@@ -65,7 +65,7 @@ Imports:

     dplyr,

     stats

 Depends:

-    R(>= 3.4.2)

+    R(<= 3.4.2)

 VignetteBuilder: knitr

 Suggests: 

     BiocStyle,

@@ -20,7 +20,10 @@

 {

     schema_name <- list.files(datasetName, pattern = "*.schema$",

                                 full.names = TRUE)

-    if(length(schema_name)==0)

+    schema_name_xml <- list.files(datasetName, pattern = "*.xml$",

+                                full.names = TRUE)

+    

+    if(length(schema_name)==0 || length(schema_name_xml) == 0)

         stop("schema not present")

     xml_schema <- xml2::read_xml(schema_name)

@@ -89,45 +89,29 @@ setMethod("merge", c("GMQLDataset","GMQLDataset"),

                     ptr_data_y <- y@value

                     joinBy = list(...)

                     gmql_join(ptr_data_x, ptr_data_y, genometric_predicate, 

-                                joinBy, region_output="contig")

+                                joinBy, region_output)

                 })

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

-                            region_output="contig")

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

+                            region_output)

 {

     if(!is.null(genometric_predicate))

     {

+        if(length(genometric_predicate) >4)

+            stop("genometric_predicate: only 4 DISTAL condition")

+        

         if(!is.list(genometric_predicate))

-            stop("genometric_predicate must be list of lists")

+            stop("genometric_predicate must be a list")

-        #if(!all(sapply(genometric_predicate, function(x) is.list(x) )))

-         #   stop("genometric_predicate must be list of lists")

-    

-        #lapply(genometric_predicate, function(list_pred) {

-           # if(length(list_pred)>4)

-            #{

-             #   warning("only 4 element per list, we cut the rest")

-              #  length(list_pred)=4

-            #}

         if(!all(sapply(genometric_predicate, function(x) {is(x,"DISTAL")} )))

             stop("All elements should be DISTAL object")

-            #})

-    

-        #genomatrix <- t(sapply(genometric_predicate, function(list_pred) {

+         

         genomatrix <- t(sapply(genometric_predicate, function(x) {

                 new_value = as.character(x)

                 array <- c(new_value)

         }))

-        na_matrix <- matrix("NA", nrow = 3, ncol = 2)

-        genomatrix <- rbind(genomatrix,na_matrix)

-        col <- dim(genomatrix)[1]

-        if(col>4)

-        {

-            array <- seq(5, to  = col)

-            genomatrix <- genomatrix[-array,]

-        }

-       # }))

+        

         genomatrix <- .jarray(genomatrix, dispatch = TRUE)

     }

     else

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