From 1aaf4bcf1faa540ae142e08f939bca0485b1f115 Mon Sep 17 00:00:00 2001
From: Simon Penel <simon.penel@univ-lyon1.fr>
Date: Tue, 16 Jul 2024 10:11:42 +0200
Subject: [PATCH] Improve fix https://github.com/lbbe-software/seqinr/issues/10
 . Just need to decrement nseq

---
 DESCRIPTION        |  2 +-
 R/read.alignment.R | 19 ++++++++++---------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1ea7ebb..c54f2e9 100755
--- a/DESCRIPTION
+++ b/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"),
diff --git a/R/read.alignment.R b/R/read.alignment.R
index b8251ee..e4fa1af 100644
--- a/R/read.alignment.R
+++ b/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))
     }