Merge commit '259602fdc08ca9835dfc6871eb477c481b4d9b40' as 'src/smith…

…lab_cpp'

src/smithlab_cpp/.gitignore

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+# no compiled object file
+*.[oa]
+*.so
+
+# no temparary file
+*~

src/smithlab_cpp/FileIterator.cpp

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+/*
+ *    Copyright (C) 2009 University of Southern California and
+ *                       Andrew D. Smith
+ *
+ *    Authors: Andrew D. Smith
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include "FileIterator.hpp"
+#include "GenomicRegion.hpp"
+#include "MappedRead.hpp"
+
+#include <iostream>
+
+using std::istream;
+using std::vector;
+using std::string;
+
+/*  THIS FUNCTION FILLS A BUFFER FOR GenomicRegion OBJECTS
+ */
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    vector<GenomicRegion> &buffer) {
+  GenomicRegion tmp;
+  size_t i = buffer_start;
+  assert(buffer_start <= buffer.size());
+  for (; i != buffer.size() && !in.eof(); ++i) {
+    in >> tmp;
+    buffer[i].swap(tmp);
+    in.peek();
+  }
+  if (i < buffer.size())
+    buffer.erase(buffer.begin() + i, buffer.end());
+}
+
+/*  THIS FUNCTION FILLS A BUFFER FOR THE ACTUAL READS, REPRESENTED AS
+ *  STRINGS, AND MUST BE IN A FASTA FORMAT FILE
+ */
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    vector<string> &buffer) {
+  string tmp;
+  size_t i = buffer_start;
+  for (; i != buffer.size() && !in.eof(); ++i) {
+    // the read name...
+    in >> tmp; // DANGER: assumes that the name of the read has no
+	       // spaces in it!!
+    // the read itself:
+    in >> buffer[i];
+    in.peek();
+  }
+  if (i < buffer.size())
+    buffer.erase(buffer.begin() + i, buffer.end());
+}
+
+
+/*  THIS FUNCTION FILLS A BUFFER FOR THE ACTUAL READS, REPRESENTED AS
+ *  RECORDS IN A FASTQ FILE, INCLUDING THE QUALITY SCORES
+ */
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    vector<FASTQRecord> &buffer) {
+  string tmp, read_seq, scores_seq;
+  size_t i = buffer_start;
+  for (; i != buffer.size() && !in.eof(); ++i) {
+    // the read name...
+    in >> tmp; // DANGER: assumes that the name of the read has no
+	       // spaces in it!!
+    // the read itself:
+    in >> read_seq;
+    in >> tmp;
+    in >> scores_seq;
+    buffer[i] = std::make_pair(read_seq, scores_seq);
+    in.peek();
+  }
+  if (i < buffer.size())
+    buffer.erase(buffer.begin() + i, buffer.end());
+}
+
+
+/*  THIS FUNCTION FILLS A BUFFER FOR THE ACTUAL READS, REPRESENTED AS
+ *  RECORDS IN A FASTQ FILE, INCLUDING THE QUALITY SCORES
+ */
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    vector<MappedRead> &buffer) {
+  size_t i = buffer_start;
+  for (; i != buffer.size() && !in.eof(); ++i) {
+    in >> buffer[i];
+    in.peek();
+  }
+  if (i < buffer.size())
+    buffer.erase(buffer.begin() + i, buffer.end());
+}

src/smithlab_cpp/FileIterator.hpp

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+/*
+ *    Copyright (C) 2009 University of Southern California and
+ *                       Andrew D. Smith
+ *
+ *    Authors: Andrew D. Smith
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef FILE_ITERATOR_HPP
+#define FILE_ITERATOR_HPP
+
+#include <string>
+#include <vector>
+#include <fstream>
+
+#include "smithlab_utils.hpp"
+
+template <class T>
+class FileIterator {
+public:
+  FileIterator(const std::string f, const size_t bs);
+  void increment_first() {
+    if (++first == buffer.end()) {
+      assert(first <= last);
+      refill_buffer();
+    }
+    assert(first <= buffer.end() && last <= buffer.end());
+  }
+  void increment_last() {
+    assert(last < buffer.end());
+    if (++last == buffer.end()) {
+      assert(first <= last);
+      refill_buffer();
+    }
+    assert(first <= buffer.end());
+    assert(last <= buffer.end());
+  }
+  void increment() {
+    increment_last();
+    increment_first();
+  }
+  typename std::vector<T>::const_iterator get_first() const {return first;}
+  typename std::vector<T>::const_iterator get_last() const {return last;}
+  bool first_is_good() const {return (!in.eof() || first < buffer.end());}
+  bool last_is_good() const {return (!in.eof() || last < buffer.end());}
+  bool is_good() const {return first_is_good() && last_is_good();}
+
+private:
+  std::ifstream in;
+  std::vector<T> buffer;
+  typename std::vector<T>::iterator first;
+  typename std::vector<T>::iterator last;
+  void refill_buffer();
+};
+
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    std::vector<std::string> &buffer);
+
+class GenomicRegion;
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    std::vector<GenomicRegion> &buffer);
+
+typedef std::pair<std::string, std::string> FASTQRecord;
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    std::vector<FASTQRecord> &buffer);
+
+struct MappedRead;
+void 
+fill_buffer(std::ifstream &in, const size_t buffer_start, 
+	    std::vector<MappedRead> &buffer);
+
+/* THIS REFILL BUFFER IS USED WHEN INCREMENTS TO EITHER THE FIRST OR
+   THE LAST CURRENTLY USED ELEMENTS IN THE BUFFER HIT THE END OF THE
+   BUFFER. HOPEFULLY THE FIRST ONE WILL NOT HIT THE END BEFORE THE
+   LAST: THE FIRST IS ALWAYS SUPPOSED TO BE LESS THAN OR EQUAL TO THE
+   LAST.
+ */
+template <class T> void
+FileIterator<T>::refill_buffer() {
+  assert(first <= last);
+  const size_t diff = last - first;
+  copy(first, last, buffer.begin());
+  // Not sure if the code below actualy works or is the best way to
+  // grow the buffer
+  // assert(diff < buffer.size());
+  if (diff == buffer.size()) {
+    std::vector<T> newbuff(2*buffer.size());
+    copy(buffer.begin(), buffer.end(), newbuff.begin());
+    buffer.swap(newbuff);
+  }
+  first = buffer.begin();
+  last = first + diff;
+  fill_buffer(in, diff, buffer);
+}
+
+template <class T>
+FileIterator<T>::FileIterator(const std::string f, const size_t bs) :
+  buffer(std::vector<T>(bs)) {
+  in.open(f.c_str());
+  if (!in) throw SMITHLABException("cannot open input file " + f);
+  fill_buffer(in, 0, buffer);
+  first = buffer.begin();
+  last = buffer.begin();
+}
+
+#endif