[Seqinr-commits] r1979 - pkg/R

[noreply at r-forge.r-project.org]

Author: jeanlobry
Date: 2016-07-12 19:08:12 +0200 (Tue, 12 Jul 2016)
New Revision: 1979

Modified:
   pkg/R/extractseqs.R
Log:
adding a zlib argument to extractseqs

Modified: pkg/R/extractseqs.R
===================================================================
--- pkg/R/extractseqs.R	2016-07-07 18:55:51 UTC (rev 1978)
+++ pkg/R/extractseqs.R	2016-07-12 17:08:12 UTC (rev 1979)
@@ -4,15 +4,15 @@
 
 
 
-###################################################################################################
+##########################################################################################
 #                                                                                                 #
 #                                         extractseqs.socket                                       #
 #                                                                                                 #
-###################################################################################################
+##########################################################################################
 
-extractseqs <- function(listname, socket = autosocket(), format="fasta",operation="simple", feature="xx", bounds="xx", minbounds="xx",verbose = FALSE, nzlines=1000){
-  if (.Platform$OS.type == "windows") {
-  	stop(paste("This function is not implemented for windows.\n"))
+extractseqs <- function(listname, socket = autosocket(), format="fasta", operation="simple", feature="xx", bounds="xx", minbounds="xx", verbose = FALSE, nzlines=1000, zlib = FALSE){
+  if (zlib == TRUE && .Platform$OS.type == "windows") {
+  	stop(paste("Zlib compressed sockets is not implemented for windows.\n"))
 	}
   debug<-0
   if (verbose) debug <- 1
@@ -52,7 +52,7 @@
 
 if ((operation == "region") && ((bounds =="xx") || (feature =="xx"))) stop(paste("You should specify bounds and region!\n"))
 
-
+#
 # Build request:
 #
 # listname is a list
@@ -67,7 +67,13 @@
   if (feature != "xx") request <- paste(request,"&feature=", feature, sep = "")
   if (bounds != "xx") request <- paste(request,"&bounds=",bounds, sep = "")
   if (minbounds != "xx") request <- paste(request,"&minbounds=",minbounds, sep = "")
-  request <- paste(request,"&zlib=T", sep = "")
+  
+  if(zlib) {
+    request <- paste(request,"&zlib=T", sep = "")
+  }
+  else {
+    request <- paste(request,"&zlib=F", sep = "")
+  }
   if(verbose) cat("request : ",request,"\n")
   
   # Write request into the socket:
@@ -75,16 +81,33 @@
   writeLines(request , socket, sep="\n")
 	
   # Read result from server:
-   
-  lastres <-  .Call("getzlibsock", socket, nzlines, debug,PACKAGE = "seqinr")
-  
-  #
-  # Remove empty lines at the end of lastres:
-  #
-  
-  return( lastres[nchar(lastres) != 0] )
+
+  if(zlib) {
+    lastres <-  .Call("getzlibsock", socket, nzlines, debug,PACKAGE = "seqinr")
+  }
+  else {
+    lastres <- readLines(socket)
+  }
+  if(zlib) {
+    #
+    # Remove empty lines at the end of lastres:
+    #
+    return( lastres[nchar(lastres) != 0] )
+  }
+  else {
+    #
+    # Remove flags from server:
+    #
+    lastres <- lastres[-1]                       # code=0
+    lastres <- lastres[-length(lastres)]         # extractseqs END. 
+    lastres <- lastres[-grep("count=", lastres)] # count=
+    return(lastres)
+  }
 }
 
+#
+# Define a shorthcut for extractseqs
+#
 exseq <- extractseqs