutate-methods

-#' 

-setGeneric("mutate", function(.data, metadata = NULL) 

-                                standardGeneric("mutate"))

 # insted of GMQL order

 # setGeneric("sort", function(data, metadata_ordering = NULL, 

@@ -51,8 +44,9 @@ setGeneric("mutate", function(.data, metadata = NULL)

 #' Wrapper to GMQL merge function

 #' 

 #' @name aggregate

-#' @rdname aggregate-methods

-#' 

+#' @rdname aggregate-GMQLDataset-method

+#' @aliases aggregate

+#'  

 setGeneric("aggregate", function(data, groupBy = NULL) 

                                     standardGeneric("aggregate"))

@@ -62,9 +56,42 @@ setGeneric("aggregate", function(data, groupBy = NULL)

 #' Wrapper to GMQL join function

 #' 

 #' @name join

-#' @rdname join-methods

+#' @rdname join-GMQLDataset-method

 #' @aliases join

 #' 

-setGeneric("join", function(x, y, by = NULL, ...) standardGeneric("join"))

+setGeneric("join", function(x, y, by = NULL,...) standardGeneric("join"))

+

+

+#' Method filter

+#' 

+#' Wrapper to GMQL select function

+#' 

+#' @name filter

+#' @rdname filter-GMQLDataset-method

+#' @aliases filter

+#' 

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

+

+#' Method cover

+#' 

+#' Wrapper to GMQL cover function

+#' 

+#' @name cover

+#' @rdname cover-GMQLDataset-method

+#' @aliases cover

+#' 

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

+

+#' Method map

+#' 

+#' Wrapper to GMQL map function

+#' 

+#' @name map

+#' @rdname map-GMQLDataset-method

+#' @aliases map

+#' 

+setGeneric("map", function(x, y, ...) standardGeneric("map"))

+

+

@@ -22,7 +22,7 @@

 #' For details of DISTAL objects see:

 #' \code{\link{DLE}}, \code{\link{DGE}}, \code{\link{DL}}, \code{\link{DG}},

 #' \code{\link{MD}}, \code{\link{UP}}, \code{\link{DOWN}}

-#' 

+#' @param ... Additional arguments for use in specific methods.

 #' @param by list of CONDITION objects where every object contains 

 #' the name of metadata to be used in semijoin, or simple string concatenation 

 #' of name of metadata, e.g. c("cell_type", "attribute_tag", "size") 

@@ -84,9 +84,7 @@

 #' region_output="RIGHT")

 #' 

-#' @name join

-#' @rdname join-methods

-#' @aliases join, join-methods

+#' @aliases join-method

 #' @export

 setMethod("join", "GMQLDataset",

                 function(x, y, by = NULL, genometric_predicate = NULL, 

@@ -94,7 +92,7 @@ setMethod("join", "GMQLDataset",

                 {

                     r_data <- x@value

                     l_data <- y@value

-                    gmql_join(x, y, genometric_predicate, by, 

+                    gmql_join(r_data, l_data, genometric_predicate, by, 

                             region_output="contig")

                 })

@@ -19,9 +19,12 @@

 #' present with equal values in both M1 and  M2

 #'

 #'

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

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

-#' @param aggregates list of element in the form \emph{key} = \emph{aggregate}.

+#' @param x GMQLDataset class object

+#' @param y GMQLDataset class object 

+#' 

+#' @param ... Additional arguments for use in specific methods.

+#' 

+#' In this case a series of element in the form \emph{key} = \emph{aggregate}.

 #' The \emph{aggregate} is an object of class AGGREGATES

 #' The aggregate functions available are: \code{\link{SUM}}, 

 #' \code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}}, 

@@ -54,7 +57,7 @@

 #' without conditon, the metadata are considered having default 

 #' evaluation: the two attributes match if both end with value.

 #' 

-#' @return DataSet class object. It contains the value to use as input 

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

 #' for the subsequent GMQL function

 #' 

 #'

@@ -74,16 +77,23 @@

 #' test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")

 #' exp = read_dataset(test_path)

 #' ref = read_dataset(test_path2)

-#' out = map(ref,exp, list(minScore = MIN("score")), 

-#' joinBy = c("cell_tissue"))

-#' 

+#' out = map(ref,exp, minScore = MIN("score"), joinBy = c("cell_tissue"))

 #' 

+#' @aliases map-method

 #' @export

-#'

-map <- function(left_input_data, right_input_data, aggregates = NULL, 

-                    joinBy = NULL)

+setMethod("map", "GMQLDataset",

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

+            {

+                r_data <- x@value

+                l_data <- y@value

+                aggregates = list(...)

+                gmql_map(r_data, l_data, aggregates, joinBy)

+            })

+

+

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

 {

-    if(!is.null(aggregates))

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

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

                                     dispatch = TRUE)

     else

@@ -96,8 +106,8 @@ map <- function(left_input_data, right_input_data, aggregates = NULL,

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

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

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

-                            left_input_data@value, right_input_data@value)

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

+                            r_data)

     error <- strtoi(response[1])

     data <- response[2]

     if(error!=0)

@@ -12,9 +12,9 @@

 #' init_gmql()

 #' test_path <- system.file("example","DATASET",package = "RGMQL")

 #' r = read_dataset(test_path)

-#' s = filter(input_data = r)

-#' m = aggregate(groupBy = c("antibody_targer","cell_karyotype"),input_data = s)

-#' materialize(input_data = m, dir_out = test_path)

+#' s = filter(r)

+#' m = aggregate(s, groupBy = c("antibody_targer","cell_karyotype"))

+#' materialize(m, dir_out = test_path)

 #' 

 #' \dontrun{

 #' execute()

@@ -65,9 +65,7 @@ execute <- function()

     }

 }

-#' @name materialize

-#' @rdname materialize-methods

-#' @aliases materialize

+#' @rdname materialize-GMQLDataset-method

 #' @export

 setGeneric("materialize", function(data, ...) standardGeneric("materialize"))

@@ -86,7 +84,7 @@ setGeneric("materialize", function(data, ...) standardGeneric("materialize"))

 #' @param data GMQLDataset class object

 #' @param dir_out destination folder path.

 #' by default is current working directory of the R process

-#'

+#' @param ... Additional arguments for use in specific methods.

 #' @return None

 #'

 #' @examples

@@ -94,13 +92,11 @@ setGeneric("materialize", function(data, ...) standardGeneric("materialize"))

 #' init_gmql()

 #' test_path <- system.file("example","DATASET",package = "RGMQL")

 #' r = read_dataset(test_path)

-#' s = filter(input_data = r)

+#' s = filter(r)

 #' m = aggregate(s, groupBy = c("antibody_targer","cell_karyotype"))

-#' materialize(input_data = m, dir_out = test_path)

+#' materialize(m, dir_out = test_path)

 #' 

-#' @name materialize

-#' @rdname materialize-methods

-#' @aliases materialize, materialize-methods

+#' @aliases materialize-method

 #' @export

 setMethod("materialize", "GMQLDataset",

             function(data, dir_out = getwd())

@@ -149,7 +145,7 @@ gmql_materialize <- function(data, dir_out)

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' r = read_dataset(test_path)

 #' m = aggregate(r, groupBy = c("antibody_target", "cell_karyotype"))

-#' g <- take(input_data = m, rows = 45)

+#' g <- take(m, rows = 45)

 #' 

 #' @export

 #'

@@ -46,18 +46,16 @@

 #' init_gmql()

 #' test_path <- system.file("example","DATASET",package = "RGMQL")

 #' exp = read_dataset(test_path)

-#' merged = aggregate(input_data = exp, groupBy = c("antibody_target"))

+#' merged = aggregate(exp, groupBy = c("antibody_target"))

 #' 

-#' @name aggregate

-#' @rdname aggregate-methods

-#' @aliases aggregate, aggregate-methods

+#' @aliases aggregate-method

 #' @export

 #' 

 setMethod("aggregate", "GMQLDataset",

             function(data, groupBy = NULL)

             {

                 val = data@value

-                gmql_merge(val, metadata)

+                gmql_merge(val, groupBy)

             })

 gmql_merge <- function(data, groupBy = NULL)

@@ -81,9 +81,8 @@

 #' num_fetch = 2)

 #' 

 #' }

-#' @name sort

-#' @rdname sort-methods

-#' @aliases sort, sort-methods

+#' 

+#' @aliases sort-method

 #' @export

 setMethod("sort", "GMQLDataset",

             function(x, decreasing = FALSE, metadata_ordering = NULL, 

@@ -14,6 +14,7 @@

 #' @importFrom rJava J

 #' @importFrom rJava .jnull

 #' @importFrom rJava .jarray

+#' @importFrom BiocGenerics subset

 #' 

 #' @param x GMQLDataset class object

 #' @param metadata vector of string made up by metadata attribute

@@ -84,11 +85,8 @@

 #' 

 #' }

 #' 

-#' @export

 #'

-#' @name subset

-#' @rdname subset-methods

-#' @aliases subset, subset-methods

+#' @aliases subset

 #' @export

 setMethod("subset", "GMQLDataset",

             function(x, metadata = NULL, metadata_update=NULL, 

@@ -96,9 +94,27 @@ setMethod("subset", "GMQLDataset",

                         regions_update = NULL, all_but_reg=FALSE)

             {

                 data = x@value

-                gmql_project(data, metadata, metadata_update,

+                r_update <- substitute(regions_update)

+                if(!is.null(r_update))

+                {

+                    reg_update <- .trasform_update(deparse(r_update))

+                    reg_update <- paste(reg_update,collapse = "")

+                }

+                else

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

+                

+                m_update <- substitute(metadata_update)

+                if(!is.null(m_update))

+                {

+                    meta_update <- .trasform_update(deparse(m_update))

+                    meta_update <- paste(meta_update,collapse = "")

+                }

+                else

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

+                

+                gmql_project(data, metadata, meta_update,

                                 all_but_meta, regions, 

-                                regions_update, all_but_reg)

+                                reg_update, all_but_reg)

             })

 gmql_project <-function(input_data, metadata = NULL, metadata_update=NULL, 

@@ -137,24 +153,7 @@ gmql_project <-function(input_data, metadata = NULL, metadata_update=NULL,

     else

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

-    reg_update <- substitute(regions_update)

-    if(!is.null(reg_update))

-    {

-        regions_update <- .trasform_update(deparse(reg_update))

-        regions_update <- paste(regions_update,collapse = "")

-    }

-    else

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

-    

-    meta_update <- substitute(metadata_update)

-    if(!is.null(meta_update))

-    {

-        metadata_update <- .trasform_update(deparse(meta_update))

-        metadata_update <- paste(metadata_update,collapse = "")

-    }

-    else

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

-    

+

     if(length(all_but_meta)>1)

         warning("all_but_meta: no multiple values")

@@ -167,7 +166,7 @@ gmql_project <-function(input_data, metadata = NULL, metadata_update=NULL,

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

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

                                 regions,regions_update,

-                                all_but_reg,input_data$value)

+                                all_but_reg,input_data)

     error <- strtoi(response[1])

     data <- response[2]

     if(error!=0)

@@ -15,14 +15,14 @@

 #' @importFrom rJava .jarray

 #' @importFrom methods isClass

 #'

-#' @param x GMQLDataset class object

+#' @param .data GMQLDataset class object

 #' @param m_predicate logical predicate made up by R logical operation 

 #' on metadata attribute. 

 #' Only !, |, ||, &, && are admitted.

 #' @param r_predicate logical predicate made up by R logical operation 

 #' on chema region values. 

 #' Only !, |, ||, &, && are admitted.

-#' @param semi_join list of CONDITION objects where every object contains 

+#' @param semi_join vector of CONDITION objects where every object contains 

 #' the name of metadata to be used in semijoin, or simple string concatenation 

 #' of name of metadata, e.g. c("cell_type", "attribute_tag", "size") 

 #' without declaring condition.

@@ -35,16 +35,17 @@

 #' as value will match; no further prefixes are allowed. }

 #' }

 #' Every condition accepts only one string value. (e.g. FULL("cell_type") )

-#' In case of single concatenation with no CONDITION or list with some value 

-#' without conditon, the metadata are considered having default 

-#' evaluation: the two attributes match if both end with value.

+#' In case of single concatenation with no CONDITION the metadata are 

+#' considered having default evaluation: 

+#' the two attributes match if both end with value.

 #' 

-#' @param semi_join_negation logical value: T => semijoin is perfomed 

+#' @param not_in logical value: T => semijoin is perfomed 

 #' considering semi_join NOT IN semi_join_dataset, F => semijoin is performed 

 #' considering semi_join IN semi_join_dataset

 #' 

 #' @param semi_join_dataset GMQLDataset class object

-#'

+#' @param ... Additional arguments for use in specific methods.

+#' 

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

 #' for the subsequent GMQL function

 #' 

@@ -56,7 +57,7 @@

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' input <- read_dataset(test_path)

-#' s <- subset(input, Patient_age < 70)

+#' s <- filter(input, Patient_age < 70)

 #' 

 #' 

 #' \dontrun{

@@ -84,25 +85,14 @@

 #' 

 #' }

 #' 

-#' @name filter

-#' @rdname GMQLDataset-class

-#' @aliases filter, filter-methods

-#' 

-setGeneric("filter", function(data, m_predicate = NULL, r_predicate = NULL, 

-                    semi_join = NULL, semi_join_negation = FALSE, 

-                    semi_join_dataset = NULL) 

-    standardGeneric("filter"))

-

-#' @name filter

-#' @rdname filter-methods

-#' @aliases filter, filter-methods

+#' @aliases filter, filter-method

 #' @export

 setMethod("filter", "GMQLDataset",

-            function(data, m_predicate = NULL, r_predicate = NULL, 

-                    semi_join = NULL, semi_join_negation = FALSE, 

+            function(.data, m_predicate = NULL, r_predicate = NULL, 

+                    semi_join = NULL, not_in = FALSE, 

                     semi_join_dataset = NULL)

             {

-                val <- data@value

+                val <- .data@value

                 meta_pred <- substitute(m_predicate)

                 if(!is.null(meta_pred))

                 {

@@ -122,12 +112,11 @@ setMethod("filter", "GMQLDataset",

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

                 gmql_select(val, predicate, region_predicate, 

-                        semi_join, semi_join_negation, semi_join_dataset)

+                        semi_join, not_in, semi_join_dataset)

             })

-gmql_select <- function(input_data, predicate = NULL, region_predicate = NULL, 

-                    semi_join = NULL, semi_join_negation = FALSE, 

-                    semi_join_dataset = NULL)

+gmql_select <- function(input_data, predicate, region_predicate, semi_join, 

+                            semi_join_negation, semi_join_dataset)

 {