[adegenet-commits] r774 - pkg/R

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

Author: jombart
Date: 2011-01-24 17:15:57 +0100 (Mon, 24 Jan 2011)
New Revision: 774

Modified:
   pkg/R/import.R
Log:
printing improved


Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R	2011-01-24 15:07:45 UTC (rev 773)
+++ pkg/R/import.R	2011-01-24 16:15:57 UTC (rev 774)
@@ -738,6 +738,11 @@
             count <- count + 1L
         }
         i <- i+1
+        if(i>10){
+            warning("No comment section at the beginning of the file. Format may be wrong.")
+            i <- 0
+            break
+        }
     }
 
     lines.to.skip <- i
@@ -769,7 +774,17 @@
 
     txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=1)
 
+    COUNT <- 0 # used to count the nb of genotypes read
+    
     while(length(grep(">", txt))>0){
+        if(!quiet) {
+            if(COUNT %% 10 == 0){
+                cat(COUNT)
+            } else {
+                cat(".")
+            }
+        }
+        
         indName <- gsub(">","", txt)
         indName <- gsub("(^[[:space:]]+)|([[:space:]]+$)", "", indName)
         temp <- strsplit(scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip + 1, nmax=1), "")[[1]]
@@ -782,6 +797,8 @@
 
 
     ## CHECK CONSISTENCY ##
+    if(!quiet) cat("\n Checking consistency... \n")
+
     n.loc <- unique(sapply(res, nLoc))
     n.ind <- length(res)
 
@@ -798,6 +815,8 @@
 
 
     ## BUILD OUTPUT ##
+    if(!quiet) cat("\n Building final object... \n")
+
     ind.names <- names(res)
     if(!is.null(misc.info$chromosome)){
         other <- list(chromosome = misc.info$chromosome)