From 4692855d75e90b1b362b01f68d7d369dd251acc0 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 19 Aug 2010 11:33:41 +0000
Subject: [PATCH] make fasta parser more robust by skipping whitespace
characters
Fixes part of BZDNG-152
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2658 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/seq/fasta_io_handler.cc | 23 ++++++++++++++---------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/modules/io/src/seq/fasta_io_handler.cc b/modules/io/src/seq/fasta_io_handler.cc
index 919902088..198171208 100644
--- a/modules/io/src/seq/fasta_io_handler.cc
+++ b/modules/io/src/seq/fasta_io_handler.cc
@@ -92,17 +92,22 @@ void FastaIOHandler::Import(seq::SequenceList& aln,
String error=str(format(error_msg) % line);
throw IOException(error);
}
- String identifier=line.substr(1);
- String sequence_str;
- while (std::getline(instream, line) && line.size()>0 && line[0]!='>') {
- if (line.find_first_not_of("\n\t ")==String::npos) {
- continue;
+ String name=line.substr(1);
+ std::stringstream seq_string;
+ while (std::getline(instream, line)) {
+ if (!line.empty() && line[0]=='>') {
+ break;
}
- sequence_str+=line;
- }
- if (sequence_str.length()>0) {
+ for (String::iterator i=line.begin(), e=line.end(); i!=e; ++i) {
+ if (isspace(*i)) {
+ continue;
+ }
+ seq_string << *i;
+ }
+ }
+ if (!seq_string.str().empty()) {
try {
- seq::SequenceHandle seq=seq::CreateSequence(identifier, sequence_str);
+ seq::SequenceHandle seq=seq::CreateSequence(name, seq_string.str());
aln.AddSequence(seq);
seq_count+=1;
} catch (seq::InvalidSequence& e) {
--
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