From 578d0743979ac62b6e55f588b004d98be6cb4c73 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 7 Sep 2006 22:49:26 +0000
Subject: [PATCH] remove commented out string conversion and prevet a possible
 shared_ptr dereference in c_str()

---
 alg/sequence.cpp | 21 +++++----------------
 alg/sequence.hpp |  6 ++----
 2 files changed, 7 insertions(+), 20 deletions(-)

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index e318207..787f2a9 100644
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -126,20 +126,6 @@ Sequence &Sequence::operator=(const Sequence& s)
   return *this;
 }
 
-/*
-Sequence::operator std::string()
-{
-  std::string s(seq.begin(), seq.end());
-  return s;
-}
-
-Sequence::operator std::string() const
-{
-  std::string s(seq.begin(), seq.end());
-  return s;
-}
-*/
-
 static void multiplatform_getline(std::istream& in, std::string& line)
 {
   line.clear();
@@ -247,7 +233,7 @@ Sequence::load_fasta(std::iostream& data_file, int seq_num,
 }
 
 void Sequence::set_filtered_sequence(const std::string &old_seq, 
-                                     std::string::size_type start, 
+                                     std::string::size_type start,
                                      std::string::size_type count)
 {
   char conversionTable[257];
@@ -612,7 +598,10 @@ Sequence::clear()
 
 const char *Sequence::c_str() const
 {
-  return seq->c_str();
+  if (seq) 
+    return seq->c_str();
+  else 
+    return 0;
 }
 
 Sequence::const_iterator Sequence::begin() const
diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 6c5b3b6..b335dcd 100644
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -129,10 +129,6 @@ public:
   //! assignment to constant sequences
   Sequence &operator=(const Sequence&);
 
-  // dangerous since they create large copies
-  //operator std::string();
-  //operator std::string() const;
-
   friend std::ostream& operator<<(std::ostream&, const Sequence&);
   friend bool operator<(const Sequence&, const Sequence&);
   friend bool operator==(const Sequence&, const Sequence&);
@@ -229,8 +225,10 @@ public:
 private:
   boost::shared_ptr<seq_string> seq;
   std::string header;
+  //! species name
   std::string species;
 
+  //! store our oldstyle annotations
   std::list<annot> annots;
   //! a seperate list for motifs since we're currently not saving them
   std::list<motif> motif_list;
-- 
2.30.2