source files: update dot begin and end to non-member functions

src/common/Alphabet.cpp

@@ -104,9 +104,9 @@ void
 get_base_comp(const vector<string>& sequences, float *base_comp) {
   std::fill(base_comp, base_comp + alphabet_size, 0.0);
   float total = 0;
-  for (vector<string>::const_iterator i = sequences.begin();
-       i != sequences.end(); ++i)
-    for (string::const_iterator j = i->begin(); j != i->end(); ++j)
+  for (vector<string>::const_iterator i = begin(sequences);
+       i != end(sequences); ++i)
+    for (string::const_iterator j = begin(*i); j != end(*i); ++j)
       if (valid_base(*j)) {
         base_comp[base2int(*j)]++;
         total++;
@@ -119,63 +119,63 @@ get_base_comp(const vector<string>& sequences, float *base_comp) {
 void
 get_base_comp(const vector<string>& sequences, vector<float>& base_comp) {
   vector<size_t> count(alphabet_size, 0);
-  for (vector<string>::const_iterator i = sequences.begin();
-       i != sequences.end(); ++i)
-    for (string::const_iterator j = i->begin(); j != i->end(); ++j)
+  for (vector<string>::const_iterator i = begin(sequences);
+       i != end(sequences); ++i)
+    for (string::const_iterator j = begin(*i); j != end(*i); ++j)
       if (valid_base(*j)) {
         count[base2int(*j)]++;
       }
-  const float total = std::accumulate(count.begin(), count.end(), 0.0);
+  const float total = std::accumulate(begin(count), end(count), 0.0);
   base_comp.clear();
-  transform(count.begin(), count.end(), back_inserter(base_comp),
+  transform(begin(count), end(count), back_inserter(base_comp),
             std::bind(std::divides<float>(), std::placeholders::_1, total));
 }
 
 
 void
 get_base_comp(const vector<string>& sequences, vector<double>& base_comp) {
   vector<size_t> count(alphabet_size, 0);
-  for (vector<string>::const_iterator i = sequences.begin();
-       i != sequences.end(); ++i)
-    for (string::const_iterator j = i->begin(); j != i->end(); ++j)
+  for (vector<string>::const_iterator i = begin(sequences);
+       i != end(sequences); ++i)
+    for (string::const_iterator j = begin(*i); j != end(*i); ++j)
       if (valid_base(*j)) {
         count[base2int(*j)]++;
       }
-  const double total = std::accumulate(count.begin(), count.end(), 0.0);
+  const double total = std::accumulate(begin(count), end(count), 0.0);
   base_comp.clear();
-  transform(count.begin(), count.end(), back_inserter(base_comp),
+  transform(begin(count), end(count), back_inserter(base_comp),
             std::bind(std::divides<double>(), std::placeholders::_1, total));
 }
 
 
 string
 reverse_complement(const string& s) {
   string r;
-  transform(s.begin(), s.end(), back_inserter(r), complement);
-  reverse(r.begin(), r.end());
+  transform(begin(s), end(s), back_inserter(r), complement);
+  reverse(begin(r), end(r));
   return r;
 }
 
 
 /*string   commented out
 revcomp(const string& s) {
   string r;
-  transform(s.begin(), s.end(), back_inserter(r), complement);
-  reverse(r.begin(), r.end());
+  transform(begin(s), end(s), back_inserter(r), complement);
+  reverse(begin(r), end(r));
   return r;
 }*/
 
 
 size_t
 count_valid_bases(const string& s) {
-  return count_if(s.begin(), s.end(), &valid_base);
+  return count_if(begin(s), end(s), &valid_base);
 }
 
 
 size_t
 count_valid_bases(const vector<string>& s) {
   size_t n_valid = 0;
-  for (vector<string>::const_iterator i = s.begin(); i != s.end(); ++i)
+  for (vector<string>::const_iterator i = begin(s); i != end(s); ++i)
     n_valid += count_valid_bases(*i);
   return n_valid;
 }

src/common/BEDFile.cpp

@@ -58,7 +58,7 @@ string
 UCSCGenomeBrowserHeader::tostring() const {
   ostringstream s;
   if (!header_lines.empty()) {
-    copy(header_lines.begin(), header_lines.end() - 1,
+    copy(begin(header_lines), end(header_lines) - 1,
 	 std::ostream_iterator<string>(s, "\n"));
     s << header_lines.back();
   }
@@ -78,7 +78,7 @@ UCSCGenomeBrowserHeader::set_position(const GenomicRegion& region) {
   ostringstream ss;
   ss << position << "\t" 
      << region.get_chrom() << "\t" 
-     << region.get_start() << "\t" << region.get_end();
+     << region.get_start() << "\t" << region.end(get);
   header_lines.push_back(ss.str());
 }
 
@@ -106,7 +106,7 @@ UCSCGenomeBrowserTrack::valid_attributes[] = {
 
 string
 UCSCGenomeBrowserTrack::get_attribute(string label) const {
-  if (attributes.find(label) != attributes.end()) 
+  if (attributes.find(label) != end(attributes)) 
     return attributes.find(label)->second;
   else return "";
 }
@@ -154,7 +154,7 @@ UCSCGenomeBrowserTrack::tostring() const {
   if (!name.empty())
     s << " name=" << name;
   typedef map<string, string>::const_iterator attr_itr;
-  for (attr_itr i = attributes.begin(); i != attributes.end(); ++i) {
+  for (attr_itr i = begin(attributes); i != end(attributes); ++i) {
     s << " " << i->first << "=";
     const bool print_quotes = (i->second.find(' ') != string::npos ||
 			       i->second.find('\t') != string::npos);
@@ -353,8 +353,8 @@ ReadBEDTrack(string filename,
     the_track = the_tracks.front();
 
   vector<vector<GenomicRegion> >::const_iterator i;
-  for (i = the_region_sets.begin(); i != the_region_sets.end(); ++i)
-    the_regions.insert(the_regions.end(), i->begin(), i->end());
+  for (i = begin(the_region_sets); i != end(the_region_sets); ++i)
+    the_regions.insert(end(the_regions), begin(*i), end(*i));
 }
 
 
@@ -380,8 +380,8 @@ ReadBEDTrack(string filename,
     the_track = the_tracks.front();
 
   vector<vector<SimpleGenomicRegion> >::const_iterator i;
-  for (i = the_region_sets.begin(); i != the_region_sets.end(); ++i)
-    the_regions.insert(the_regions.end(), i->begin(), i->end());
+  for (i = begin(the_region_sets); i != end(the_region_sets); ++i)
+    the_regions.insert(end(the_regions), begin(*i), end(*i));
 }
 
 

src/common/FastaFile.cpp

@@ -51,9 +51,9 @@ size_t
 BigFastaFile::SequenceInfo::count_newlines(size_t range_start,
                                            size_t range_end) const {
   vector<size_t>::const_iterator lower =
-    lower_bound(newlines.begin(), newlines.end(), range_start - start);
+    lower_bound(cbegin(newlines), cend(newlines), range_start - start);
   vector<size_t>::const_iterator upper =
-    lower_bound(newlines.begin(), newlines.end(), range_end - start);
+    lower_bound(cbegin(newlines), cend(newlines), range_end - start);
   return upper - lower;
 }
 
@@ -115,7 +115,7 @@ BigFastaFile::make_index(string filename) {
 
 BigFastaFile::SeqInfoIter
 BigFastaFile::find_containing_sequence(size_t position) const {
-  return lower_bound(SequenceTable.begin(), SequenceTable.end(), position);
+  return lower_bound(begin(SequenceTable), end(SequenceTable), position);
 }
 
 
@@ -125,12 +125,12 @@ BigFastaFile::get_names(const size_t chunk_start,
   SeqInfoIter start_index = find_containing_sequence(chunk_start);
   //   SeqInfoIter end_index = (chunk_start + chunk_size < filesize) ?
   //     find_containing_sequence(chunk_start + chunk_size) + 1 :
-  //     SequenceTable.end();
+  //     end(SequenceTable);
 
   SeqInfoIter end_index = find_containing_sequence(chunk_start + chunk_size);
   // This check is needed because the end could be between sequences:
   // in the name part
-  if (end_index != SequenceTable.end() &&
+  if (end_index != end(SequenceTable) &&
       chunk_start + chunk_size > end_index->start)
     ++end_index;
 
@@ -174,12 +174,12 @@ BigFastaFile::get_sequences(const size_t chunk_start,
   // chunk
   //   SeqInfoIter end_index = (chunk_start + chunk_size < filesize) ?
   //     find_containing_sequence(chunk_start + chunk_size) + 1 :
-  //     SequenceTable.end();
+  //     end(SequenceTable);
 
   SeqInfoIter end_index = find_containing_sequence(chunk_start + chunk_size);
   // This check is needed because the end could be between sequences:
   // in the name part
-  if (end_index != SequenceTable.end() &&
+  if (end_index != end(SequenceTable) &&
       chunk_start + chunk_size > end_index->start)
     ++end_index;
 
@@ -293,7 +293,7 @@ vector<string>
 FastaFile::get_ids() const {
   if (names.empty()) read();
   vector<string> ids;
-  for (vector<string>::iterator i = names.begin(); i != names.end(); ++i)
+  for (vector<string>::iterator i = begin(names); i != end(names); ++i)
     ids.push_back(i->substr(0, i->find_first_of(" \t")));
   return ids;
 }
@@ -303,7 +303,7 @@ vector<string>
 FastaFile::get_descriptions() const {
   if (names.empty()) read();
   vector<string> descriptions;
-  for (vector<string>::iterator i = names.begin(); i != names.end(); ++i) {
+  for (vector<string>::iterator i = begin(names); i != end(names); ++i) {
     const size_t desc_offset = i->find_first_of(" \t");
     if (desc_offset != string::npos)
       descriptions.push_back(i->substr(desc_offset));
@@ -418,7 +418,7 @@ FastaFile::base_comp_from_files(const vector<string>& fns,
   delete[] buffer;
 
   // get the total number of valid bases
-  const double total = std::accumulate(count.begin(), count.end(), 0.0);
+  const double total = std::accumulate(begin(count), end(count), 0.0);
   base_comp.clear();
   transform(cbegin(count), cend(count), back_inserter(base_comp),
             [&](const char x) {return x/total;});