Improve fix #10 . Just need to decrement nseq

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: seqinr
 Title: Biological Sequences Retrieval and Analysis
-Version: 4.2-40
+Version: 4.2-41
 Depends: R (>= 2.10.0)
 Imports: ade4,segmented
 Authors@R: c(person("Delphine", "Charif", role = "aut"),

R/read.alignment.R

@@ -54,7 +54,6 @@ read.alignment <- function(file, format, forceToLower = TRUE,
       white <- characters[-length(characters)] == " "
       black <- characters[-1] != " "
       istart <- which(white & black)[1]
-
       # Get sequence names
       nam <- character()
       nseq <- 1
@@ -74,7 +73,12 @@ read.alignment <- function(file, format, forceToLower = TRUE,
           nseq <- nseq - 1
           break # alredy seen
         }
-        if (seqname == 'NA')  {break}
+        # this happens with short alignments because seqname is never found
+        # in mam
+        if (seqname == 'NA')  {
+          nseq <- nseq - 1
+          break
+        }
         nam[nseq] <- seqname
         nseq <- nseq + 1
       }
@@ -98,14 +102,11 @@ read.alignment <- function(file, format, forceToLower = TRUE,
       # Concatenation of sequence lines in a single string
       seq <- vector(mode = "list")
       for(iseq in seq_len(nseq)){
-        if (iseq <= length(filecontent)) {
-          ii <- seq(iseq, length(filecontent), by = nseq)
-          seq[[iseq]] <- paste0(filecontent[ii], collapse = "")
-          if(forceToLower) seq[[iseq]] <- tolower(seq[[iseq]])
-        }
+        ii <- seq(iseq, length(filecontent), by = nseq)
+        seq[[iseq]] <- paste0(filecontent[ii], collapse = "")
+        if(forceToLower) seq[[iseq]] <- tolower(seq[[iseq]])
       }
-
-      return(as.alignment(nb = length(seq), nam = nam, seq = seq, com = NA))
+      return(as.alignment(nb = nseq, nam = nam, seq = seq, com = NA))
     }