@@ -1,7 +1,7 @@

 Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

-Version: 0.99.43

+Version: 0.99.44

 Author: Simone Pallotta, Marco Masseroli

 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>

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

@@ -155,9 +155,10 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,

         else

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

-        ouput <- toupper(region_output)

-        if(ouput %in% c("CAT","INT"))

-            stop("reg_attributes is defined: output cannot be INT or CAT")

+        if(is.null(genometric_predicate) && length(reg_attributes))

+            if(ouput %in% c("CAT","INT"))

+                stop("Both reg_attributes and genometric_predicate are defined: 

+                        output cannot be INT or CAT")

     }

     else

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

@@ -168,6 +169,7 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,

         stop("region_output must be cat, left, right, right_dist, left_dist 

                 or int (intersection)")

+    

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

     response <- WrappeR$join(genomatrix, join_matrix, ouput,reg_attributes,

                                 left_data, right_data)

@@ -47,9 +47,14 @@ execute <- function()

     {

         if(remote_proc)

         {

+            isGTF <- FALSE

+            outformat <- WrappeR$outputMaterialize()

+            if(identical(outformat, "gtf"))

+                isGTF <- TRUE

+            

             url <- WrappeR$get_url()

             .download_or_upload()

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

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

         }

     }

 }