X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fsequence.cpp;h=521496d3497b2b96d4786819438d170f6ac50ce4;hb=f3c0553a22b0e4ddc39ee45f51725352d92e97f1;hp=f0cb6e5178fbc19cdabbc9e7c37154ed4210e4fa;hpb=a852aac4f69fd5eb7d5a1c6e4118a5e7477f4d36;p=mussa.git

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index f0cb6e5..521496d 100644
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -22,205 +22,323 @@
 //                           ---------- sequence.cc -----------
 //                        ----------------------------------------
 #include <boost/filesystem/fstream.hpp>
+#include <boost/filesystem/operations.hpp>
 namespace fs = boost::filesystem;
 
 #include <boost/spirit/core.hpp>
 #include <boost/spirit/actor/push_back_actor.hpp>
 #include <boost/spirit/iterator/file_iterator.hpp>
+#include <boost/spirit/utility/chset.hpp>
 namespace spirit = boost::spirit;
 
 #include "alg/sequence.hpp"
+#include "io.hpp"
 #include "mussa_exceptions.hpp"
 
 #include <string>
+#include <stdexcept>
 #include <iostream>
 #include <sstream>
+#include <set>
 
-annot::annot() 
- : start(0),
-   end(0),
-   type(""),
-   name("")
+bool operator==(const motif& left, const motif& right)
 {
+  return ((left.begin== right.begin) and
+          (left.end == right.end) and
+          (left.type == right.type) and
+          (left.name == right.name));
 }
 
-annot::annot(int start, int end, std::string type, std::string name)
- : start(start),
-   end(end),
-   type(type),
-   name(name)
+motif::motif() 
+ : begin(0),
+   end(0),
+   type("motif"),
+   name(""),
+   sequence("")
 {
 }
 
-motif::motif(int start, std::string motif)
- : annot(start, start+motif.size(), "motif", motif),
+motif::motif(int begin_, std::string motif)
+ : begin(begin_),
+   end(begin_+motif.size()),
+   type("motif"),
+   name(motif),
    sequence(motif)
 {
 }
-  
-Sequence::Sequence()
-  : sequence(""),
-    header(""),
-    species("")
+
+motif::~motif()
+{
+}
+
+Sequence::Sequence(AlphabetRef alphabet)
+  : seq(new SeqSpan("", alphabet, SeqSpan::PlusStrand)),
+    annotation_list(new SeqSpanRefList), 
+    motif_list(new MotifList)
+{
+}
+
+Sequence::~Sequence()
+{
+}
+
+Sequence::Sequence(const char *seq, AlphabetRef alphabet_, SeqSpan::strand_type strand_)
+  : header(""),
+    species(""),
+    annotation_list(new SeqSpanRefList),
+    motif_list(new MotifList)
 {
-  annots.clear();
-  motif_list.clear();
+  set_filtered_sequence(seq, alphabet_, 0, npos, strand_);
 }
 
-Sequence::Sequence(std::string seq)
+Sequence::Sequence(const std::string& seq, 
+                   AlphabetRef alphabet_,
+                   SeqSpan::strand_type strand_) 
+  : header(""),
+    species(""),
+    annotation_list(new SeqSpanRefList),
+    motif_list(new MotifList)
+{
+  set_filtered_sequence(seq, alphabet_, 0, seq.size(), strand_);
+}
+
+Sequence::Sequence(const Sequence& o)
+  : seq(o.seq),
+    header(o.header),
+    species(o.species),
+    annotation_list(o.annotation_list),
+    motif_list(o.motif_list)
+{
+}
+
+Sequence::Sequence(const Sequence* o)
+  : seq(o->seq),
+    header(o->header),
+    species(o->species),
+    annotation_list(o->annotation_list),
+    motif_list(o->motif_list)
+{
+}
+
+Sequence::Sequence(const SequenceRef o)
+  : seq(new SeqSpan(o->seq)),
+    header(o->header),
+    species(o->species),
+    annotation_list(new SeqSpanRefList),
+    motif_list(o->motif_list)
+{
+  // copy over the annotations in the other sequence ref, 
+  // attaching them to our current sequence ref
+  for(SeqSpanRefList::const_iterator annot_i = o->annotation_list->begin();
+      annot_i != o->annotation_list->end();
+      ++annot_i)
+  {
+    size_type annot_begin= (*annot_i)->start();
+    size_type annot_count = (*annot_i)->size();
+    
+    SeqSpanRef new_annot(seq->subseq(annot_begin, annot_count));
+    new_annot->setAnnotations((*annot_i)->annotations());
+    annotation_list->push_back(new_annot);
+  }  
+}
+
+Sequence::Sequence(const SeqSpanRef& seq_ref)
+  : seq(seq_ref),
+    header(""),
+    species(""),
+    annotation_list(new SeqSpanRefList),
+    motif_list(new MotifList)
 {
-  set_filtered_sequence(seq);
 }
 
 Sequence &Sequence::operator=(const Sequence& s)
 {
   if (this != &s) {
-    sequence = s.sequence;
+    seq = s.seq;
     header = s.header;
     species = s.species;
-    annots = s.annots;
+    annotation_list = s.annotation_list;
+    motif_list = s.motif_list;
   }
   return *this;
 }
 
-Sequence &Sequence::operator=(const std::string& s)
+void Sequence::load_fasta(fs::path file_path, int seq_num, int start_index, int end_index)
 {
-  set_filtered_sequence(s);
-  return *this;
+  load_fasta(file_path, reduced_nucleic_alphabet, seq_num, start_index, end_index);
 }
 
-char Sequence::operator[](int index) const
+//! load a fasta file into a sequence
+void Sequence::load_fasta(fs::path file_path, AlphabetRef a, 
+                          int seq_num, int start_index, int end_index)
 {
-  return sequence[index];
+  fs::fstream data_file;
+  data_file.open(file_path, std::ios::in);
+
+  if (!data_file.good())
+  {    
+    throw mussa_load_error("Sequence File: "+file_path.string()+" not found"); 
+  } else {
+    try {
+      load_fasta(data_file, a, seq_num, start_index, end_index);
+    } catch(sequence_empty_error e) {
+      // there doesn't appear to be any sequence
+      // catch and rethrow to include the filename
+      std::stringstream msg;
+      msg << "The selected sequence in " 
+          << file_path.native_file_string()
+          << " appears to be empty"; 
+      throw sequence_empty_error(msg.str());
+    } catch(sequence_empty_file_error e) {
+      std::stringstream errormsg;
+      errormsg << file_path.native_file_string()
+               << " did not have any fasta sequences" << std::endl;
+      throw sequence_empty_file_error(errormsg.str());
+    } catch(sequence_invalid_load_error e) {
+      std::ostringstream msg;
+      msg << file_path.native_file_string();
+      msg << " " << e.what();
+      throw sequence_invalid_load_error(msg.str());
+    }
+  }
 }
 
-std::ostream& operator<<(std::ostream& out, const Sequence& seq)
+void Sequence::load_fasta(std::istream& file, 
+                          int seq_num, int start_index, int end_index)
 {
-  out << "Sequence(" << seq.get_seq() << ")";
-  return out;
+  load_fasta(file, reduced_nucleic_alphabet, seq_num, start_index, end_index);
 }
 
-//! load a fasta file into a sequence
-/*! 
- * \param file_path the location of the fasta file in the filesystem
- * \param seq_num which sequence in the file to load
- * \param start_index starting position in the fasta sequence, 0 for beginning
- * \param end_index ending position in the fasta sequence, 0 for end
- * \return error message, empty string if no error. (gag!)
- */
 void
-Sequence::load_fasta(fs::path file_path, int seq_num, 
+Sequence::load_fasta(std::istream& data_file, AlphabetRef a, 
+                     int seq_num, 
                      int start_index, int end_index)
 {
-  fs::fstream data_file;
   std::string file_data_line;
   int header_counter = 0;
+  size_t line_counter = 0;
   bool read_seq = true;
   std::string rev_comp;
   std::string sequence_raw;
-  std::string seq_tmp;             // holds sequence during basic filtering
-
-  data_file.open(file_path, std::ios::in);
+  std::string seq_tmp;      // holds sequence during basic filtering
+  const Alphabet &alpha = Alphabet::get_alphabet(a);
 
   if (seq_num == 0) {
     throw mussa_load_error("fasta sequence number is 1 based (can't be 0)");
   }
-  if (!data_file)
-  {    
-    throw mussa_load_error("Sequence File: " + file_path.string() + " not found"); 
-  }
-  // if file opened okay, read it
-  else
+
+  // search for the header of the fasta sequence we want
+  while ( (!data_file.eof()) && (header_counter < seq_num) )
   {
-    // search for the header of the fasta sequence we want
-    while ( (!data_file.eof()) && (header_counter < seq_num) )
-    {
-      getline(data_file,file_data_line);
-      if (file_data_line.substr(0,1) == ">")
-        header_counter++;
-    }
+    multiplatform_getline(data_file, file_data_line);
+    ++line_counter;
+    if (file_data_line.substr(0,1) == ">")
+      header_counter++;
+  }
 
-    if (header_counter > 0) {
-      header = file_data_line.substr(1);
+  if (header_counter > 0) {
+    header = file_data_line.substr(1);
 
-      sequence_raw = "";
+    sequence_raw = "";
 
-      while ( !data_file.eof() && read_seq ) {
-        getline(data_file,file_data_line);
-        if (file_data_line.substr(0,1) == ">")
-          read_seq = false;
-        else sequence_raw += file_data_line;
+    while ( !data_file.eof() && read_seq ) {
+      multiplatform_getline(data_file,file_data_line);
+      ++line_counter;
+      if (file_data_line.substr(0,1) == ">")
+        read_seq = false;
+      else {
+        for (std::string::const_iterator line_i = file_data_line.begin();
+             line_i != file_data_line.end();
+             ++line_i)
+         {
+           if(alpha.exists(*line_i)) {
+             sequence_raw += *line_i;
+           } else {
+            std::ostringstream msg;
+            msg << "Unrecognized characters in fasta sequence at line ";
+            msg << line_counter;
+            throw sequence_invalid_load_error(msg.str());
+           }
+         }
       }
+    }
 
-      // Lastly, if subselection of the sequence was specified we keep cut out
-      // and only keep that part
-      // end_index = 0 means no end was specified, so cut to the end 
-      if (end_index == 0)
-        end_index = sequence_raw.size();
+    // Lastly, if subselection of the sequence was specified we keep cut out
+    // and only keep that part
+    // end_index = 0 means no end was specified, so cut to the end 
+    if (end_index == 0)
+      end_index = sequence_raw.size();
 
-      // sequence filtering for upcasing agctn and convert non AGCTN to N
-      set_filtered_sequence(sequence_raw, start_index, end_index-start_index);
-    } else {
-      std::stringstream errormsg;
-      errormsg << file_path.native_file_string()
-               << " did not have any fasta sequences" << std::endl;
-      throw mussa_load_error(errormsg.str());
+    // sequence filtering for upcasing agctn and convert non AGCTN to N
+    if (end_index-start_index <= 0) {
+      std::string msg("The selected sequence appears to be empty"); 
+      throw sequence_empty_error(msg);
     }
-    data_file.close();
+    set_filtered_sequence(sequence_raw, a, start_index, end_index-start_index, SeqSpan::PlusStrand);
+  } else {
+    std::string errormsg("There were no fasta sequences");
+    throw sequence_empty_file_error(errormsg);
   }
 }
 
-void Sequence::set_filtered_sequence(const std::string &old_seq, 
-                                     std::string::size_type start, 
-                                     std::string::size_type count)
+void Sequence::set_filtered_sequence(const std::string &in_seq,
+                                     AlphabetRef alphabet_,
+                                     size_type start,
+                                     size_type count,
+                                     SeqSpan::strand_type strand_)
 {
-  char conversionTable[257];
-
-  if ( count == 0)
-    count = old_seq.size() - start;
-  sequence.clear();
-  sequence.reserve(count);
-
-  // Make a conversion table
-
-  // everything we don't specify below will become 'N'
-  for(int table_i=0; table_i < 256; table_i++)
-  {
-    conversionTable[table_i] = 'N';
-  }
-  // add end of string character for printing out table for testing purposes
-  conversionTable[256] = '\0';
-
-  // we want these to map to themselves - ie not to change
-  conversionTable[(int)'A'] = 'A';
-  conversionTable[(int)'T'] = 'T';
-  conversionTable[(int)'G'] = 'G';
-  conversionTable[(int)'C'] = 'C';
-  // this is to upcase
-  conversionTable[(int)'a'] = 'A';
-  conversionTable[(int)'t'] = 'T';
-  conversionTable[(int)'g'] = 'G';
-  conversionTable[(int)'c'] = 'C';
+  if ( count == npos)
+    count = in_seq.size() - start;
+  std::string new_seq;
+  new_seq.reserve(count);
 
   // finally, the actual conversion loop
-  for(std::string::size_type seq_index = 0; seq_index < count; seq_index++)
+  const Alphabet& alpha_impl = Alphabet::get_alphabet(alphabet_); // go get one of our actual alphabets
+  std::string::const_iterator seq_i = in_seq.begin()+start;
+  for(size_type i = 0; i != count; ++i, ++seq_i)
   {
-    sequence += conversionTable[ (int)old_seq[seq_index+start]];
+    if (alpha_impl.exists(*seq_i)) {
+      new_seq.append(1, toupper(*seq_i));
+    } else {
+      new_seq.append(1, 'N');
+    }
   }
+  SeqSpanRef new_seq_ref(new SeqSpan(new_seq, alphabet_, strand_)); 
+  seq = new_seq_ref;
 }
 
-  // this doesn't work properly under gcc 3.x ... it can't recognize toupper
-  //transform(sequence.begin(), sequence.end(), sequence.begin(), toupper);
-
 void
 Sequence::load_annot(fs::path file_path, int start_index, int end_index)
 {
+  if (not fs::exists(file_path)) {
+    throw mussa_load_error("Annotation File " + file_path.string() + " was not found");
+  }
+  if (fs::is_directory(file_path)) {
+    throw mussa_load_error(file_path.string() +
+            " is a directory, please provide a file for annotations."
+          );
+  }    
   fs::fstream data_stream(file_path, std::ios::in);
   if (!data_stream)
   {
-    throw mussa_load_error("Sequence File: " + file_path.string() + " not found");
+    throw mussa_load_error("Error loading annotation file " + file_path.string());
+  }
+
+  try {  
+    load_annot(data_stream, start_index, end_index);
+  }  catch(annotation_load_error e) {
+    std::ostringstream msg;
+    msg << file_path.native_file_string()
+        << " "
+        << e.what();
+    throw annotation_load_error(msg.str());
   }
+  data_stream.close();
+}
 
+void
+Sequence::load_annot(std::istream& data_stream, int start_index, int end_index)
+{
   // so i should probably be passing the parse function some iterators
   // but the annotations files are (currently) small, so i think i can 
   // get away with loading the whole file into memory
@@ -230,8 +348,7 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
     data_stream.get(c);
     data.push_back(c);
   }
-  data_stream.close();
-        
+
   parse_annot(data, start_index, end_index);
 }
 
@@ -253,30 +370,36 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
  */
   
 struct push_back_annot {
-  std::list<annot>& annot_list;
+  Sequence* parent;
+  SeqSpanRefListRef children;
   int& begin;
   int& end;
   std::string& name;
   std::string& type;
+  int &parsed;
 
-  push_back_annot(std::list<annot>& annot_list_, 
+  push_back_annot(Sequence* parent_seq,
+                  SeqSpanRefListRef children_list,
                   int& begin_, 
                   int& end_, 
                   std::string& name_, 
-                  std::string& type_) 
-  : annot_list(annot_list_), 
+                  std::string& type_,
+                  int &parsed_) 
+  : parent(parent_seq),
+    children(children_list),
     begin(begin_),
     end(end_),
     name(name_),
-    type(type_)
+    type(type_),
+    parsed(parsed_)
   {
   }
 
   void operator()(std::string::const_iterator, 
                   std::string::const_iterator) const 
   {
-    std::cout << "adding annot: " << begin << " " << end << " " << name << " " << type << std::endl;
-    annot_list.push_back(annot(begin, end, name, type));
+    children->push_back(parent->make_annotation(name, type, begin, end));
+    ++parsed;
   };
 };
 
@@ -284,23 +407,36 @@ struct push_back_seq {
   std::list<Sequence>& seq_list;
   std::string& name;
   std::string& seq;
+  int &parsed;
 
   push_back_seq(std::list<Sequence>& seq_list_,
                 std::string& name_, 
-                std::string& seq_)
+                std::string& seq_,
+                int &parsed_)
   : seq_list(seq_list_), 
     name(name_),
-    seq(seq_)
+    seq(seq_),
+    parsed(parsed_)
   {
   }
 
   void operator()(std::string::const_iterator, 
                   std::string::const_iterator) const 
   {
-    std::cout << "adding seq: " << name << " " << seq << std::endl;
-    Sequence s(seq);
-    s.set_header(name);
+    // filter out newlines from our sequence
+    std::string new_seq;
+    for(std::string::const_iterator seq_i = seq.begin();
+        seq_i != seq.end();
+        ++seq_i)
+    {
+      if (*seq_i != '\015' && *seq_i != '\012') new_seq += *seq_i;
+    }
+    //std::cout << "adding seq: " << name << " " << new_seq << std::endl;
+    
+    Sequence s(new_seq);
+    s.set_fasta_header(name);
     seq_list.push_back(s);
+    ++parsed;
   };
 };
 
@@ -311,271 +447,235 @@ Sequence::parse_annot(std::string data, int start_index, int end_index)
   int end=0;
   std::string name;
   std::string type;
-  std::string seq;
+  std::string seqstr;
+  SeqSpanRefListRef parsed_annots(new SeqSpanRefList);
   std::list<Sequence> query_seqs;
-
-  bool status = spirit::parse(data.begin(), data.end(),
-                //begin grammar
-                (
-                (+(spirit::alpha_p))[spirit::assign_a(species)] >> 
-                    *(
-                       // parse an absolute location name
-                       (spirit::uint_p[spirit::assign_a(start)] >> 
-                        spirit::uint_p[spirit::assign_a(end)] >> 
-                        (*(spirit::alpha_p))[spirit::assign_a(name)]/* >> 
-                        (*(spirit::alpha_p))[spirit::assign_a(type)]*/
-                        // to understand how this group gets set
-                        // read the comment above struct push_back_annot
-                       )[push_back_annot(annots, start, end, type, name)]
-                     |
-                      (spirit::ch_p('>') >> 
-                       (*(spirit::alpha_p))[spirit::assign_a(name)] >>
-                       (+(spirit::ch_p('A')|
-                          spirit::ch_p('G')|
-                          spirit::ch_p('C')|
-                          spirit::ch_p('T'))[spirit::assign_a(seq)])
-                       )[push_back_seq(query_seqs, name, seq)]
+  int parsed=0;
+
+  bool ok = spirit::parse(data.begin(), data.end(),
+              (
+               //begin grammar
+                 !(
+                    (
+                      spirit::alpha_p >> 
+                      +(spirit::graph_p)
+                    )[spirit::assign_a(species)] >> 
+                    +(spirit::space_p)
+                  ) >>
+                  *(
+                     ( // ignore html tags
+                       *(spirit::space_p) >>
+                       spirit::ch_p('<') >> 
+                       +(~spirit::ch_p('>')) >>
+                       spirit::ch_p('>') >>
+                       *(spirit::space_p)
                      )
-                ),
-                //end grammar
-                spirit::space_p).full;
+                   |
+                    ( // parse an absolute location name
+                     (spirit::uint_p[spirit::assign_a(start)] >> 
+                      +spirit::space_p >>
+                      spirit::uint_p[spirit::assign_a(end)] >> 
+                      +spirit::space_p >>
+                      ( 
+                         spirit::alpha_p >> 
+                         *spirit::graph_p
+                      )[spirit::assign_a(name)] >> 
+                      // optional type
+                      !(
+                          +spirit::space_p >>
+                          (
+                            spirit::alpha_p >>
+                            *spirit::graph_p
+                          )[spirit::assign_a(type)]
+                      )
+                      // to understand how this group gets set
+                      // read the comment above struct push_back_annot
+                     )[push_back_annot(this, parsed_annots, start, end, name, type, parsed)]
+                   |
+                    ((spirit::ch_p('>')|spirit::str_p("&gt;")) >> 
+                       (*(spirit::print_p))[spirit::assign_a(name)] >>
+                       spirit::eol_p >> 
+                       (+(spirit::chset<>(Alphabet::nucleic_cstr)))[spirit::assign_a(seqstr)]
+                     )[push_back_seq(query_seqs, name, seqstr, parsed)]
+                    ) >>
+                    *spirit::space_p
+                   )
+              //end grammar
+              )).full;
+  if (not ok) {
+    std::stringstream msg;
+    msg << "Error parsing annotation #" << parsed;
+    throw annotation_load_error(msg.str());
+  }
+  // If everything loaded correctly add the sequences to our annotation list
+  // add newly parsed annotations to our sequence
+  std::copy(parsed_annots->begin(), parsed_annots->end(), std::back_inserter(*annotation_list));  
+  // go search for query sequences 
+  find_sequences(query_seqs.begin(), query_seqs.end());
 }
 
-/*
-void
-Sequence::load_annot(std::istream& data_stream, int start_index, int end_index)
+void Sequence::add_annotation(const SeqSpanRef a)
 {
-  std::string file_data_line;
-  annot an_annot;
-  std::string::size_type space_split_i;
-  std::string annot_value;
-  std::list<annot>::iterator list_i;
-  std::string err_msg;
+  annotation_list->push_back(a);
+}
 
-  annots.clear();
+void Sequence::add_annotation(std::string name, std::string type, size_type start, size_type stop)
+{
+  add_annotation(make_annotation(name, type, start, stop));
+}
 
-  getline(data_stream,file_data_line);
-  species = file_data_line;
+SeqSpanRef 
+Sequence::make_annotation(std::string name, std::string type, size_type start, size_type stop) const
+{
+  // we want things to be in the positive direction
+  if (stop < start) {
+    size_type tmp = start;
+    start = stop;
+    stop = tmp;
+  }
+  size_type count = stop - start;
+  SeqSpanRef new_annot(seq->subseq(start, count,  SeqSpan::UnknownStrand));
+  AnnotationsRef metadata(new Annotations(name));
+  metadata->set("type", type);
+  new_annot->setAnnotations(metadata);
+  return new_annot;
+}
 
-  // end_index = 0 means no end was specified, so cut to the end 
-  if (end_index == 0)
-    end_index = sequence.length();
+const SeqSpanRefList& Sequence::annotations() const
+{
+  return *annotation_list;
+}
 
-  //std::cout << "START: " << start_index << " END: " << end_index << std::endl;
+void Sequence::copy_children(Sequence &new_seq, size_type start, size_type count) const
+{
+  new_seq.motif_list = motif_list;
+  new_seq.annotation_list.reset(new SeqSpanRefList);
 
-  while ( !data_stream.eof() )
+  for(SeqSpanRefList::const_iterator annot_i = annotation_list->begin();
+      annot_i != annotation_list->end();
+      ++annot_i)
   {
-    getline(data_stream,file_data_line);
-    if (file_data_line != "")
-    {
-      // need to get 4 values...almost same code 4 times...
-      // get annot start index
-      space_split_i = file_data_line.find(" ");
-      annot_value = file_data_line.substr(0,space_split_i);
-      an_annot.start = atoi (annot_value.c_str());
-      file_data_line = file_data_line.substr(space_split_i+1);
-      // get annot end index
-      space_split_i = file_data_line.find(" ");
-      annot_value = file_data_line.substr(0,space_split_i);
-      an_annot.end = atoi (annot_value.c_str());
-      file_data_line = file_data_line.substr(space_split_i+1);
-
-      //std::cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
-      //     << std::endl;
-
-      // get annot name
-      space_split_i = file_data_line.find(" ");
-      if (space_split_i == std::string::npos)  // no entries for name & type
-      {
-        std::cout << "seq, annots - no name or type\n";
-        an_annot.name = "";
-        an_annot.type = "";
+    size_type annot_begin= (*annot_i)->start();
+    size_type annot_end = (*annot_i)->stop();
+
+    if (annot_begin < start+count) {
+      if (annot_begin >= start) {
+        annot_begin -= start;
+      } else {
+        annot_begin = 0;
       }
-      else
-      {
-        annot_value = file_data_line.substr(0,space_split_i);
-        an_annot.name = annot_value;
-        file_data_line = file_data_line.substr(space_split_i+1);
-        // get annot type
-        space_split_i = file_data_line.find(" ");
-        if (space_split_i == std::string::npos)  // no entry for type
-          an_annot.type = "";
-        else
-        {
-          annot_value = file_data_line.substr(0,space_split_i);
-          an_annot.type = annot_value;
-        }
-      }
-
 
-      // add annot to list if it falls within the range of sequence specified
-      if ((start_index <= an_annot.start) && (end_index >= an_annot.end)) 
-      {
-        an_annot.start -= start_index;
-        an_annot.end -= start_index;
-        annots.push_back(an_annot);
+      if (annot_end < start+count) {
+        annot_end -= start;
+      } else {
+        annot_end = count;
       }
-      // else no (or bogus) annotations
+      SeqSpanRef new_annot(new_seq.seq->subseq(annot_begin, annot_end));
+      new_annot->setAnnotations((*annot_i)->annotations());
+      new_seq.annotation_list->push_back(new_annot);
     }
   }
 }
-*/
 
-const std::string& Sequence::get_species() const
+Sequence
+Sequence::subseq(size_type start, size_type count, SeqSpan::strand_type strand) const
 {
-  return species;
-}
-
-bool Sequence::empty() const
-{
-  return (size() == 0);
-}
-
-const std::list<annot>& Sequence::annotations() const
-{
-  return annots;
-}
+  // FIXME: should i really allow a subsequence of an empty sequence?
+  if (!seq) {
+    Sequence new_seq;
+    return new_seq;
+  }
 
-std::string::size_type Sequence::length() const
-{
-  return size();
+  Sequence new_seq(*this);
+  new_seq.seq = seq->subseq(start, count, strand);
+  if (seq->annotations()) {
+    AnnotationsRef a(new Annotations(*(seq->annotations())));
+    new_seq.seq->setAnnotations(a);
+  }
+  copy_children(new_seq, start, count);
+  
+  return new_seq;
 }
 
-std::string::size_type Sequence::size() const
-{
-  return sequence.size();
-}
 
-Sequence::iterator Sequence::begin()
+// FIXME: This needs to be moved into SeqSpan
+Sequence Sequence::rev_comp() const
 {
-  return sequence.begin();
+  // a reverse complement is the whole opposite strand 
+  return subseq(0, npos, SeqSpan::OppositeStrand);
 }
 
-Sequence::const_iterator Sequence::begin() const
+const Alphabet& Sequence::get_alphabet() const
 {
-  return sequence.begin();
+  return (seq) ? seq->get_alphabet() : Alphabet::empty_alphabet(); 
 }
 
-Sequence::iterator Sequence::end()
+void Sequence::set_fasta_header(std::string header_)
 {
-  return sequence.end();
+  header = header_;
 }
 
-Sequence::const_iterator Sequence::end() const
+void Sequence::set_species(const std::string& name)
 {
-  return sequence.end();
+  species = name;
 }
 
-
-const std::string&
-Sequence::get_seq() const
+std::string Sequence::get_species() const
 {
-  return sequence;
+  return species;
 }
 
 
 std::string
-Sequence::subseq(int start, int end) const
-{
-  return sequence.substr(start, end);
-}
-
-
-const char *
-Sequence::c_seq() const
+Sequence::get_fasta_header() const
 {
-  return sequence.c_str();
+  return header;
 }
 
 std::string
-Sequence::rev_comp() const
+Sequence::get_name() const
 {
-  std::string rev_comp;
-  char conversionTable[257];
-  int seq_i, table_i, len;
-
-  len = sequence.length();
-  rev_comp.reserve(len);
-  // make a conversion table
-  // init all parts of conversion table to '~' character
-  // '~' I doubt will ever appear in a sequence file (jeez, I hope)
-  // and may the fleas of 1000 camels infest the genitals of any biologist (and
-  // seven generations of their progeny) who decides to make it mean
-  // something special!!!
-  // PS - double the curse for any smartass non-biologist who tries it as well
-  for(table_i=0; table_i < 256; table_i++)
-  {
-    conversionTable[table_i] = '~';
-  }
-  // add end of string character for printing out table for testing purposes
-  conversionTable[256] = '\0';
-
-  // add in the characters for the bases we want to convert
-  conversionTable[(int)'A'] = 'T';
-  conversionTable[(int)'T'] = 'A';
-  conversionTable[(int)'G'] = 'C';
-  conversionTable[(int)'C'] = 'G';
-  conversionTable[(int)'N'] = 'N';
-
-  // finally, the actual conversion loop
-  for(seq_i = len - 1; seq_i >= 0; seq_i--)
-  {
-    table_i = (int) sequence[seq_i];
-    rev_comp += conversionTable[table_i];
-  }
-
-  return rev_comp;
+  if (header.size() > 0) 
+    return header;
+  else if (species.size() > 0)
+    return species;
+  else
+    return "";
 }
 
-void Sequence::set_header(std::string &header_)
+void Sequence::set_sequence(const std::string& s, AlphabetRef a) 
 {
-  header = header_;
+  set_filtered_sequence(s, a, 0, s.size(), SeqSpan::PlusStrand);
 }
 
-const std::string&
-Sequence::get_header() const
-{
-  return header;
-}
-/*
-//FIXME: i don't think this code is callable
-std::string 
-Sequence::sp_name() const
+std::string Sequence::get_sequence() const
 {
-  return species;
+  return seq->sequence();
 }
-*/
 
-void
-Sequence::set_seq(const std::string& a_seq)
+Sequence::const_reference Sequence::operator[](Sequence::size_type i) const
 {
-  set_filtered_sequence(a_seq);
+  return at(i);
 }
 
-
-/*
-std::string 
-Sequence::species()
-{
-  return species;
-}
-*/
-
 void
 Sequence::clear()
 {
-  sequence = "";
-  header = "";
-  species = "";
-  annots.clear();
+  seq.reset();
+  header.clear();
+  species.clear();
+  annotation_list.reset(new SeqSpanRefList);
+  motif_list.reset(new MotifList);
 }
 
 void
 Sequence::save(fs::fstream &save_file)
-               //std::string save_file_path)
 {
+  std::string type("type");
+  std::string empty_str("");
   //fstream save_file;
-  std::list<annot>::iterator annots_i;
+  SeqSpanRefList::iterator annots_i;
+  AnnotationsRef metadata;
 
   // not sure why, or if i'm doing something wrong, but can't seem to pass
   // file pointers down to this method from the mussa control class
@@ -583,49 +683,154 @@ Sequence::save(fs::fstream &save_file)
   //save_file.open(save_file_path.c_str(), std::ios::app);
 
   save_file << "<Sequence>" << std::endl;
-  save_file << sequence << std::endl;
+  save_file << *this << std::endl;
   save_file << "</Sequence>" << std::endl;
 
   save_file << "<Annotations>" << std::endl;
   save_file << species << std::endl;
-  for (annots_i = annots.begin(); annots_i != annots.end(); ++annots_i)
+  for (annots_i = annotation_list->begin(); 
+       annots_i != annotation_list->end(); 
+       ++annots_i)
   {
-    save_file << annots_i->start << " " << annots_i->end << " " ;
-    save_file << annots_i->name << " " << annots_i->type << std::endl;
+    metadata = (*annots_i)->annotations();
+    save_file << (*annots_i)->parentStart() << " " << (*annots_i)->parentStop() << " " ;
+    save_file << metadata->name() << " " 
+              << metadata->getdefault(type, empty_str) << std::endl;
   }
   save_file << "</Annotations>" << std::endl;
   //save_file.close();
 }
 
-void
-Sequence::load_museq(fs::path load_file_path, int seq_num)
+//void
+//Sequence::load_museq(fs::path load_file_path, int seq_num)
+//{
+//  fs::fstream load_file;
+//  std::string file_data_line;
+//  int seq_counter;
+//  //annot an_annot;
+//  int annot_begin;
+//  int annot_end;
+//  std::string annot_name;
+//  std::string annot_type;
+//  
+//  std::string::size_type space_split_i;
+//  std::string annot_value;
+//
+//  annotation_list.reset(new SeqSpanRefList);
+//  
+//  load_file.open(load_file_path, std::ios::in);
+//
+//  seq_counter = 0;
+//  // search for the seq_num-th sequence 
+//  while ( (!load_file.eof()) && (seq_counter < seq_num) )
+//  {
+//    getline(load_file,file_data_line);
+//    if (file_data_line == "<Sequence>")
+//      seq_counter++;
+//  }
+//  getline(load_file, file_data_line);
+//  // looks like the sequence is written as a single line
+//  set_filtered_sequence(file_data_line, reduced_dna_alphabet, 0, file_data_line.size(), SeqSpan::PlusStrand);
+//  getline(load_file, file_data_line);
+//  getline(load_file, file_data_line);
+//  if (file_data_line == "<Annotations>")
+//  {
+//    getline(load_file, file_data_line);
+//    species = file_data_line;
+//    while ( (!load_file.eof())  && (file_data_line != "</Annotations>") )
+//    {
+//      getline(load_file,file_data_line);
+//      if ((file_data_line != "") && (file_data_line != "</Annotations>"))  
+//      {
+//        // need to get 4 values...almost same code 4 times...
+//        // get annot start index
+//        space_split_i = file_data_line.find(" ");
+//        annot_value = file_data_line.substr(0,space_split_i);
+//        annot_begin = atoi (annot_value.c_str());
+//        file_data_line = file_data_line.substr(space_split_i+1);
+//        // get annot end index
+//        space_split_i = file_data_line.find(" ");
+//        annot_value = file_data_line.substr(0,space_split_i);
+//        annot_end = atoi (annot_value.c_str());
+//
+//        if (space_split_i == std::string::npos)  // no entry for type or name
+//        {
+//          std::cout << "seq, annots - no type or name\n";
+//          annot_name = "";
+//          annot_type = "";
+//        }
+//        else   // else get annot type
+//        {
+//          file_data_line = file_data_line.substr(space_split_i+1);
+//          space_split_i = file_data_line.find(" ");
+//          annot_value = file_data_line.substr(0,space_split_i);
+//          //an_annot.type = annot_value;
+//          annot_type = annot_value;
+//          if (space_split_i == std::string::npos)  // no entry for name
+//          {
+//            std::cout << "seq, annots - no name\n";
+//            annot_name = "";
+//          }
+//          else          // get annot name
+//          {
+//            file_data_line = file_data_line.substr(space_split_i+1);
+//            space_split_i = file_data_line.find(" ");
+//            annot_value = file_data_line.substr(0,space_split_i);
+//            // this seems like its wrong?
+//            annot_type = annot_value;
+//          }
+//        }
+//        add_annotation(annot_name, annot_type, annot_begin, annot_end);
+//      }
+//      //std::cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
+//      //     << "-->" << an_annot.type << "::" << an_annot.name << std::endl;
+//    }
+//  }
+//  load_file.close();
+//}
+
+SequenceRef Sequence::load_museq(boost::filesystem::fstream& load_file)
 {
-  fs::fstream load_file;
+  boost::shared_ptr<Sequence> seq(new Sequence);
   std::string file_data_line;
   int seq_counter;
-  annot an_annot;
+  //annot an_annot;
+  int annot_begin;
+  int annot_end;
+  std::string annot_name;
+  std::string annot_type;
+  
   std::string::size_type space_split_i;
   std::string annot_value;
 
-  annots.clear();
-  load_file.open(load_file_path, std::ios::in);
+  //seq->annotation_list.reset(new SeqSpanRefList);
 
   seq_counter = 0;
-  // search for the seq_num-th sequence 
+  // search for the next sequence
+  int seq_num = 1;
   while ( (!load_file.eof()) && (seq_counter < seq_num) )
   {
     getline(load_file,file_data_line);
     if (file_data_line == "<Sequence>")
       seq_counter++;
   }
+  
+  // Could not find next sequence
+  if (load_file.eof())
+  {
+    seq.reset();
+    return seq;
+  }
+  
   getline(load_file, file_data_line);
-  sequence = file_data_line;
+  // looks like the sequence is written as a single line
+  seq->set_filtered_sequence(file_data_line, reduced_dna_alphabet, 0, file_data_line.size(), SeqSpan::PlusStrand);
   getline(load_file, file_data_line);
   getline(load_file, file_data_line);
   if (file_data_line == "<Annotations>")
   {
     getline(load_file, file_data_line);
-    species = file_data_line;
+    seq->set_species(file_data_line);
     while ( (!load_file.eof())  && (file_data_line != "</Annotations>") )
     {
       getline(load_file,file_data_line);
@@ -635,151 +840,52 @@ Sequence::load_museq(fs::path load_file_path, int seq_num)
         // get annot start index
         space_split_i = file_data_line.find(" ");
         annot_value = file_data_line.substr(0,space_split_i);
-        an_annot.start = atoi (annot_value.c_str());
+        annot_begin = atoi (annot_value.c_str());
         file_data_line = file_data_line.substr(space_split_i+1);
         // get annot end index
         space_split_i = file_data_line.find(" ");
         annot_value = file_data_line.substr(0,space_split_i);
-        an_annot.end = atoi (annot_value.c_str());
+        annot_end = atoi (annot_value.c_str());
 
         if (space_split_i == std::string::npos)  // no entry for type or name
         {
           std::cout << "seq, annots - no type or name\n";
-          an_annot.type = "";
-          an_annot.name = "";
+          annot_name = "";
+          annot_type = "";
         }
         else   // else get annot type
         {
           file_data_line = file_data_line.substr(space_split_i+1);
           space_split_i = file_data_line.find(" ");
           annot_value = file_data_line.substr(0,space_split_i);
-          an_annot.type = annot_value;
+          //an_annot.type = annot_value;
+          annot_type = annot_value;
           if (space_split_i == std::string::npos)  // no entry for name
           {
             std::cout << "seq, annots - no name\n";
-            an_annot.name = "";
+            annot_name = "";
           }
           else          // get annot name
           {
             file_data_line = file_data_line.substr(space_split_i+1);
             space_split_i = file_data_line.find(" ");
             annot_value = file_data_line.substr(0,space_split_i);
-            an_annot.type = annot_value;
+            // this seems like its wrong?
+            annot_type = annot_value;
           }
         }
-        annots.push_back(an_annot);  // don't forget to actually add the annot
+        seq->add_annotation(annot_name, annot_type, annot_begin, annot_end);
       }
       //std::cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
       //     << "-->" << an_annot.type << "::" << an_annot.name << std::endl;
     }
   }
-  load_file.close();
+  //load_file.close();
+  return seq;
 }
 
 
-std::string
-Sequence::rc_motif(std::string a_motif)
-{
-  std::string rev_comp;
-  char conversionTable[257];
-  int seq_i, table_i, len;
-
-  len = a_motif.length();
-  rev_comp.reserve(len);
-
-  for(table_i=0; table_i < 256; table_i++)
-  {
-    conversionTable[table_i] = '~';
-  }
-  // add end of std::string character for printing out table for testing purposes
-  conversionTable[256] = '\0';
-
-  // add in the characters for the bases we want to convert (IUPAC)
-  conversionTable[(int)'A'] = 'T';
-  conversionTable[(int)'T'] = 'A';
-  conversionTable[(int)'G'] = 'C';
-  conversionTable[(int)'C'] = 'G';
-  conversionTable[(int)'N'] = 'N';
-  conversionTable[(int)'M'] = 'K';
-  conversionTable[(int)'R'] = 'Y';
-  conversionTable[(int)'W'] = 'W';
-  conversionTable[(int)'S'] = 'S';
-  conversionTable[(int)'Y'] = 'R';
-  conversionTable[(int)'K'] = 'M';
-  conversionTable[(int)'V'] = 'B';
-  conversionTable[(int)'H'] = 'D';
-  conversionTable[(int)'D'] = 'H';
-  conversionTable[(int)'B'] = 'V';
-
-  // finally, the actual conversion loop
-  for(seq_i = len - 1; seq_i >= 0; seq_i--)
-  {
-    //std::cout << "** i = " << seq_i << " bp = " << 
-    table_i = (int) a_motif[seq_i];
-    rev_comp += conversionTable[table_i];
-  }
-
-  //std::cout << "seq: " << a_motif << std::endl;
-  //std::cout << "rc:  " << rev_comp << std::endl;
-
-  return rev_comp;
-}
-
-std::string
-Sequence::motif_normalize(std::string a_motif)
-{
-  std::string valid_motif;
-  int seq_i, len;
-
-  len = a_motif.length();
-  valid_motif.reserve(len);
-
-  // this just upcases IUPAC symbols.  Eventually should return an error if non IUPAC is present.
-  // current nonIUPAC symbols are omitted, which is not reported atm
-  for(seq_i = 0; seq_i < len; seq_i++)
-  {
-    if ((a_motif[seq_i] == 'a') || (a_motif[seq_i] == 'A'))
-      valid_motif += 'A';
-    else if ((a_motif[seq_i] == 't') || (a_motif[seq_i] == 'T'))
-      valid_motif += 'T';
-    else if ((a_motif[seq_i] == 'g') || (a_motif[seq_i] == 'G'))
-      valid_motif += 'G';
-    else if ((a_motif[seq_i] == 'c') || (a_motif[seq_i] == 'C'))
-      valid_motif += 'C';
-    else if ((a_motif[seq_i] == 'n') || (a_motif[seq_i] == 'N'))
-      valid_motif += 'N';
-    else if ((a_motif[seq_i] == 'm') || (a_motif[seq_i] == 'M'))
-      valid_motif += 'M';
-    else if ((a_motif[seq_i] == 'r') || (a_motif[seq_i] == 'R'))
-      valid_motif += 'R';
-    else if ((a_motif[seq_i] == 'w') || (a_motif[seq_i] == 'W'))
-      valid_motif += 'W';
-    else if ((a_motif[seq_i] == 's') || (a_motif[seq_i] == 'S'))
-      valid_motif += 'S';
-    else if ((a_motif[seq_i] == 'y') || (a_motif[seq_i] == 'Y'))
-      valid_motif += 'Y';
-    else if ((a_motif[seq_i] == 'k') || (a_motif[seq_i] == 'K'))
-      valid_motif += 'G';
-    else if ((a_motif[seq_i] == 'v') || (a_motif[seq_i] == 'V'))
-      valid_motif += 'V';
-    else if ((a_motif[seq_i] == 'h') || (a_motif[seq_i] == 'H'))
-      valid_motif += 'H';
-    else if ((a_motif[seq_i] == 'd') || (a_motif[seq_i] == 'D'))
-      valid_motif += 'D';
-    else if ((a_motif[seq_i] == 'b') || (a_motif[seq_i] == 'B'))
-      valid_motif += 'B';
-    else {
-      std::string msg = "Letter ";
-      msg += a_motif[seq_i];
-      msg += " is not a valid IUPAC symbol";
-      throw motif_normalize_error(msg);
-    }
-  }
-  //std::cout << "valid_motif is: " << valid_motif << std::endl;
-  return valid_motif;
-}
-
-void Sequence::add_motif(std::string a_motif)
+void Sequence::add_motif(const Sequence& a_motif)
 {
   std::vector<int> motif_starts = find_motif(a_motif);
 
@@ -787,113 +893,96 @@ void Sequence::add_motif(std::string a_motif)
       motif_start_i != motif_starts.end();
       ++motif_start_i)
   {
-    motif_list.push_back(motif(*motif_start_i, a_motif));
+    motif_list->push_back(motif(*motif_start_i, a_motif.get_sequence()));
   }
 }
 
 void Sequence::clear_motifs()
 {
-  motif_list.clear();
+  if (motif_list) 
+    motif_list->clear();
+  else 
+    motif_list.reset(new MotifList);
 }
 
-const std::list<motif>& Sequence::motifs() const
+const Sequence::MotifList& Sequence::motifs() const
 {
-  return motif_list;
+  return *motif_list;
 }
 
 std::vector<int>
-Sequence::find_motif(std::string a_motif)
+Sequence::find_motif(const Sequence& a_motif) const
 {
   std::vector<int> motif_match_starts;
-  std::string a_motif_rc;
+  Sequence norm_motif_rc;
 
   motif_match_starts.clear();
+  // std::cout << "motif is: " << norm_motif << std::endl;
 
-  //std::cout << "motif is: " << a_motif << std::endl;
-  a_motif = motif_normalize(a_motif);
-  //std::cout << "motif is: " << a_motif << std::endl;
-
-  if (a_motif != "")
+  if (a_motif.size() > 0)
   {
     //std::cout << "Sequence: none blank motif\n";
     motif_scan(a_motif, &motif_match_starts);
 
-    a_motif_rc = rc_motif(a_motif);
+    norm_motif_rc = a_motif.rev_comp();;
     // make sure not to do search again if it is a palindrome
-    if (a_motif_rc != a_motif)
-      motif_scan(a_motif_rc, &motif_match_starts);
+    if (norm_motif_rc != a_motif) {
+      motif_scan(norm_motif_rc, &motif_match_starts);
+    }
   }
   return motif_match_starts;
 }
 
 void
-Sequence::motif_scan(std::string a_motif, std::vector<int> * motif_match_starts)
+Sequence::motif_scan(const Sequence& a_motif, std::vector<int> * motif_match_starts) const
 {
-  char * seq_c;
-  std::string::size_type seq_i;
-  int motif_i, motif_len;
-
-  // faster to loop thru the sequence as a old c std::string (ie char array)
-  seq_c = (char*)sequence.c_str();
-  //std::cout << "Sequence: motif, seq len = " << sequence.length() << std::endl; 
-  motif_len = a_motif.length();
+  // if there's no sequence we can't scan for it?
+  // should this throw an exception?
+  if (!seq) return;
 
-  //std::cout << "motif_length: " << motif_len << std::endl;
-  //std::cout << "RAAARRRRR\n";
+  std::string::size_type seq_i = 0;
+  Sequence::size_type motif_i = 0;
+  Sequence::size_type motif_len = a_motif.length();
+  Sequence::value_type motif_char;
+  Sequence::value_type seq_char;
 
-  motif_i = 0;
-
-  //std::cout << "motif: " << a_motif << std::endl;
-
-  //std::cout << "Sequence: motif, length= " << length << std::endl;
-  seq_i = 0;
-  while (seq_i < sequence.length())
+  while (seq_i < size())
   {
-    //std::cout << seq_c[seq_i];
-    //std::cout << seq_c[seq_i] << "?" << a_motif[motif_i] << ":" << motif_i << " ";
     // this is pretty much a straight translation of Nora's python code
     // to match iupac letter codes
-    if (a_motif[motif_i] =='N')
+    motif_char = toupper(a_motif[motif_i]);
+    seq_char = toupper(seq->at(seq_i));
+    if (motif_char =='N')
       motif_i++;
-    else if (a_motif[motif_i] == seq_c[seq_i])
+    else if (motif_char == seq_char)
       motif_i++;
-    else if ((a_motif[motif_i] =='M') && 
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C')))
+    else if ((motif_char =='M') && ((seq_char=='A') || (seq_char=='C')))
       motif_i++;
-    else if ((a_motif[motif_i] =='R') && 
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G')))
+    else if ((motif_char =='R') && ((seq_char=='A') || (seq_char=='G')))
       motif_i++;
-    else if ((a_motif[motif_i] =='W') && 
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='T')))
+    else if ((motif_char =='W') && ((seq_char=='A') || (seq_char=='T')))
       motif_i++;
-    else if ((a_motif[motif_i] =='S') && 
-             ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G')))
+    else if ((motif_char =='S') && ((seq_char=='C') || (seq_char=='G')))
       motif_i++;
-    else if ((a_motif[motif_i] =='Y') && 
-             ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='T')))
+    else if ((motif_char =='Y') && ((seq_char=='C') || (seq_char=='T')))
       motif_i++;
-    else if ((a_motif[motif_i] =='K') && 
-             ((seq_c[seq_i]=='G') || (seq_c[seq_i]=='T')))
+    else if ((motif_char =='K') && ((seq_char=='G') || (seq_char=='T')))
       motif_i++;
-    else if ((a_motif[motif_i] =='V') && 
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
-              (seq_c[seq_i]=='G')))
+    else if ((motif_char =='V') && 
+             ((seq_char=='A') || (seq_char=='C') || (seq_char=='G')))
       motif_i++;
-    else if ((a_motif[seq_i] =='H') && 
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
-              (seq_c[seq_i]=='T')))
+    else if ((motif_char =='H') && 
+             ((seq_char=='A') || (seq_char=='C') || (seq_char=='T')))
       motif_i++;
-    else if ((a_motif[motif_i] =='D') &&
-             ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G') ||
-              (seq_c[seq_i]=='T')))
+    else if ((motif_char =='D') &&
+             ((seq_char=='A') || (seq_char=='G') || (seq_char=='T')))
       motif_i++;
-    else if ((a_motif[motif_i] =='B') &&
-             ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G') ||
-              (seq_c[seq_i]=='T')))
+    else if ((motif_char =='B') &&
+             ((seq_char=='C') || (seq_char=='G') || (seq_char=='T')))
       motif_i++;
-
     else
     {
+      // if a motif doesn't match, erase our current trial and try again
       seq_i -= motif_i;
       motif_i = 0;
     }
@@ -901,8 +990,6 @@ Sequence::motif_scan(std::string a_motif, std::vector<int> * motif_match_starts)
     // end Nora stuff, now we see if a match is found this pass
     if (motif_i == motif_len)
     {
-      //std::cout << "!!";
-      annot new_motif;
       motif_match_starts->push_back(seq_i - motif_len + 1);
       motif_i = 0;
     }
@@ -916,15 +1003,12 @@ void Sequence::add_string_annotation(std::string a_seq,
                                      std::string name)
 {
   std::vector<int> seq_starts = find_motif(a_seq);
-
+  
   for(std::vector<int>::iterator seq_start_i = seq_starts.begin();
       seq_start_i != seq_starts.end();
       ++seq_start_i)
   {
-    annots.push_back(annot(*seq_start_i, 
-                           *seq_start_i+a_seq.size(),
-                           "",
-                           name));
+    add_annotation(name, "", *seq_start_i, *seq_start_i+a_seq.size()); 
   }
 }
 
@@ -932,8 +1016,91 @@ void Sequence::find_sequences(std::list<Sequence>::iterator start,
                               std::list<Sequence>::iterator end)
 {
   while (start != end) {
-    add_string_annotation(start->get_seq(), start->get_header());
+    add_string_annotation(start->get_sequence(), start->get_fasta_header());
     ++start;
   }
 }
 
+
+std::ostream& operator<<(std::ostream& out, const Sequence& s)
+{
+  if (s.seq) {
+    for(Sequence::const_iterator s_i = s.begin(); s_i != s.end(); ++s_i) {
+      out << *s_i;
+    }
+  }
+  return out;
+}
+
+bool operator<(const Sequence& x, const Sequence& y)
+{
+  Sequence::const_iterator x_i = x.begin();
+  Sequence::const_iterator y_i = y.begin();
+  // for sequences there's some computation associated with computing .end
+  // so lets cache it.
+  Sequence::const_iterator xend = x.end();
+  Sequence::const_iterator yend = y.end();
+  while(1) {
+    if( x_i == xend and y_i == yend ) {
+      return false;
+    } else if ( x_i == xend ) {
+      return true;
+    } else if ( y_i == yend ) {
+      return false;
+    } else if ( (*x_i) < (*y_i)) {
+      return true;
+    } else if ( (*x_i) > (*y_i) ) {
+      return false;
+    } else {
+      ++x_i;
+      ++y_i;
+    }
+  }
+}
+
+template <typename Iter1, typename Iter2>
+static
+bool sequence_insensitive_equality(Iter1 abegin, Iter1 aend, Iter2 bbegin, Iter2 bend)
+{
+  Iter1 aseq_i = abegin;
+  Iter2 bseq_i = bbegin;
+  if (aend-abegin == bend-bbegin) {
+    // since the length of the two sequences is equal, we only need to
+    // test one.
+    for(; aseq_i != aend; ++aseq_i, ++bseq_i) {
+      if (toupper(*aseq_i) != toupper(*bseq_i)) {
+        return false;
+      }
+    }
+    return true;
+  } else {
+    return false;
+  }
+}
+
+bool operator==(const Sequence& x, const Sequence& y) 
+{
+  if (x.seq and y.seq) {
+    // both x and y are defined
+    if (SeqSpan::isFamily(x.seq, y.seq)) {
+      // both are part of the same SeqSpan tree
+      return *(x.seq) == *(y.seq);
+    } else {
+      // we'll have to do a real comparison
+      return sequence_insensitive_equality<SeqSpan::const_iterator, SeqSpan::const_iterator>(
+               x.begin(), x.end(),
+               y.begin(), y.end()
+             );
+    }
+  } else {
+    // true if they're both empty (with either a null SeqSpanRef or 
+    // a zero length string
+    return (x.size() == y.size());
+  }
+}
+
+bool operator!=(const Sequence& x, const Sequence& y) 
+{
+  return not operator==(x, y);
+}
+